From ca5acf9005b32711912b4f4387208f87d8c3a527 Mon Sep 17 00:00:00 2001 From: Adam English Date: Wed, 21 Feb 2024 14:53:03 -0500 Subject: [PATCH] cleaning unused msa --- .../fm_01dec88038cc997632b9d399594d58bd.msa | 325 --------- .../fm_025e148dfa15d03cf2f4a4fffa42166a.msa | 30 - .../fm_02d8c59aa7cd0c43327d9132316379b9.msa | 160 ----- .../fm_03c47b81edc7fd199d3060b4b5aafe34.msa | 105 --- .../fm_046a78a601e1df55d59e59ee9193f41b.msa | 100 --- .../fm_048024c0ae8f1cb7cc70270fc649fef6.msa | 140 ---- .../fm_0553a98462cadf062d1641cfeb97a0df.msa | 85 --- .../fm_06433b401328232c8c4a2f2278e2fb4c.msa | 195 ----- .../fm_0653f2abc01702903c57c997585cf824.msa | 90 --- .../fm_06caad6b783fc99e81d125bbb065c601.msa | 115 --- .../fm_08113059453960271e05afa618f756b8.msa | 175 ----- .../fm_082a2851433961fb945bb0581d40050c.msa | 165 ----- .../fm_09e5224f3ed49d0a0d63118c15970e8f.msa | 45 -- .../fm_0a842177b0a019f7a4fb813c41b08d1e.msa | 170 ----- .../fm_0b060e62331ab50c5edfcb210d920370.msa | 70 -- 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repo_utils/test_files/external/fake_mafft/lookup/fm_dee2cded414817616e5f55ad21aa4281.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_df30169fc031a64138ca04f54efb8ec9.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_df55c8c1ea86802a42a7e9b21d75a6f1.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_e1c1e1257e2af6edd925e90941014ba6.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_e2cfd5d9ad8fc19fe505a047e91b24e1.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_e4c97851db02dffe002380caf62d4e79.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_e561cd35a9c0baa7a6bc82299c357dd6.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_e58988b4a4cd0e0f7c0d5df1b61a5eb9.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_e5c29704e745bf1432e1c17b5cccc7f5.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_e6f9cd298d13f4ee45a91c7ce72023a5.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_e82174c474aa4624f7a1c120a21eed8b.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_e89731d3c39c6c9c40860a9bcd465472.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_e8eb923241a4227ce80f8e8413e57b9f.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_ebf476a7f02b11a3b6ed6aeba24742c2.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_f328fb5ed3385e1b3cad0fe424579df0.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_f6c1a597d80bac4f7dabc75d287d7e0e.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_f7c5ca36d463cc7cabf9cb401fc27789.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_f948393d54df6d4839d008016d5b4721.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_fa91a80c012b3dea4b79f7b64e5bca29.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_fab829612d8c5cf9d944a8e0df516b52.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_fb0cbaa1eb297ef09be0ae1b7c267a30.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_fb1e3d08ab0d6833b9dcb209316bd32a.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_fb2c7d222388665a15e2429f8ef24422.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_fba649023d92213d13abd6e375f45b15.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_fbe2022855d4e2527c86f41fc179b80f.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_fc40819c3b411d6b2869794670b475f9.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_fee04a9e0fd9ad6a70af99f071a34ce2.msa delete mode 100644 repo_utils/test_files/external/fake_mafft/lookup/fm_ff0d5a6f324c029d8b72f511a97c8b88.msa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_01dec88038cc997632b9d399594d58bd.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_01dec88038cc997632b9d399594d58bd.msa deleted file mode 100644 index edaa1c65..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_01dec88038cc997632b9d399594d58bd.msa +++ /dev/null @@ -1,325 +0,0 @@ ->syndip_1_chr20:62057392-62058978 -cctcattctaaaacctaatgtcaaatttgatagacagaaaaaactgtttctggggtttcc -tgactattcggaaatggtccctccaagatccatgtaccccaacaccaccctacctggcta -cgctcctctcacaactttgagatcaagatgccacgtgtgccttcctcacatcggcgcttt -ccagtgatgcccagtgggggacacaaagggcccagcaagacctcaggaaggacggacaca -ggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcag -gaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacctc -agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc -ggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccac -agacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggccta -cacaccaggccacagacaatggggctcg-------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc -aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac -aggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca -ggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacct -cagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggct -c-gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcca -cagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcc -tacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagg -acggacacaggtc----------------------------------------------- ---------------------------tacacaccaggccacagacaatggggctcggggg -gccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagaca -atggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacaca -ccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggac -acaggtctacacaccaggccacagacaatggggctc-gggggccaacctcagcaagacct -caggaaggacggacacaggtctacacaccaggccacagacaatggggctcg--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------------gg -gggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacaga -caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctaca -caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg -acacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacc -tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc-gggggcca -acctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatgg -ggctcgggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccagg -ccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacag -gcctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcagg -aaggacggacacaggtctacacaccaggccacagacagtggggctcggggggccaacctc -agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc -gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca -gacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggccta -cacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaagga -cggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaag -acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggg -ccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaa -tggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac -caggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggaca -caggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctc -aggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacc -tcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggc -tcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcca -cagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtct -acacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaagg -acggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagca -agacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggg -gccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagaca -atggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac -caggccacagaca ->syndip_2_chr20:62057392-62058978 -cctcattctaaaacctaatgtcaaatttgatagacagaaaaaactgtttctggggtttcc -tgactattcggaaatggtccctccaagatccatgtaccccaacaccaccctacctggcta -cgctcctctcacaactttgagatcaagatgccacgtgtgccttcctcacatcggcgcttt -ccagtgatgcccagtgggggacacaaagggcc---------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------cagcaagacctcaggaaggacggacacaggtctacaca -ccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggac -acaggtctacacaccaggccacagacaatggggctc-gggggccaacctcagcaagacct -caggaaggacggacacaggtctacacaccaggccacagacaatggggctc---------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------gggggccaacctcagcaagacctcaggaaggacggacacaggcctaca -caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg -acacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacc -tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac -caggccacagaca ->p:HG002_1_chr20:62057392-62058978 -cctcattctaaaacctaatgtcaaatttgatagacagaaaaaactgtttctggggtttcc -tgactattcggaaatggtccctccaagatccatgtaccccaacaccaccctacctggcta -cgctcctctcacaactttgagatcaagatgccacgtgtgccttcctcacatcggcgcttt -ccagtgatgcccagtgggggacacaaagggcc---------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------cagcaagacctcaggaaggacggacacaggtctacaca -ccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggac -acaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacct -caggaaggacggacacaggcctacacaccaggccacagacaatggggctcg--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------gggggccaacctcagcaagacctcaggaaggacggacacaggcctaca -caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg -acacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacc -tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac -caggccacagaca ->p:HG002_2_chr20:62057392-62058978 -cctcattctaaaacctaatgtcaaatttgatagacagaaaaaactgtttctggggtttcc -tgactattcggaaatggtccctccaagatccatgtaccccaacaccaccctacctggcta -cgctcctctcacaactttgagatcaagatgccacgtgtgccttcctcacatcggcgcttt -ccagtgatgcccagtgggggacacaaagggcccagcaagacctcaggaaggacggacaca -ggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcag -gaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctc -agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc -ggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccac -agacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggccta -cacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaagga -cggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaag -acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggg -ccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaa -tggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc -aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac -aggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca -ggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacct -cagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggct -cggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcca -cagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtc -tacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagg -acggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaa -gacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggg -gccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagaca -atggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacaca -ccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggac -acaggtctacacaccaggccacagacaatggggctc-gggggccaacctcagcaagacct -caggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaac -ctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatgggg -ctcgggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggcc -acagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggc -ctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaa -ggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcag -caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg -gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga -caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctaca -caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg -acacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacc -tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggcca -acctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatgg -ggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccagg -ccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacag -gtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcagg -aaggacggacacaggtctacacaccaggccacagacaatggggctc-------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------gggggccaacctcagcaagacctcaggaagga -cggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaag -acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggg -ccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaa -tggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacac -caggccacagacaatggggctc-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------gggggccaacctcagca -agacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggg -gccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagaca -atggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac -caggccacagaca ->ref_chr20:62057392-62058978 -cctcattctaaaacctaatgtcaaatttgatagacagaaaaaactgtttctggggtttcc -tgactattcggaaatggtccctccaagatccatgtaccccaacaccaccctacctggcta -cgctcctctcacaactttgagatcaagatgccacgtgtgccttcctcacatcggcgcttt -ccagtgatgcccagtgggggacacaaagggcccagcaagacctcaggaaggacggacaca -ggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcag -gaaggacggacacaggcctacacaccaggccacagacaatggggctcg------------ ------------------------------------------------------------- ------------------------------------------------------------- ---------------gggggccaacctcagcaagacctcaggaaggacggacacaggccta -cacaccaggccacagacaatggggctcg-------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc -aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac -aggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca -ggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacct -cagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggct -c-gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcca -cagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcc -tacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagg -acggacacaggtc----------------------------------------------- ---------------------------tacacaccaggccacagacaatggggctcggggg -gccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagaca -atggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacaca -ccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggac -acaggtctacacaccaggccacagacaatggggctc-gggggccaacctcagcaagacct -caggaaggacggacacaggtctacacaccaggccacagacaatggggctcg--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------------gg -gggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacaga -caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctaca -caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg -acacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacc -tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac -caggccacagaca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_025e148dfa15d03cf2f4a4fffa42166a.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_025e148dfa15d03cf2f4a4fffa42166a.msa deleted file mode 100644 index 4c51a2dd..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_025e148dfa15d03cf2f4a4fffa42166a.msa +++ /dev/null @@ -1,30 +0,0 @@ ->syndip_1_chr20:60702942-60703115 -tgtcgctacatattaccaacatttgtcattgtctttctttcttttctttctctctctctc -tttcttttccttctttctttctttctttctttctttctttctttctttctttctttcttt -ctttcttttctttccttcttctttctttctttctttctttctttctttctttctttcttt -ctttctttctttctttctttctttctttctttctttcttctttctttctttttctttctt -ttttttttgggatggagtctcgctctg ->syndip_2_chr20:60702942-60703115 -tgtcgctacatattaccaacatttgtcattgtctttctttcttttctttctctctctctc -tctctttcttttccttctttctttctttctttctttctttcttcctttctttctttcttt -ctttctttctttctttctttctttct---tttctttccttctttctttctttctttcttt -tttttt------------------------------------------------------ ---------gggatggagtctcgctctg ->p:HG002_1_chr20:60702942-60703115 -tgtcgctacatattaccaacatttgtcattgtctttctttcttttctttctctctctctc -tctctttcttttccttctttctttctttctttctttctttcttcctttctttctttcttt -ctttctttctttctttctttctttct---tttctttccttctttctttctttctttcttt -tttttt------------------------------------------------------ ---------gggatggagtctcgctctg ->p:HG002_2_chr20:60702942-60703115 -tgtcgctacatattaccaacatttgtcattgtctttctttcttttctttctctctctctc -tttcttttccttctttctttctttctttctttctttctttctttctttctttctttcttt -ctttcttttctttccttcttctttctttctttctttctttctttctttctttctttcttt -ctttctttctttctttctttctttctttctttctttcttctttctttctttttctttctt -ttttttttgggatggagtctcgctctg ->ref_chr20:60702942-60703115 -tgtcgctacatattaccaacatttgtcattgtctttctttcttttctttctctctctctc -tttct----------------------------tttccttctttctttctttctttcttt -ctttctttctttctttctttcttttc---tttccttctttctttctttctttctttcttt -tttttt------------------------------------------------------ ---------gggatggagtctcgctctg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_02d8c59aa7cd0c43327d9132316379b9.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_02d8c59aa7cd0c43327d9132316379b9.msa deleted file mode 100644 index c8f2b8ea..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_02d8c59aa7cd0c43327d9132316379b9.msa +++ /dev/null @@ -1,160 +0,0 @@ ->syndip_1_chr20:61282306-61283869 -ccaagattgcgccactgcactccagcctgggagacagcgtcagactcagtctcaaaaaag -aaaaaagaaattcacctttggctctatccctcttactttcataaaacattctgtattttc -aaaatgccaaaaaaattattgttaaagactttagaaaacagaaaagtacaaagaataaaa -gggtaacttcatttccctcctctgaacaaaccacttttaatctttggcatggtgtgtgtg ---tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgtacttgtacctgcacacacaac -tggatgagcatggtgtgtgtgtacacatgtattgtgttcatatgtacatatgtgggtgcc -ttgtgcacacgtgtgtggctgtgggatgttcagatgtgcatgtgagttggtgtgtgtgca -tgcccacaagcatgcatgtaaatgtgatgtgctgtgtatgcacacggataagcatgtgtg -aaggagtgcatgagagtggtgcatggctgtggtgtgcacgtgtgtgcgtgtgatgcatgt -gcatttgcacgcatgtgctgtggtgtgtgtgatgtacgtgcatttgcacgcatgtgctgt -ggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtgtgtgtgatgtacgtgcattt -gcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtg -tgtgatgtacgtgcgtttgcacgcgt---------------------------------- ----gtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtga -tgtacgtgcgtttgcacgcgtgtgctgtg----------------gtgtgtgatgtacgt -gcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgt -ggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcg -tttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgttctgtggc -gtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgttt -gcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtg -tgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgca -cgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgt -gatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgc -gtgtgc------------------------------------------------------ ------------------------------tgtgtgatgtgtgtgcgtttgcacgcgtgtg -ctgtggtgtgtgatgtaggtgcatttacacgcgtgtgctgtggtgtgtgatgtaggtgca -tttgcacgcgtgtgctgtggtgtgtgtgatgtgtgtgcgtttgcacgtgtgtgctgtggt -gtgtgtgtggtgagtggatgggaggatatttccagtgctctcctcctgggactgatgcca -tgatgaaaatctgtgtaaaccagacagcacatctctcatcatttctttgtgatgggtcat -tagaagcaggattctgaatttctggttcagaagctctgttacgtggccctggatccacac -atctaaacgatgtttcagaaaggtggtgccaatttatattcccagcaaggacactggct ->syndip_2_chr20:61282306-61283869 -ccaagattgcgccactgcactccagcctgggagacagcgtcagactcagtctcaaaaaag -aaaaaagaaattcacctttggctctatccctcttactttcataaaacattctgtattttc -aaaatgccaaaaaaattattgttaaagactttagaaaacagaaaagtacaaagaataaaa -gggtaacttcatttccctcctctgaacaaaccacttttaatctttggcatggtgtgtgtg ---tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgtacttgtacctgcacacacaac -tggatgagcatggtgtgtgtgtacacatgtaatgtgttcatatgtacatatgtgggtgcc -ttgtgcacacgtgtgtggctgtgggatgttcagatgtgcatgtgagttggtgtgtgtgca -tgcccacaagcatgcatgtaaatgtgatgtgctgtgtatgcacacggataagcatgtgtg -aaggagtgcatgagagtggtgcatggctgtggtgtgcacgtgtgtgcgtgtgatgcatgt -gcatttgcacgcatgtgctgtggtgtgtgtgatgtacgtgcatttgcacgcgtgtgctgt -ggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtgtgtgtgatgtacgtgcattt -gcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtg -tgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgatgtacgtgcgtttgcacg -cgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtga -tgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtggcgtgtgtgatgtacgt -gcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgt -ggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcg -tttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggc -gtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgttt -gcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtg -tgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgca -cgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgt -gatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgc -gcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgat -gtgtgtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcgtttgcacgcgtgtg -ctgtggtgtgtgatgtaggtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgca -tttgcacgtgtgtgctgtggtgtgtgtgatgtgtgtgcatttgcacgtgtgtgctgtggt -gtgtgtgtggtgagtggatgggaggatatttccagtgctctcctcctgggactgatgcca -tgatgaaaatctgtgtaaaccagacagcacatctctcatcatttctttgtgatgggtcat -tagaagcaggattctgaatttctggttcagaagctctgttacgtggccctggatccacac -atctaaacgatgtttcagaaaggtggtgccaatttatattcccagcaaggacactggct ->p:HG002_1_chr20:61282306-61283869 -ccaagattgcgccactgcactccagcctgggagacagcgtcagactcagtctcaaaaaag -aaaaaggaaattcacctttggctctatccctcttactttcataaaacattctgtattttc -aaaatgccaaaaaaattattgttaaagactttagaaaacagaaaagtacaaagaataaaa -gggtaacttcatttccctcctctgaacaaaccacttttaatctttggcatggtgtgtgtg ---tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgtacttgtacctgcacacacaac -tggatgagcatggtgtgtgtgtacacatgtaatgtgttcatatgtacatatgtgggtgcc -ttgtgcacacgtgtgtggctgtgggatgtttagatgtgcatgtgagttggtgtgtgtgca -tgcccacaagcatgcatgtaaatgtgatgtgctgtgtatgcacacggataagcatgtgtg -aaggagtgcatgagagtggtgcatggctgtggtgtgcacgtgtgtgcgtgtgatgcatgt -gcatttgcacgcatgtgctgtggtgtgtgtgatgtacgtgcatttgcacgcgtgtgctgt -ggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtgtgtgtgatgtacgtgcattt -gcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtg -tgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgatgtacgtgcgtttgcacg -cgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtga -tgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtggcgtgtgtgatgtacgt -gcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgt -ggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcg -tttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggc -gtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgttt -gcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtg -tgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgca -cgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgt -gatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgc -gcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgat -gtgtgtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcgtttgcacgcgtgtg -ctgtggtgtgtgatgtaggtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgca -tttgcacgtgtgtgctgtggtgtgtgtgatgtgtgtgcatttgcacgtgtgtgctgtggt -gtgtgtgtggtgagtggatgggaggatatttccagtgctctcctcctgggactgatgcca -tgatgaaaatctgtgtaaaccagacagcacatctctcatcatttctttgtgatgggtcat -tagaagcaggattctgaatttctggttcagaagctctgttacgtggccctggatccacac -atctaaacgatgtttcagaaaggtggtgccaatttatattcccagcaaggacactggct ->p:HG002_2_chr20:61282306-61283869 -ccaagattgcgccactgcactccagcctgggagacagcgtcagactcagtctcaaaaaag -aaaaaggaaattcacctttggctctatccctcttactttcataaaacattctgtattttc -aaaatgccaaaaaaattattgttaaagactttagaaaacagaaaagtacaaagaataaaa -gggtaacttcatttccctcctctgaacaaaccacttttaatctttggcatggtgtgtgtg ---tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgtacttgtacctgcacacacaac -tggatgagcatggtgtgtgtgtacacatgtattgtgttcatatgtacatatgtgggtgcc -ttgtgcacacgtgtgtggctgtgggatgttcggatgtgcatgtgagttggtgtgtgtgca -tgcccacaagcatgcatgtaaatgtgatgtgctgtgtatgcacacggataagcatgtgtg -aaggagtgcatgagagtggtgcatggctgtggtgtgcacgtgtgtgcgtgtgatgcatgt -gcatttgcacgcatgtgctgtggtgtgtgtgatgtacgtgcatttgcacgcatgtgctgt -ggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtgtgtgtgatgtacgtgcattt -gcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtg -tgtgatgtacgtgcgtttgcacgcgt---------------------------------- ----gtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtga -tgtacgtgcgtttgcacgcgtgtgctgtg----------------gtgtgtgatgtacgt -gcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgt -ggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcg -tttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgttctgtggc -gtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgttt -gcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtg -tgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgca -cgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgt -gatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgc -gtgtgc------------------------------------------------------ ------------------------------tgtgtgatgtgtgtgcgtttgcacgcgtgtg -ctgtggtgtgtgatgtaggtgcatttacacgcgtgtgctgtggtgtgtgatgtaggtgca -tttgcacgcgtgtgctgtggtgtgtgtgatgtgtgtgcgtttgcacgtgtgtgctgtggt -gtgtgtgtggtgagtggatgggaggatatttccagtgctctcctcctgggactgatgcca -tgatgaaaatctgtgtaaaccagacagcacatctctcatcatttctttgtgatgggtcat -tagaagcaggattctgaatttctggttcagaagctctgttacgtggccctggatccacac -atctaaacgatgtttcagaaaggtggtgccaatttatattcccagcaaggacactggct ->ref_chr20:61282306-61283869 -ccaagattgcgccactgcactccagcctgggagacagcgtcagactcagtctcaaaaaag -aaaaaagaaattcacctttggctctatccctcttactttcataaaacattctgtattttc -aaaatgccaaaaaaattattgttaaagactttagaaaacagaaaagtacaaagaataaaa -gggtaacttcatttccctcctctgaacaaaccacttttaatctttggcatggtgtgtgtg -catgtgtgtgtgtgtgtgtgtgtgtgtatgtctatctgtacttgtacctgcacacacaac -tggatgagcatggtgtgtgtgtacacatgtaatgtgttcatatgtacatatgtgggtgcc -ttgtgcacacgtgtgtggctgtgggatgttcagatgtgcatgtgagttggtgtgtgtgca -tgcccacaagcatgcatgtaaatgtgatgtgctgtgtatgcacacggataagcatgtgtg -aaggagtgcatgagagtggtgcatggctgtggtgtgcacgtgtgtgcgtgtgatgcatgt -gcatttgcacgcatgtgctgtggtgtgtgtgatgtacgtgcatttgcacgcgtgtgctgt -ggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtg-------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------gcgtgtga -tgtacgtgcgtttgcacgcgcgtgctgtg----------------gcgtgtgatgtacgt -gcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgt -ggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcg -tttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggc -gtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgttt -gcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtg -tgtgatgtacgtgcgtttgcacgcgcgtgctgtggc---------gtgtgtgcgtttgca -cgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgt -gatgtgtgtgcgtttgcacgcgtgtgctgtggtgtgtgtgatgtgtgtgcgtttgcacgc -gtgtgc------------------------------------------------------ -------------------------tgtggtgtgtgatgtaggtgcatttgcacgcgtgtg -ctgtggtgtgtgatgtaggtgcatttacacgcgtgtgctgtggtgtgtgatgtaggtgca -tttgcacgtgtgtgctgtggtgtgtgtgatgtgtgtgcatttgcacgtgtgtgctgtggt -gtgtgtgtggtgagtggatgggaggatatttccagtgctctcctcctgggactgatgcca -tgatgaaaatctgtgtaaaccagacagcacatctctcatcatttctttgtgatgggtcat -tagaagcaggattctgaatttctggttcagaagctctgttacgtggccctggatccacac -atctaaacgatgtttcagaaaggtggtgccaatttatattcccagcaaggacactggct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_03c47b81edc7fd199d3060b4b5aafe34.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_03c47b81edc7fd199d3060b4b5aafe34.msa deleted file mode 100644 index e0c871c5..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_03c47b81edc7fd199d3060b4b5aafe34.msa +++ /dev/null @@ -1,105 +0,0 @@ ->syndip_1_chr20:32722224-32723412 -gacaagagcaaaactctgtctcg--aaaaaaaaaaaaaaaaaaaaaaaggatacagtgtg -gtggggtgaggaagacagggaagactggggacagggacactagacagaggtctcctgaaa -attagtgcccataacaggtgtttggtagacaggtctcagccctcagacaaacccatttcc -aaagatgaaggccagagaatgagaataatgatttatcgttctggccgggtgtgatggctc -atgcctgtaatcccagcgctgtgggaggcgtggccggcagatcacctgaggtcaggagtt -caagaccagcctggccaacatggtgaaacttggtctctactaaaaatacaaaaattagcc -aggcatggtggtgggcgcctgcaatcccagctacccagaaggctgagtcagaagaatcac -ttgaacccgggaggtggaggttgcagtgagccgagatcgtgccactgcactccagcctgg -gtgacagagtgagactcaggaaaaaaaaaaaaaagacttggccgagcccagtggctcaca -cctgtaatcccagcactttgggaggctgaggcgggtggatcacgaggtcaagagatcgag -accatcctggctaacacggtgaaaccccatctctactaaaaaatacaaaaaattagccgg -gcgtggtggtgggcacctgtagtcccagctactcgggaggctgaggcagaatggcgtgaa -cctggtaggcagagcttgcagtgagctgagatcacgccactgcactccagcctgggtgac -agagcaagactccatctcaaaaataaataaataaataaataaata-------aataataa -taataataataaagacttgtgatcctctccctctccctctccctctccgtctccctctcc -ctctccctctccctccctctccgtctccgtctccgtctccgtctccctctccctctcccc -acggtctccctctcatgcggagccgaagctggactgtactgctgccatctcggctcactg -caacctccctgcctgattctcctgcctcagcctgccgagtgcctgcgattgcaggcacgc -gccgccacgcctgactggttttggtggagacggggtttcgctgtgttggccgggccggtc -tccagcccctaaccgcgagtgatccgccaacctcggcctcccgaggtgccgggattgca ->syndip_2_chr20:32722224-32723412 -gacaagagcaaaactctgtctcgaaaaaaaaaaaaaaaaaaaaaaaaaggatacagtgtg -gtggggtgaggaagacagggaagactggggacagggacactagacagaggtctcctgaaa -attagtgcccataacaggtgtttggtagacaggtctcagccctcagacaaacccatttcc -aaagatgaaggccagagaatgagaataatgatttatcgttctggccgggtgtgatggctc -atgcctgtaatcccagcgctgtgggaggcgtggccggcagatcacctgaggtcaggagtt -caagaccagcctggccaacatggtgaaacttggtctctactaaaaatacaaaaattagcc -aggcatggtggtgggcgcctgcaatcccagctacccagaaggctgagtcagaagaatcac -ttgaacccgggaggtggaggttgcagtgagccgagatcgtgccactgcactccagcctgg -gtgacagagtgagactcaggaaaaaaaaaaaaaagacttggccgagcccagtggctcaca -cctgtaatcccagcactttgggaggctgaggcgggtggatcacgaggtcaagagatcgag -accatcctggctaacacggtgaaaccccatctctactaaaaaatacaaaaaattagccgg -gcgtggtggtgggcacctgtagtcccagctactcgggaggctgaggcagaatggcgtgaa -cctggtaggcagagcttgcagtgagctgagatcacaccactgcactccagcctgggtgac -agagcaagactccatctcaaaaataaataaataaataaataaataaataaataataataa -taataataataaagacttgtgatcctctccctctccctctccctctccgtctccctctcc -ctctccctctccctccctctccgtctccgtctccgtctccgtctccctctccctctcccc -acggtctccctctcatgcggagccgaagctggactgtactgctgccatctcggctcactg -caacctccctgcctgattctcctgcctcagcctgccgagtgcctgcgattgcaggcacgc -gccgccacgcctgactggttttggtggagacggggtttcgctgtgttggccgggccggtc -tccagcccctaaccgcgagtgatccgccaacctcggcctcccgaggtgccgggattgca ->p:HG002_1_chr20:32722224-32723412 -gacaagagcaaaactctgtctcgaaaaaaaaaaaaaaaaaaaaaaaaaggatacagtgtg -gtggggtgaggaagacagggaagactggggacagggacactagacagaggtctcctgaaa -attagtgcccataacaggtgtttggtagacaggtctcagccctcagacaaacccatttcc -aaagatgaaggccagagaatgagaataatgatttatcgttctggccgggtgtgatggctc -atgcctgtaatcccagcgctgtgggaggcgtggccggcagatcacctgaggtcaggagtt -caagaccagcctggccaacatggtgaaacttggtctctactaaaaatacaaaaattagcc -aggcatggtggtgggcgcctgcaatcccagctacccagaaggctgagtcagaagaatcac -ttgaacccgggaggtggaggttgcagtgagccgagatcgtgccactgcactccagcctgg -gtgacagagtgagactcaggaaaaaaaaaaaaaagacttggccgagcccagtggctcaca -cctgtaatcccagcactttgggaggctgaggcgggtggatcacgaggtcaagagatcgag -accatcctggctaacacggtgaaaccccatctctactaaaaaatacaaaaaattagccgg -gcgtggtggtgggcacctgtagtcccagctactcgggaggctgaggcagaatggcgtgaa -cctggtaggcagagcttgcagtgagctgagatcacaccactgcactccagcctgggtgac -agagcaagactccatctcaaaaataaataaataaataaataaata-------aataataa -taataataataaagacttgtgatcctctccctctccctctccctctccgtctccctctcc -ctctccctctccctccctctccgtctccgtctccgtctccgtctccctctccctctcccc -acggtctccctctcatgcggagccgaagctggactgtactgctgccatctcggctcactg -caacctccctgcctgattctcctgcctcagcctgccgagtgcctgcgattgcaggcacgc -gccgccacgcctgactggttttggtggagacggggtttcgctgtgttggccgggccggtc -tccagcccctaaccgcgagtgatccgccaacctcggcctcccgaggtgccgggattgca ->p:HG002_2_chr20:32722224-32723412 -gacaagagcaaaactctgtctcg--aaaaaaaaaaaaaaaaaaaaaaaggatacagtgtg -gtggggtgaggaagacagggaagactggggacagggacactagacagaggtctcctgaaa -attagtgcccataacaggtgtttggtagacaggtctcagccctcagacaaacccatttcc -aaagatgaaggccagagaatgagaataatgatttatcgttctggccgggtgtgatggctc -atgcctgtaatcccagcgctgtgggaggcgtggccggcagatcacctgaggtcaggagtt -caagaccagcctggccaacatggtgaaacttggtctctactaaaaatacaaaaattagcc -aggcatggtggtgggcgcctgcaatcccagctacccagaaggctgagtcagaagaatcac -ttgaacccgggaggtggaggttgcagtgagccgagatcgtgccactgcactccagcctgg -gtgacagagtgagactcaggaaaaaaaaaaaaaagacttggccgagcccagtggctcaca -cctgtaatcccagcactttgggaggctgaggcgggtggatcacgaggtcaagagatcgag -accatcctggctaacacggtgaaaccccatctctactaaaaaatacaaaaaattagccgg -gcgtggtggtgggcacctgtagtcccagctactcgggaggctgaggcagaatggcgtgaa -cctggtaggcagagcttgcagtgagctgagatcacgccactgcactccagcctgggtgac -agagcaagactccatctcaaaaataaataaataaataaataaata-------aataataa -taataataataaagacttgtgatcctctccctctccctctccctctccgtctccctctcc -ctctccctctccctccctctccgtctccgtctccgtctccgtctccctctccctctcccc -acggtctccctctcatgcggagccgaagctggactgtactgctgccatctcggctcactg -caacctccctgcctgattctcctgcctcagcctgccgagtgcctgcgattgcaggcacgc -gccgccacgcctgactggttttggtggagacggggtttcgctgtgttggccgggccggtc -tccagcccctaaccgcgagtgatccgccaacctcggcctcccgaggtgccgggattgca ->ref_chr20:32722224-32723412 -gacaagagcaaaactctgtctcg---aaaaaaaaaaaaaaaaaaaaaaggatacagtgtg -gtggggtgaggaagacagggaagactggggacagggacactagacagaggtctcctgaaa -attagtgcccataacaggtgtttggtagacaggtctcagccctcagacaaacccatttcc -aaagatgaaggccagagaatgagaataatgatttatcgttctggccgggtgtgatggctc -atgcctgtaatcccagcgctgtgggaggcgtggccggcagatcacctgaggtcaggagtt -caagaccagcctggccaacatggtgaaacttggtctctactaaaaatacaaaaattagcc -aggcatggtggtgggcgcctgcaatcccagctacccagaaggctgagtcagaagaatcac -ttgaacccgggaggtggaggttgcagtgagccgagatcgtgccactgcactccagcctgg -gtgacagagtgagactcaggaaaaaaaaaaaaaagacttggccgagcccagtggctcaca -cctgtaatcccagcactttgggaggctgaggcgggtggatcacgaggtcaagagatcgag -accatcctggctaacacggtgaaaccccatctctactaaaaaatacaaaaaattagccgg -gcgtggtggtgggcacctgtagtcccagctactcgggaggctgaggcagaatggcgtgaa -cctggtaggcagagcttgcagtgagctgagatcacgccactgcactccagcctgggtgac -agagcaagactccatctcaaaaataaataaataaataaataaata-------aataataa -taataataataaagacttgtgatcctctccctctccctctccctctccgtctccctctcc -ctctccctctccctccctctccgtctccgtctccgtctccgtctccctctccctctcccc -acggtctccctctcatgcggagccgaagctggactgtactgctgccatctcggctcactg -caacctccctgcctgattctcctgcctcagcctgccgagtgcctgcgattgcaggcacgc -gccgccacgcctgactggttttggtggagacggggtttcgctgtgttggccgggccggtc -tccagcccctaaccgcgagtgatccgccaacctcggcctcccgaggtgccgggattgca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_046a78a601e1df55d59e59ee9193f41b.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_046a78a601e1df55d59e59ee9193f41b.msa deleted file mode 100644 index e78f1c2d..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_046a78a601e1df55d59e59ee9193f41b.msa +++ /dev/null @@ -1,100 +0,0 @@ ->syndip_1_chr20:20295804-20296540 -gaggaaacacacgggaatgagcaaagcccatgtggcatccaggcctagagagatgcctgt -ggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagccagaggctca -gtcctggctttttccaaactcttctccagaggagcccgcccttgcacaccaacgcctgca -tgcttccctccttccttccttccttccctcctttccttccttctttcttttcttcctccc -tcccttcct---tcccttccttcccttccttccctccttttcttccttctttccttcctt -ccttccctccctccttcccttccttccttccttcccttccttccttctctccttccttcc -ttccctccctccttcccttccttccttctctccttccttc--ccttccttccttctctcc -ttccttcccttccttccttctctccttccttcccttccttccttctctccttccttccct -tccttccttctctccttccttcccttgctt--cctttcttccttcctttgcttccttgct -tccttctttcctttcttcatccctccctccctccttccttcctttccttccttccctcta -tccttccttccttcctttctttctccctcccttccttcccttccttccttccctcttttc -cttccatctttcctttcttcctccctccctccctccttccctccttcattccttccttcc -ctcctttccttccttcacctccttcccttctctcctcccttcatcccttccttcctttct -tccttccctccctcttccttcctttcttcacccctcccccttccctcatcccttccctcc -ttcccttccttccttccttccctccttccttcccttccttccttccttgcttccttcctt -ctttcctttcttcatccctccttccctccctccctccttcctgccttccttctttctttc -ttttctttcttcctccctccctccttccttccctccttcctgccttccttccttcctttc -tttttcctccctccctccttccttctttactcccttccttccttccttcctcccctcact -caattt ->syndip_2_chr20:20295804-20296540 -gaggaaacacacgggaatgagcaaagcccatgtggcatccaggcctagagagatgcctgt -ggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagccagaggctca -gtcctggctttttccaaactcttctccagaggagcccgcccttgcacaccaacgcctgca -tgcttccctccttccttccttccttccctcct-tccttccttccttccttccttcctgcc -tgcctgcctgccttcctgccttcccttcctccctccc--tccctacctccctccctcctt -ccttcccttcctccctccctcccttctttacttccttcc-------tccttccctcctcc -tttcctccatccttccctcccttctttcctttcttcctcctgccctccctccttctttcc -cttcctccctcccttccttcccatcctccttccc-tccctccttccttcctgccttcctt -ccttccctccatccttccttccttcctttcttcctccctcccttccttcctcccttcctt -cccttccttcct-----------tccctcttttccttccatctttcctttcttcctccct -ccctccctccttccctccttcattccttccttccctcctttccttccttcacctccttcc -cttctctcctcccttcatcccttccttcctttcttccttccctccctcttccttcctttc -ttcacccctcccccttccctcatcccttccctccttcccttccttccttccttccctcct -tccttccct---tccttccttccttccctccttccttcccttccttccttgcttccttcc -ttccttcccttccttccttgcttccttccttccttcccttccttccttgcttccttcctt -ctttcctttcttcatccctccttccctccctccctccttcctgccttccttctttctttc -ttttctttcttcctccctccctccttccttccctccttcctgccttccttccttcctttc -tttttcctccctccctccttccttctttactcccttccttccttccttcctcccctcact -caattt ->p:HG002_1_chr20:20295804-20296540 -gaggaaacacacgggaatgagcaaagcccatgtggcatccaggcctagagagatgcctgt -ggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagccagaggctca -gtcctggctttttccaaactcttctccagaggagcccgcccttgcacaccaacgcctgca -tgcttccctccttccttccttccttccctcct-tccttccttccttccttccttcctgcc -tgcctgcctgccttcctgccttcccttcctccctccc--tccctacctccctccctcctt -ccttcccttcctccctccctcccttctttacttccttcc-------tccttccctcctcc -tttcctccatccttccctcccttctttcctttcttcctcctgccctccctccttctttcc -cttcctccctcccttccttcccatcctccttccc-tccctccttccttccttctttcttt -tcttcctccctcccttccttcccttccttc--ccttccttccctccttttcttccttctt -tccttccttcct-----------tccctccctccttcccttccttccttccttcctccct -ccctccctccttccctccttcattccttccttccctcctttccttccttcacctccttcc -cttctctcctcccttcatcccttccttcctttcttccttccctccctcttccttcctttc -ttcacccctcccccttccctcatcccttccctccttcccttccttccttccttccctcct -tccttccct---tccttccttccttccctccttccttcccttccttccttgcttccttcc -ttccttcccttccttccttgcttccttccttccttcccttccttccttgcttccttcctt -ctttcctttcttcatccctccttccctccctccctccttcctgccttccttctttctttc -ttttctttcttcctccctccctccttccttccctccttcctgccttccttccttcctttc -tttttcctccctccctccttccttctttactcccttccttccttccttcctcccctcact -caattt ->p:HG002_2_chr20:20295804-20296540 -gaggaaacacacgggaatgagcaaagcccatgtggcatccaggcctagagagatgcctgt -ggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagccagaggctca -gtcctggctttttccaaactcttctccagaggagcccgcccttgcacaccaacgcctgca -tgcttccctccttccttccttccttccctcctttccttccttctttcttttcttcctccc -tcccttcct---tcccttccttcccttccttccctccttttcttccttctttccttcctt -ccttccctccctccttcccttccttccttccttcccttccttccttctctccttccttcc -ttccctccctccttcccttccttccttctctccttccttc--ccttccttccttctctcc -ttccttcccttccttccttctctccttccttcccttccttccttctctccttccttccct -tccttccttctctccttccttcccttgctt--cctttcttccttcctttgcttccttgct -tccttctttcctttcttcatccctccctccctccttccttcctttccttccttccctcta -tccttccttccttcctttctttctccctcccttccttcccttccttccttccctcttttc -cttccatctttcctttcttcctccctccctccctccttccctccttcattccttccttcc -ctcctttccttccttcacctccttcccttctctcctcccttcatcccttccttcctttct -tccttccctccctcttccttcctttcttcacccctcccccttccctcatcccttccctcc -ttcccttccttccttccttccctccttccttcccttccttccttccttgcttccttcctt -ctttcctttcttcatccctccttccctccctccctccttcctgccttccttctttctttc -ttttctttcttcctccctccctccttccttccctccttcctgccttccttccttcctttc -tttttcctccctccctccttccttctttactcccttccttccttccttcctcccctcact -caattt ->ref_chr20:20295804-20296540 -gaggaaacacacgggaatgagcaaagcccatgtggcatccaggcctagagagatgcctgt -ggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagccagaggctca -gtcctggctttttccaaactcttctccagaggagcccgcccttgcacaccaacgcctgca -tgcttccctccttccttccttccttccctcctttccttccttctttcttttcttcctccc -tcccttcct---tcccttccttc------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------ccttccttccctccttttcttccttctt -tccttccttcct-----------tccctccctccttcccttccttccttccttcctccct -ccctccctccttccctccttcattccttccttccctcctttccttccttcacctccttcc -cttctctcctcccttcatcccttccttcctttcttccttccctccctcttccttcctttc -ttcacccctcccccttccctcatcccttccctccttcccttccttccttccttccctcct -tccttccct--------------------------------------------------- ------------------------------------tccttccttccttgcttccttcctt -ctttcctttcttcatccctccttccctccctccctccttcctgccttccttctttctttc -ttttctttcttcctccctccctccttccttccctccttcctgccttccttccttcctttc -tttttcctccctccctccttccttctttactcccttccttccttccttcctcccctcact -caattt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_048024c0ae8f1cb7cc70270fc649fef6.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_048024c0ae8f1cb7cc70270fc649fef6.msa deleted file mode 100644 index c272df87..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_048024c0ae8f1cb7cc70270fc649fef6.msa +++ /dev/null @@ -1,140 +0,0 @@ ->syndip_1_chr20:14861937-14862741 -cttccaaagtgaaataggacattggaggttttatatataaatatatatatatatttatat -atatatttatatatatatatatttatatatatttatatatatatttatatatatatttat -atatatatttatatatatatttatatatatatttatatatatatttatatatatatttat -atatatatttatatatatttatatatatttatatatatttttatatatttttatatatat -aaatatataaaaatatatataaatatataaaaatatataaaaatatataaatatatataa -atatataaatatatataaatatatataaatatatatttatatataaatatatataaatat -atatttatacataaatatatataaatatatatttatacataaatatataaatatatataa -tatatataaatatatattatacataaatatataaatatatattatacataaatatataaa -tatatataaatatatataaatatatatttatacataaatatataaatatatatataaata -tatataaatatatataaatatatatataaatatatatataaatatatataaatatatata -taaatatatatataaatatatataaatatatataaatatatatataaatatatataaata -tatataaatatatatttatatattaatatataaatatatataa-atatatatttatatat -t-------aatatataaatatat-----------atatattaatatatataaatatatat -aaatatatatttatatattaatatatatatattaatatatatatatttatatattaatat -atatatttatatattaatatatataaatatattactatgtatatttatatatatttatat -aaatatatataaatatatgtaaatatatatataaaaatatatattaatatataaaatata -tatataaatataaataaatatatatataaatatatataaataaatatatatataaatata -tataaataaatatataaatatatataaatatatatataaatatatataaatatatataaa -tatatataaaaatatatataaatatatatataaatatatataaatatatatataaatata -tatataaatatatatataaatatatataaatatatatataaatatatataaatatatata -taattatatataaatatatataaatatatataaatatatatataaatatatataaatata -tataaatatatataaatatatatataaatatatataaatatatatatataaatatatata -aatatatatataaatatatataaatatatatatataaatatatataaatatatatataaa -tatatataaatatatatataaatataaatatatatgtataaatatatatataaatataaa -tatatatgtataaatatatatataaatatatatatataaatatatatatacatatataaa -tatatatataaatatatataaaaatatatatatatatatttttttaatagagaggatgaa -ga ->syndip_2_chr20:14861937-14862741 -cttccaaagtgaaataggacattggaggtttt---------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------atatataaa -tatatatatatatatttatatatatatttatatatatatatttatatatatttatatata -tttatatatatatttttatatatatttatatatatttatatatttatatatatttatata -tatttttatatatataaatatataaaaatatataaatatatat----aaatatataaata -tatataaatatatatttatacataaatatataaatatatataatatatataaatatatat -tatacataaatatataaatatatattatacataaatatataaatatatataaatatatat -aaatatatatttatacataaatatataaat----atatatatatataaatatatataaat -atatatttatatattaatatatataaatatattactatgtatatttatatatatttatat -aa--atatataaatatatgtaaatatatatataaaaatatatattaatatataaaa---- ------atatatatataaatatatatataaatatatataaataaatatatataaatatata -tataaat--atatataaatatatataaatatatatataaatatatataaatatatataaa -tatatatataaatatatatataaatatatataaatatatataaataaatatataaatata -tatataaatatatataaatatatatataaatatatataaatatatatataaatatatata -aatatatatataaatatatataaat--------atatatataaatatatatataaatata -tataaatatatataaatatatatatataaatatatataaatatatatataaatataaata -tatataaatatataaaaatatatatataaatataaatatatataaatatatatgtataaa -tatatatataaatataaatatatataaatatatatatataaatatatatataaatatata -taaatatatataaaaatatatataaatatatatataaatatatatataaatatatataaa -tatatatataaatatatataaaaatatatatatatttttttttttaatagagaggatgaa -ga ->p:HG002_1_chr20:14861937-14862741 -cttccaaagtgaaataggacattggaggtttt---------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------atatataaa -tatatatatatatatttatatatatatttatatatatatatttatatatatttatatata -tttatatatatatttttatatatatttatatatatttatatatttatatatatttatata -tatttttatatatataaatatataaaaatatataaatatatat----aaatatataaata -tatataaatatatatttatacataaatatataaatatatataatatatataaatatatat -tatacataaatatataaatatatattatacataaatatataaatatatataaatatatat -aaatatatatttatacataaatatataaat----atatatatatataaatatatataaat -atatatttatatattaatatatataaatatattactatgtatatttatatatatttatat -aa--atatataaatatatgtaaatatatatataaaaatatatattaatatataaaa---- ------atatatatataaatatatatataaatatatataaataaatatatataaatatata -tataaat--atatataaatatatataaatatatatataaatatatataaatatatataaa -tatatatataaatatatatataaatatatataaatatatataaataaatatataaatata -tatataaatatatataaatatatatataaatatatataaatatatatataaatatatata -aatatatatataaatatatataaat--------atatatataaatatatatataaatata -tataaatatatataaatatatatatataaatatatataaatatatatataaatataaata -tatataaatatataaaaatatatatataaatataaatatatataaatatatatgtataaa -tatatatataaatataaatatatataaatatatatatataaatatatatataaatatata -taaatatatataaaaatatatataaatatatatataaatatatatataaatatatataaa -tatatatataaatatatataaaaatatatatatatttttttttttaatagagaggatgaa -ga ->p:HG002_2_chr20:14861937-14862741 -cttccaaagtgaaataggacattggaggttttatatataaatatatatatatatttatat -atatatttatatatatatatatttatatatatttatatatatatttatatatatatttat -atatatatttatatatatatttatatatatatttatatatatatttatatatatatttat -atatatatttatatatatttatatatatttatatatatttttatatatttttatatatat -aaatatataaaaatatatataaatatataaaaatatataaaaatatataaatatatataa -atatataaatatatataaatatatataaatatatatttatatataaatatatataaatat -atatttatacataaatatatataaatatatatttatacataaatatataaatatatataa -tatatataaatatatattatacataaatatataaatatatattatacataaatatataaa -tatatataaatatatataaatatatatttatacataaatatataaatatatatataaata -tatataaatatatataaatatatatataaatatatatataaatatatataaatatatata -taaatatatatataaatatatataaatatatataaatatatatataaatatatataaata -tatataaatatatatttatatattaatatataaatatatataa-atatatatttatatat -t-------aatatataaatatat-----------atatattaatatatataaatatatat -aaatatatatttatatattaatatatatatattaatatatatatatttatatattaatat -atatatttatatattaatatatataaatatattactatgtatatttatatatatttatat -aaatatatataaatatatgtaaatatatatataaaaatatatattaatatataaaatata -tatataaatataaataaatatatatataaatatatataaataaatatatatataaatata -tataaataaatatataaatatatataaatatatatataaatatatataaatatatataaa -tatatataaaaatatatataaatatatatataaatatatataaatatatatataaatata -tatataaatatatatataaatatatataaatatatatataaatatatataaatatatata -taattatatataaatatatataaatatatataaatatatatataaatatatataaatata -tataaatatatataaatatatatataaatatatataaatatatatatataaatatatata -aatatatatataaatatatataaatatatatatataaatatatataaatatatatataaa -tatatataaatatatatataaatataaatatatatgtataaatatatatataaatataaa -tatatatgtataaatatatatataaatatatatatataaatatatatatacatatataaa -tatatatataaatatatataaaaatatatatatatatatttttttaatagagaggatgaa -ga ->ref_chr20:14861937-14862741 -cttccaaagtgaaataggacattggaggtttt---------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------atatataaa -tatatatatatatatttatatatatatttatatatatatatttatatatatttatatata -tttatatatatatttatat----------------------------------------- ----------------------------atatataaatatatat----aaatatataaata -tatataaatatatatttatacataaatatataaatatata-------------------- --------atatatataaatatatattatacataaatatataaatatatataaatatatat -aaatatatatttatacataaatatataaat----atatatatatataaatatatataaat -atatatttatatattaatatatataaatatattactatgtatatttatatatatttatat -aaatatatataaatatatgtaaatatatatataaaaatatatattaatatataaaa---- ------atatatat--------------------------ataaatatatataaatatata -tataaat--atatataaat----------------------------------------- ------------------------------------------------------------- ------------------atatatatataaatatatataaatatatatataaatatatata -aatatatatataaatatatataaat--------atatatatataaatatatataa----- ------------------atatatatataaatatatataaatatatatataaatataaata -tatataaatatataaaaatatatatataaatataaatatatataaatatatatgtataaa -tatatatataaatataaatatatataaatatatatatataaatatatatataaat----- --------------------------atatatatataaatatatatataaatatatataaa -tatatatataaatatatataaatatatatatatatatttttttttaatagagaggatgaa -ga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_0553a98462cadf062d1641cfeb97a0df.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_0553a98462cadf062d1641cfeb97a0df.msa deleted file mode 100644 index 69c4f1a4..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_0553a98462cadf062d1641cfeb97a0df.msa +++ /dev/null @@ -1,85 +0,0 @@ ->syndip_1_chr20:63641637-63642225 -cgagcttccttcagggcactttcaatataatgaatttagccatctattactgcggctagt -tactgtcccgccaggaccagactctggacctgcctcgtgcgctgctggggacgcccagta -aacacgggaggagcccccgacccccaccccagctcagcgcctcggagtccccggccccgc -tctgcgcccctccgagctccgccctagccccgcccccgcccagtgccccgccccctgcct -gctgctagccctgcccccgccccggcccctgcccgctccgagctccgccctggccccgcc -ccggcccctgcccgctccgagctccgccctggccccgccccccgcccagtgccccgcccc -ctgcctgctgctagccctgcccccgccccggcccctgcccgctccgagctccgccccgg- ------------------------------------------------------------- ------------------------------------------------------------- -------------ccccgccccggcccctgcccgctccgagctccgccctggccccgcccc -cgcccagtgccccgccccctgactgctgctagccctgcccccgccccggcccctgcccgc -tccgagctccgccccggccccgccccggcccctgcccgctccgagctccgccccggcccc -gccccggcccctgcccgctccgagcttcgccccggccccgccccggcccctgcccgctcc -gagctccgccccggccccgcccccgcaccttctcgcgcagccgctcgcgcagtgcggcca -ggtgtgcctcgcggatctccttgctgagctccatcttgtagttgagcttctcctccgcct -ggcggctgaagttgttattctcctcc ->syndip_2_chr20:63641637-63642225 -cgagcttccttcagggcactttcaatataatgaatttagccatctattactgcggctagt -tactgtcccgccaggaccagactctggacctgcctcgtgcgctgctggggacgcccagta -aacacgggaggagcccccgacccccaccccagctcagcgcctcggagtccccggccccgc -tctgcgcccctccgagctccgccctagccccgcccccgcccagtgccccgccccctgcct -gctgctagccctgcccccgccccggcccctgcccgctccgagctccgccccggccccgcc -ccggcccctgcccgctccgagctccgccctggccccg-cccccgcccagtgccccgcccc -ctgactgctgctagccctgcccccgccccggcccctgcccgctccgagctccaccctggc -cccgcccccgcccagtgccccgccccctgcctgctgcttgccctgccccctccccggccc -ctgcccgctccgagctccgccccggccccgccccggcccagtgccccgccccctgcctgc -tgctagccctgcccccgccccggcccctgcccgctccgagctccgccctggccccgcccc -cgcccagtgccccgccccctgcctgctgcttgccctgccccctccccggcccctgcccgc -tccgagctccgccccggcctcgccccggcccctgcccgctccgagcttcgccccggcccc -gccccggcccctgcccgctccgagcttcgccccggccccgccccggcccctgcccgctcc -gagctccgccccggccccgcccccgcaccttctcgcgcagccgctcgcgcagtgcggcca -ggtgtgcctcgcggatctccttgctgagctccatcttgtagttgagcttctcctccgcct -ggcggctgaagttgttattctcctcc ->p:HG002_1_chr20:63641637-63642225 -cgagcttccttcagggcactttcaatataatgaatttagccatctattactgcggctagt -tactgtcccgccaggaccagactctggacctgcctcgtgcgctgctggggacgcccagta -aacacgggaggagcccccgacccccaccccagctcagcgcctcggagtccccggccccgc -tctgcgcccctccgagctccgccctagccccgcccccgcccagtgccccgccccctgcct -gctgctagccctgcccccgccccggcccctgcccgctccgagctccgccccggccccgcc -ccggcccctgcccgctccgagctccgccctggccccg-cccccgcccagtgccccgcccc -ctgactgctgctagccctgcccccgccccggcccctgcccgctccgagctccaccctggc -cccgcccccgcccagtgccccgccccctgcctgctgcttgccctgccccctccccggccc -ctgcccgctccgagctccgccccggccccgccccggcccagtgccccgccccctgcctgc -tgctagccctgcccccgccccggcccctgcccgctccgagctccgccctggccccgcccc -cgcccagtgccccgccccctgcctgctgcttgccctgccccctccccggcccctgcccgc -tccgagctccgccccggcctcgccccggcccctgcccgctccgagcttcgccccggcccc -gccccggcccctgcccgctccgagcttcgccccggccccgccccggcccctgcccgctcc -gagctccgccccggccccgcccccgcaccttctcgcgcagccgctcgcgcagtgcggcca -ggtgtgcctcgcggatctccttgctgagctccatcttgtagttgagcttctcctccgcct -ggcggctgaagttgttattctcctcc ->p:HG002_2_chr20:63641637-63642225 -cgagcttccttcagggcactttcaatataatgaatttagccatctattactgcggctagt -tactgtcccgccaggaccagactctggacctgcctcgtgcgctgctggggacgcccagta -aacacgggaggagcccccgacccccaccccagctcagcgcctcggagtccccggccccgc -tctgcgcccctccgagctccgccctagccccgcccccgcccagtgccccgccccctgcct -gctgctagccctgcccccgccccggcccctgcccgctccgagctccgccccggccccgcc -ccggcccctgcccgctccgagctccgccctggccccg-cccccgcccagtgccccgcccc -ctgactgctgctagccctgcccccgccccggcccctgcccgctccgagctccgccccgg- ------------------------------------------------------------- ------------------------------------------------------------- -------------ccccgccccggcccctgcccgctccgagctccgccctggccccgcccc -cgcccagtgccccgccccctgactgctgctagccctgcccccgccccggcccctgcccgc -tccgagctccgccccggccccgccccggcccctgcccgctccgagctccgccccggcccc -gccccggcccctgcccgctccgagcttcgccccggccccgccccggcccctgcccgctcc -gagctccgccccggccccgcccccgcaccttctcgcgcagccgctcgcgcagtgcggcca -ggtgtgcctcgcggatctccttgctgagctccatcttgtagttgagcttctcctccgcct -ggcggctgaagttgttattctcctcc ->ref_chr20:63641637-63642225 -cgagcttccttcagggcactttcaatataatgaatttagccatctattactgcggctagt -tactgtcccgccaggaccagactctggacctgcctcgtgcgctgctggggacgcccagta -aacacgggaggagcccccgacccccaccccagctcagcgcctcggagtccccggccccgc -tctgcgcccctccgagctccgccctagccccgcccccgcccagtgccccgccccctgcct -gctgctagccctgcccccgccccggcccctgcccgctccgagctccgccccggccccgcc -ccggcccctgcccgctccgagctccgccctggccccg-cccccgcccagtgccccgcccc -ctgactgctgctagccctgc---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------cccc -gccccggcccctgcccgctccgagcttcgccccggccccgccccggcccctgcccgctcc -gagctccgccccggccccgcccccgcaccttctcgcgcagccgctcgcgcagtgcggcca -ggtgtgcctcgcggatctccttgctgagctccatcttgtagttgagcttctcctccgcct -ggcggctgaagttgttattctcctcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_06433b401328232c8c4a2f2278e2fb4c.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_06433b401328232c8c4a2f2278e2fb4c.msa deleted file mode 100644 index ee0d8578..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_06433b401328232c8c4a2f2278e2fb4c.msa +++ /dev/null @@ -1,195 +0,0 @@ ->syndip_1_chr20:56280441-56282013 -aaaaaggtaacatccatatacagatataatatctataacatatatagatatatggatata -acatccatatatagatatatctatatatctatctatagctac------------------ -----------------------------------------------atctacagatatct -atagctacatctacagatatctatagctacatctacagatatctacagatatctacagct -acatctacagatatctatagatatctatagctatatctacagatatctatcgatagatat -atctatcgatagatatatccacatagatatctagatatatatggatatatctatagatat -ctatctggatatatctatcgatagatatatagatatatatagataaagctatatagatat -atatagataaacctatatagatacatagatatatagagagaaacctatatacatatatag -atatatagagagaaacctatatagatatatagatatatagagagaaacctatatagatgt -atagataaacctatatagatatatagataaacctatgtagatatatagatatatatagat -aaatctatatagatatataaaatagataaatctatatagatatatatacataaatctata -tagatatatatacataaatctatatatatacataaatctatatatacataaatctatata -gatatatatacataaatctatatagatatatatacataaatctatatagatatatataca -taaatctatatagatatatatacataaatctatatagatatatacataaatctatataga -tatatatacataaatctatatagatatatatacataaatctatatagatatatatacata -aatctatatagatacatatagataaatctatacagatatatagatacatatagataaatc -tatacagatatatagatacatatagataaatctatacagatatatagatacatatagata -aatctatacagatatatagatacatatagataaatctatacagatatatagatacatata -gataaatctatacagatatatagatacatatagataaatctatacagatatatagataca -tatagatacatctatacagatatatagatacatatagatacatctatacagatatataga -tacatatagatacatctatacagatatattgatacatatagatacatctatatagatata -tagat--atatagatacatctatatagatatatagatatatagatacatctatatagata -tattgatacat--atagatacatctatatagattagatatatatagatacatctatatag -attagatatatatagatacatctatatagattagatatatatagatacatctatatatag -atatatagatatatatagatacatctatatatagacatatagatatatatagatacatct -atatatagatatatagatgtatatagatacatctatatatagatatatagatgtatatag -atacatctatatatagatatatagatgtatatagatacatctatatatagatatatagat -gtatatagatacatctatatatagatatatagatgtatatagatacatctatatatagat -atatagatgtatatagatacatctatatatagatatatagatgtatatagatacatctat -atatagatatatagatgtatatagatacatctatatatagatatatagatgtatatagat -acatctatatatagatatatagatgtatatagatacatagatatatatagatacatttat -gtatatatatatgtatatatagatatatagatatatatagatacatctacacagagagat -atatagaaacatctacacagggagatatatagatacatctacatagagagatatatagat -acatctacatagagagatatatagatacatctacatagagagatatatagatacatctac -atagagagatatatagatacatctacacagagagatatatagaaacatctacacagggag -atatatagatacatctacacagagagatatatagatacatctacatagagagatatatag -atacatctacatagagagatatatagatacatctacatagagagatatatagatacatct -acatagagagatatatagatacat ->syndip_2_chr20:56280441-56282013 -aaaaaggtaacatccatatacagatataatatctataacatatatagatatatggatata -acatccatatatagatatatctatatatctatctatagctacatctacagatatctatag -ctacatctacagatatctacagatatctatagctacatctacagatatctacagatatct -atagctacatctacagatatctatagctacatctacagatatctacagatatctacagct -acatctacagatatctatagatatctatagctatatctacagatatctatcgatagatat -atctatcgatagatatatccacatagatatctagatatatatggatatatctatagatat -ctatctggatatatctatcgatagatatatagatatatatagataaagctatatagatat -atatagataaacctatatagatacatagatatatagagagaaacctatatacatatatag -atatatagagagaaacctatatagatatatagatatatagagagaaacctatatagatgt -atagataaacctatatagatatatagataaacctatgtagatatatagatatatatagat -aaatctatatagatatataaaatag------------------------ataaatctata -tagatatatatacataaatctatatagatatatatacataaatctatatatatacataaa -tctatatatacataaatctatatagatatatatacataaatctatatagatatatataca -taaatctatatagatatatatacataaatctatatagatatatatacataaatctatata -gatatatacataaatctatatagatatatatacataaatctatatagatatatatacata -aatctatataga------------------------tatatagatacatatagataaatc -tatacagatatatagatacatatagataaatctatacagatatatagatacatatagata -aatctatacagatatatagatacatatagataaatctatacagatatatagatacatata -gataaatctatacagatatatagatacatatagataaatctatacagatatatagataca -tatagataaatctatacagatatatagatacatatagatacatctatacagatatataga -tacatatagatacatctatacagatatatagatacatatagatacatctatacagatata -ttgatacatatagatacatctatatagatatatagatatatagatacatctata------ ------------------------------------------------------------- --------------------------------tagatatatatagatacatctatatatag -acatatagatatatatagatacatctatatatagacatatagatatatatagatacatct -atatatagatatatagatatatatagatacatctacacagag------agatatatagaa -acatctacacagggagatatatagatacatctacacagagagatatatagatacatctac -atagagagatatatagatacatctatatagagagatatatagatacatctacatagagag -a--------tatatagatacatctacatagagaga--------tatatagatacatctac -atagagagatatatagatacat-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------- ->p:HG002_1_chr20:56280441-56282013 -aaaaaggtaacatccatatacagatataatatctataacatatatagatatatggatata -acatccatatatagatatatctatatatctatctatagctacatctacagatatctatag -ctacatctacagatatctacagatatctatagctacatctacagatatctacagatatct -atagctacatctacagatatctatagctacatctacagatatctacagatatctacagct -acatctacagatatctatagatatctatagctatatctacagatatctatcgatagatat -atctatcgatagatatatccacatagatatctagatatatatggatatatctatagatat -ctatctggatatatctatcgatagatatatagatatatatagataaagctatatagatat -atatagataaacctatatagatacatagatatatagagagaaacctatatacatatatag -atatatagagagaaacctatatagatatatagatatatagagagaaacctatatagatgt -atagataaacctatatagatatatagataaacctatgtagatatatagatatatatagat -aaatctatatagatatataaaatagataaatctatatagatatatatacataaatctata -tagatatatatacataaatctatatagatatatatacataaatctatatatatacataaa -tctatatatacataaatctatatagatatatatacataaatctatatagatatatataca -taaatctatatagatatatatacataaatctatatagatatatatacataaatctatata -gatatatacataaatctatatagatatatatacataaatctatatagatatatata---- -----tatatagatatatatacataaatc--------tatatagatacatatagataaatc -tatacagatatatagatacatatagataaatctatacagatatatagatacatatagata -aatctatacagatatatagatacatatagataaatctatacagatatatagatacatata -gataaatctatacagatatatagatacatatagataaatctatacagatatatagataca -tatagataaatctatacagatatatagatacatatagatacatctatacagatatataga -tacatatagatacatctatacagatatatagatacatatagatacatctatacagatata -ttgatacatatagatacatctatatagatatatagatatatagatacatctata------ ------------------------------------------------------------- --------------------------------tagatatatagatata----tagatacat -ctatatagatatatatagatacatctatatatagacatatagatatatatagatacatct -atatatagatatatagatatatatagatacatctacacagag------agatatatagaa -acatctacacagggagatatatagatacatctacacagagagatatatagatacatctac -atagagagatatatagatacatctacatagagagatatatagatacatctacatagagag -a--------tatatagatacatctacatagagaga--------tatatagatacat---- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------- ->p:HG002_2_chr20:56280441-56282013 -aaaaaggtaacatccatatacagatataatatctataacatatatagatatatggatata -acatccatatatagatatatctatatatctatctatagctac------------------ -----------------------------------------------atctacagatatct -atagctacatctacagatatctatagctacatctacagatatctacagatatctacagct -acatctacagatatctatagatatctatagctatatctacagatatctatcgatagatat -atctatcgatagatatatccacatagatatctagatatatatggatatatctatagatat -ctatctggatatatctatcgatagatatatagatatatatagataaagctatatagatat -atatagataaacctatatagatacatagatatatagagagaaacctatatacatatatag -atatatagagagaaacctatatagatatatagatatatagagagaaacctatatagatgt -atagataaacctatatagatatatagataaacctatgtagatatatagatatatatagat -aaatctatatagatatataaaatagataaatctatatagatatatatacataaatctata -tagatatatatacataaatctatatagatatatatacataaatctatatatatacataaa -tctatatatacataaatctatatagatatatatacataaatctatatagatatatataca -taaatctatatagatatatatacataaatctatatagatatatatacataaatctatata -gatatatacataaatctatatagatatatatacataaatctatatagatatatatacata -aatctatatagatatatatacataaatctatacagatatatagatacatatagataaatc -tatacagatatatagatacatatagataaatctatacagatatatagatacatatagata -aatctatacagatatatagatacatatagataaatctatacagatatatagatacatata -gataaatctatacagatatatagatacatatagataaatctatacagatatatagataca -tatagataaatctatacagatatatagatacatatagatacatctatacagatatataga -tacatatagatacatctatacagatatatagatacatatagatacatctatacagatata -ttgatacatatagatacatctatatagatatatagatatatagatacatctatatagata -tatagatatatagatacatacatctatatagattagatatatatagatacatctatatag -attagatatatatagatacatctatatagattagatatatatagatacatctatatatag -atatatagatatatatagatacatctatatatagatatatagatatatatagatacatct -atatatagatatatagatgtatatagatacatctatatatagatatatagatgtatatag -atacatctatatatagatatatagatgtatatagatacatctatatatagatatatagat -gtatatagatacatctatatatagatatatagatgtatatagatacatctatatatagat -atatagatgtatatagatacatctatatatagatatatagatgtatatagatacatctat -atatagatatatagatgtatatagatacatctatatatagatatatagatgtatatagat -acatctatatatagatatatagatgtatatagatacatagatatatatagatacatttat -gtatatatatatgtatatatagatatatagatatatatagatacatctacacagagagat -atatagaaacatctacacagggagatatatagatacatctacatagagagctatatagat -atatatagatacatctatatatagacatatagatatatatagatacatctatatatagat -atatagatatatatagatacatctacacagagagatatatagaaacatctacacagggag -atatatagatacatctacacagagagatatatagatacatctacatagagagatatatag -atacatctacatagagagatatatagatacatctacatagagagatatatagatacatct -acatagagagatatatagatacat ->ref_chr20:56280441-56282013 -aaaaaggtaacatccatatacagatataatatctataacatatatagatatatggatata -acatccatatatagatatatctatatatctatctatagctac------------------ ---------------atctacagatatctatagctacatctacagatatctacagatatct -atagctacatctacagatatctatagctacatctacagatatctacagatatctacagct -acatctacagatatctatagatatctatagctatatctacagatatctatcgatagatat -atctatcgatagatatatccacatagatatctagatatatatggatatatctatagatat -ctatctggatatatctatcgatagatatatagatatatatagataaagctatatagatat -atatagataaacctatatagatacatagatatatagagagaaacctatatacatatatag -atatatagagagaaacctatatagatatatagatatatagagagaaacctatatagatgt -atagataaacctatatagatatatagataaacctatgtagatatatagatatatatagat -aaatctatatagatatataaaatagataaatctatatagatatatatacataaatctata -tagatatatatacataaatctatatagatatatatacataaatctatatatatacataaa -tctatatatacataaatctatatagatatatatacataaatctatatagatatatataca -taaatctatatagatatatatacataaatctatatagatatatatacataaatctatata -gatatatacataaatctatatagatatatatacataaatctatatagatatatatacata -aatctatatagatatatatacataaatc--------tatatagatacatatagataaatc -tatacagatatatagatacatatagataaatctatacagatatatagatacatatagata -aatctatacagatatatagatacatatagataaatctatacagatatatagatacatata -gataaatctatacagatatatagatacatatagataaatctatacagatatatagataca -tatagataaatctatacagatatatagatacatatagatacatctatacagatatataga -tacatatagatacatctatacagatatatagatacatatagatacatctatacagatata -ttgatacatatagatacatctatatagatatatagatatatagatacatctata------ ------------------------------------------------------------- --------------------------------tagatatatagatata----tagatacat -ctatatagatatatatagatacatctatatatagacatatagatatatatagatacatct -atatatagatatatagatatatatagatacatctacacagag------agatatatagaa -acatctacacagggagatatatagatacatctacacagagagatatatagatacatctac -atagagagatatatagatacatctacatagagagatatatagatacatctacatagagag -a--------tatatagatacatctacatagagaga--------tatatagatacat---- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_0653f2abc01702903c57c997585cf824.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_0653f2abc01702903c57c997585cf824.msa deleted file mode 100644 index ecd9b57d..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_0653f2abc01702903c57c997585cf824.msa +++ /dev/null @@ -1,90 +0,0 @@ ->syndip_1_chr20:13847964-13848849 -aggatcacttgaggtcaggagtttgagaccagcctggccaacatggtgaaaccccatctc -tactaaaaatacaaaaattagccgggcgtggtggcaggcatctgtaatcccagttattca -ggaggctgaggcaggagaatcacctgaacccgggaggcagaggttccagtgagtcgagat -cttgccactgcactccagcctgggggacagagggaaattgcgtctcaaaaaaaaaaaaga -a-aagaaaagtagaagacgaagatgaagaagaataagaagagagaaaagaagaagagaag -gttagagaaaagaagagaaggagaaggagaaggaggaggagaaggagaaggagaagaaga -agaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagt -caaatatctggagaagaagaagaagaagaggaagaagaagaagaggaagaagaagaagaa -gaggaagaggaagaaagaagaagaacaagaagaagaagaagtcaaatatctggagaagaa -gaagaagaagaggaggaagaagaagaagaagaggaggaggaagaagaagaagaagaagaa -gaagaagaagcaggagcaggagaagaagaagaagaagaagaagaagaggaagaggaagag -gaagaggaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaa -gaagaagaagaagaagaagaagaagaagaagaagagaagacaaatatctggagccgggat -ttgagcctggcccttgacatatgtcctaggcctcttacactctccttaccagcccctgtc -ccttaggcctgggcccctgatttgcctgtcagagaagccagagaatctgggccttttagc -tttcatcctaggaggcttgaataatctccttctaagggggtactaagggggacgccccag -ggagaacagggttctgatgagggatg ->syndip_2_chr20:13847964-13848849 -aggatcacttgaggtcaggagtttgagaccagcctggccaacatggtgaaaccccatctc -tactaaaaatacaaaaattagccgggcgtggtggcaggcatctgtaatcccagttattca -ggaggctgaggcaggagaatcacctgaacccgggaggcagaggttccagtgagtcgagat -cttgccactgcactccagcctgggggacagagggaaattgcgtctcaaaaaaaaaaaaga -a-aagaaaagtagaagacgaagatgaagaagaataagaagagagaaaagaagaagagaag -gttagagaaaagaagagaaggagaaggagaaggaggaggagaaggagaaggagaagaaga -agaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagt -caaatatctggagaagaagaagaagaagaggaagaagaagaagaggaagaagaagaagaa -gaggaagaggaagaaagaagaagaacaagaagaagaagaagtcaaatatctggagaagaa -gaagaagaagaggaggaagaagaagaagaagaggaggaggaagaagaagaagaagaagaa -gaagaagaagcaggagcaggagaagaagaagaagaagaagaagaagaggaagaggaagag -gaagag---------------gaagaagaagaagaagaagaagaagaagaagaagaagaa -gaagaagaagaagaagaagaagaagaagaagaagagaagacaaatatctggagccgggat -ttgagcctggcccttgacatatgtcctaggcctcttacactctccttaccagcccctgtc -ccttaggcctgggcccctgatttgcctgtcagagaagccagagaatctgggccttttagc -tttcatcctaggaggcttgaataatctccttctaagggggtactaagggggacgccccag -ggagaacagggttctgatgagggatg ->p:HG002_1_chr20:13847964-13848849 -aggatcacttgaggtcaggagtttgagaccagcctggccaacatggtgaaaccccatctc -tactaaaaatacaaaaattagccgggcgtggtggcaggcatctgtaatcccagttattca -ggaggctgaggcaggagaatcacctgaacccgggaggcagaggttccagtgagtcgagat -cttgccactgcactccagcctgggggacagagggaaattgcgtctcaaaaaaaaaaaaga -a-aagaaaagtagaagacgaagatgaagaagaataagaagagagaaaagaagaagagaag -gttagagaaaagaagagaaggagaaggagaaggaggaggagaaggagaaggagaagaaga -agaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagt -caaatatctggagaagaagaagaagaagaggaagaagaagaagaggaagaagaagaagaa -gaggaagaggaagaaagaagaagaacaagaagaagaagaagtcaaatatctggagaagaa -gaagaagaagaggaggaagaagaagaagaagaggaggaggaagaagaagaagaagaagaa -gaagaagaagcaggagcaggagaagaagaagaagaagaagaagaagaggaagaggaagag -gaagag---------------gaagaagaagaagaagaagaagaagaagaagaagaagaa -gaagaagaagaagaagaagaagaagaagaagaagagaagacaaatatctggagccgggat -ttgagcctggcccttgacatatgtcctaggcctcttacactctccttaccagcccctgtc -ccttaggcctgggcccctgatttgcctgtcagagaagccagagaatctgggccttttagc -tttcatcctaggaggctggaataatctccttctaagggggtactaagggggacgccccag -ggagaacagggttctgatgagggatg ->p:HG002_2_chr20:13847964-13848849 -aggatcacttgaggtcaggagtttgagaccagcctggccaacatggtgaaaccccatctc -tactaaaaatacaaaaattagccgggcgtggtggcaggcatctgtaatcccagttattca -ggaggctgaggcaggagaatcacctgaacccgggaggcagaggttccagtgagtcgagat -cttgccactgcactccagcctgggggacagagggaaattgcgtctcaaaaaaaaaaaaga -a-aagaaaagtagaagacgaagatgaagaagaataagaagagagaaaagaagaagagaag -gttagagaaaagaagagaaggagaaggagaaggaggaggagaaggagaaggagaagaaga -agaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagt -caaatatctggagaagaagaagaagaagaggaagaagaagaagaggaagaagaagaagaa -gaggaagaggaagaaagaagaagaacaagaagaagaagaagtcaaatatctggagaagaa -gaagaagaagaggaggaagaagaagaagaagaggaggaggaagaagaagaagaagaagaa -gaagaagaagcaggagcaggagaagaagaagaagaagaagaagaagaggaagaggaagag -gaagaggaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaa -gaagaagaagaagaagaagaagaagaagaagaagagaagacaaatatctggagccgggat -ttgagcctggcccttgacatatgtcctaggcctcttacactctccttaccagcccctgtc -ccttaggcctgggcccctgatttgcctgtcagagaagccagagaatctgggccttttagc -tttcatcctaggaggctggaataatctccttctaagggggtactaagggggacgccccag -ggagaacagggttctgatgagggatg ->ref_chr20:13847964-13848849 -aggatcacttgaggtcaggagtttgagaccagcctggccaacatggtgaaaccccatctc -tactaaaaatacaaaaattagccgggcgtggtggcaggcatctgtaatcccagttattca -ggaggctgaggcaggagaatcacctgaacccgggaggcagaggttccagtgagtcgagat -cttgccactgcactccagcctgggggacagagggaaattgcgtctcaaaaaaaaaaaaga -agaagaaaagtagaagacgaagatgaagaagaataagaagagagaaaagaagaagagaag -gttagagaaaagaagagaa-------------------------gagaaggagaaggaga -aggaggaggagaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagt -caaatatctgg---agaagaagaagaagaggaagaagaagaaaaggaagaagaagaagaa -gaggaagaggaagaaagaagaagaacaagaagaagaagaagtcaaatatctggagaagaa -gaagaagaagaggaagaagaagaagaagaggaggaggaagaaggagaaggagaaggagaa -ggagaagga--------------------------------------------------- ----------------------gaaggagaaggagaagaagaagaagaagaagaagaagaa -gaagaagaagaagaagaagaagaagaagaagaagaaaatacaaatatctggagccgggat -ttgagcctggcccttgacatatgtcctaggcctcttacactctccttaccagcccctgtc -ccttaggcctgggcccctgatttgcctgtcagagaagccagagaatctgggccttttagc -tttcatcctaggaggcttgaataatctccttctaagggggtactaagggggacgccccag -ggagaacagggttctgatgagggatg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_06caad6b783fc99e81d125bbb065c601.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_06caad6b783fc99e81d125bbb065c601.msa deleted file mode 100644 index f668f347..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_06caad6b783fc99e81d125bbb065c601.msa +++ /dev/null @@ -1,115 +0,0 @@ ->syndip_1_chr20:48449705-48450461 -ttaagctgggataagtggaataggaaggagtggagtggagcatgatggtatgggatggga -tggatgggatgggatggatggatggatggggtgggatgggatgggatg-----ggatgga -tggatgggatggatggatgggatgggataggatggatggggtgagatgggatggaatgga -tgggatgggatggatggatgggatgggatggatgggatgggatggatgggatgggatgga -tgggatggatgggatggaatgggatggatgggatgggatgggattggatggggtgggatg -ggatggatggatgggatggatggatgggatggaatggatggatgggatgggatggatggg -atgggatggatggatgggatgggatggatgcaatggatggatgggatgggatgggatggg -atggatggaatggatggatgggatgggatgggatggatggggtgggatgagatggatggg -atggatgggatgggatggatggat-----------------------ggatgggatggga -tggatggatgggatgggatgggatggggtggatgggatggatggatggatgggatgggat -ggatggatgggatggaatggat-gaatgggatgtgatggatgggatggaatgggat-aga -tgggatgggattggatgggatggggtgggatggggtaagatggggtgggatgggatggta -tgggatggatggatgagatgggatgggatgagatgggattggatggggtgggatgcaatg -ggatgagatgagatgagatgagatgggatggatggcatgggatgggatgggattggatgg -ggtgggatgggatggggtaggatgggatgggatgggatgggatgggatgggatgggatgg -gatgggatggggtgggatgggttgggatgggatggggtgggttgggatggggtggggtgg -gatgggatgggatgggatggggtggggtggggtggggtgggatggggtgggatggggtgg -gatgggatggggtgggatgggatgggatggggtgggatgggatggggtggggtggggtgg -ggtgggatgaggtggggtgggatgggatgggatggggtggggtggggtgggatgggatgg -gatggggtggggtgggatgggattggatggggtgggatgcgatgg-----gatgagatga -gatggatggcatgggatgggtgggaggggatgggatattatcagatggcaaaagtaagaa -gtgttc ->syndip_2_chr20:48449705-48450461 -ttaagctgggataagtggaataggaaggagtggagtggagcatgatggtatgggatggga -tggatgggatgggatggatggatggatggggtgggatgggatgggatg------------ --ggatggggtggatggatgggatgggataggatggatggggtgagatgggatggaatgga -tggaatgggatggatggatgggatgggatggatgggatgggatggatgggatggatggga -tgggatggatgggatggaatgggatggatgggatgggatgggattggatggggtgggatg -ggatggatggatgggatggatggatgggatggaatggatggatgggatgggatggatggg -atgggatggatggatgggatgggatggatgcaatggatggatgggatgggatgggatggg -atggatggaatggatggatgggatgggatgggatggatggggtgggatgagatggatggg -atggatgggatgggatggatggatggatgggatgggatggatggatgggatgggatggga -tggatggatgggatgggatgggatggggtggatgggatggatggatggatgggatgggat -ggatggatgggatggaatggat-gaatgggatgtgatggatgggatggaatgggat-aga -tgggatgggattggatgggatggggtgggatggggtaagatggggtgggatgggatggta -tgggatggatggatgagatgggatgggatgagatgggattggatggggtgggatgcaatg -ggatgagatgagatgagatgagatgggatggatggcatgggatggaatgggattggatgg -ggtgggatgggatggggtaggatgggatgggatgggatgggatgggatgggatggggtgg -gatgggttgggatgggatggggtgggttgggatgggg----------tggggtgggatgg -gatgggatggggtgggatggggtgggatggggtgggatggggtgggatgggatggggtgg -gatgggatgggatgggatggggtgggatggggtgggatgggatggggtggggtggggtgg -ggtgggatgaggtggggtgggatgggatgggatggggtggggtggggtgggatgggatgg -gatggggtggggtgggatgggattggatggggtgggatgcgatgggatgagatgagatga -gatgaatggcatgggatgggtgggaggggatgggatattatcagatggcaaaagtaagaa -gtgttc ->p:HG002_1_chr20:48449705-48450461 -ttaagctgggataagtggaataggaaggagtggagtggagcatgatggtatgggatggga -tggatgggatgggatggatggatggatggggtgggatgggatgggatg------------ --ggatggggtggatggatgggatgggataggatggatggggtgagatgggatggaatgga -tggaatgggatggatggatgggatgggatggatgggatgggatggatgggatggatggga -tgggatggatgggatggaatgggatggatgggatgggatgggattggatggggtgggatg -ggatggatggatgggatggatggatgggatggaatggatggatgggatgggatggatggg -atgggatggatggatgggatgggatggatgcaatggatggatgggatgggatgggatggg -atggatggaatggatggatgggatgggatgggatggatggggtgggatgagatggatggg -atggatgggatgggatggatggatggatgggatgggatggatggatgggatgggatggga -tggatggatgggatgggatgggatggggtggatgggatggatggatggatgggatgggat -ggatggatgggatggaatggat-gaatgggatgtgatggatgggatggaatgggat-aga -tgggatgggattggatgggatggggtgggatggggtaagatggggtgggatgggatggta -tgggatggatggatgagatgggatgggatgagatgggattggatggggtgggatgcaatg -ggatgagatgagatgagatgagatgggatggatggcatgggatggaatgggattggatgg -ggtgggatgggatggggtaggatgggatgggatgggatgggatgggatgggatggggtgg -gatgggttgggatgggatggggtgggttgggatgggg----------tggggtgggatgg -gatgggatggggtgggatggggtgggatggggtgggatggggtgggatgggatggggtgg -gatgggatgggatgggatggggtgggatggggtgggatgggatggggtggggtggggtgg -ggtgggatgaggtggggtgggatgggatgggatggggtggggtggggtgggatgggatgg -gatggggtggggtgggatgggattggatggggtgggatgcgatgggatgagatgagatga -gatgaatggcatgggatgggtgggaggggatgggatattatcagatggcaaaagtaagaa -gtgttc ->p:HG002_2_chr20:48449705-48450461 -ttaagctgggataagtggaataggaaggagtggagtggagcatgatggtatgggatggga -tggatgggatgggatggatggatggatggggtgggatgggatgggatg-----ggatgga -tggatgggatggatggatgggatgggataggatggatggggtgagatgggatggaatgga -tgggatgggatggatggatgggatgggatggatgggatgggatggatgggatgggatgga -tgggatggatgggatggaatgggatggatgggatgggatgggattggatggggtgggatg -ggatggatggatgggatggatggatgggatggaatggatggatgggatgggatggatggg -atgggatggatggatgggatgggatggatgcaatggatggatgggatgggatgggatggg -atggatggaatggatggatgggatgggatgggatggatggggtgggatgagatggatggg -atggatgggatgggatggatggat-----------------------ggatgggatggga -tggatggatgggatgggatgggatggggtggatgggatggatggatggatgggatgggat -ggatggatgggatggaatggat-gaatgggatgtgatggatgggatggaatgggat-aga -tgggatgggattggatgggatggggtgggatggggtaagatggggtgggatgggatggta -tgggatggatggatgagatgggatgggatgagatgggattggatggggtgggatgcaatg -ggatgagatgagatgagatgagatgggatggatggcatgggatgggatgggattggatgg -ggtgggatgggatggggtaggatgggatgggatgggatgggatgggatgggatgggatgg -gatgggatggggtgggatgggttgggatgggatggggtgggttgggatggggtggggtgg -gatgggatgggatgggatggggtggggtggggtggggtgggatggggtgggatggggtgg -gatgggatggggtgggatgggatgggatggggtgggatgggatggggtggggtggggtgg -ggtgggatgaggtggggtgggatgggatgggatggggtggggtggggtgggatgggatgg -gatggggtggggtgggatgggattggatggggtgggatgcgatgg-----gatgagatga -gatggatggcatgggatgggtgggaggggatgggatattatcagatggcaaaagtaagaa -gtgttc ->ref_chr20:48449705-48450461 -ttaagctgggataagtggaataggaaggagtggagtggagcatgatggtatgggatggga -tggatgggatgggatggatggatggatggggtgggatgggatgggatgggatgggatgga -tggatgggatggatggatgggatgggataggatggatggggtgagatgggatggaatgga -tgggatgggatggatggatgggatgggatggatgggatgggatggatgggatgggatgga -tgggatggatgggatggaatgggatggatgggatgggatgggattggatggggtgggatg -ggatggatggatgggatggatggatgggatggaatggatggatgggatgggatggatggg -atgggatggatggatgggatgggatggatgcaatggatggatgggatgggatgggatggg -atggatggaatggatggatgggatgggatgggatggatggggtgggatgagatggatggg -atggatgggatgggatggatggat-----------------------ggatgggatggga -tggatggatgggatgggatgggatggggtggatgggatggatggatggatgggatgggat -ggatggatgggatgggatggatgggatgggatg----gggtggggtggggtgggatggga -tgggatggggtggggtgggatgggattggatggggtgggatgcgatgggatgagatgaga -tggatggcatgggatgggtgggaggggatgggatattatcagatgg-------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------caaaagtaagaa -gtgttc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_08113059453960271e05afa618f756b8.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_08113059453960271e05afa618f756b8.msa deleted file mode 100644 index 60fd2d0c..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_08113059453960271e05afa618f756b8.msa +++ /dev/null @@ -1,175 +0,0 @@ ->syndip_1_chr20:55943919-55945807 -taaaattagctagcatttcagccaggtgcagtggctcaagcctgtaatcccagcactttg -ggaggccaaggtgggtggatcacttgaggttaggagtttgagaccagcctggccaacatg -gtgaaacctcgcctctactaaaaatacaaaaattagctgggcatgctggcatgtgcctgt -aatcccagctactcaggaggctgaggcaggagaactgcttgagcctgggaggcagaggtt -gcagtgagctgagatggcaccactgcattccagctgggcaacagagagagactctttctt -aaatatatatattttatatatatatagatacacacacacacacacacacacacac----- ------------------------------atatatatatatatatatatatatatatata -tatgcatgcatgccagatgcagtggctcacgcctgtaatcccagcactttgagaggccaa -ggtgggcagatcatctgaggtcaggagttccagaccagcctagccaacatggtgaaactc -catctctactaaaaatacaaaattagctggctgtggtggctcatgctggtaatcccagct -acttgggaggctgaggcaggagaatcacttgaacctgggaggtggaggttgcagtgagcc -gagatcacaccactgcactccagcctggatgacagagcgagactccattaaaaaaatata -tctatatctatagatatctatagatatatatctagatatagatctatgagtatatatcta -tagatatctagatatatatttatagatagatatatctatagatatctatatatttctatc -gatagagatatctatagatatctatcaatatatctatagatttctagagatatgtatcta -gatataaatctatagacatagatatagatatatagatatttaactgccaatgtcctaaac -actttatactcaacacattttttataaaaaaaaatagatatcggtctagatagtatctat -ctagatatcggtctagatagtatctatctagatatctgtgtagatgtctagatatctatc -tagatattatctatctagatatct--gtcgctatctagatatctatctagatatctgtcg -ctatctagatatctatctagatatctgtcgctatctagatatctatctagatagtatctg -tcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatag -tatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatct -agatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatat -ctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatct -agatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcg -ctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtat -ctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctaga -tagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatcta -tctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctaga -tatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgcta -tctagatatctagatagtatctgtcgctatctagatatctagatagtatctgtctagata -gctatctagatagtatctgtctagatagctatctagatagtatctgtccagatatctgta -gctatctagattgtatctgtctagatatctgtagatatctagatatctatatctatctgg -atatctatagatatttaactgccgggcaatgtcctaaacccttt ->syndip_2_chr20:55943919-55945807 -taaaattagctagcatttcagccaggtgcagtggctcaagcctgtaatcccagcactttg -ggaggccaaggtgggtggatcacttgaggttaggagtttgagaccagcctggccaacatg -gtgaaacctcgcctctactaaaaatacaaaaattagctgggcatgctggcatgtgcctgt -aatcccagctactcaggaggctgaggcaggagaactgcttgagcctgggaggcagaggtt -gcagtgagctgagatggcaccactgcattccagctgggcaacagagagagactctttctt -aaatatatatattttatatatatatagatacacacacacacacacacacacacacacaca -cacacacacacacacatatatatatatatatatatatatatatatatatatatatatata -tatgcatgcatgccagatgcagtggctcacgcctgtaatcccagcactttgagaggccaa -ggtgggcagatcatctgaggtcaggagttccagaccagcctagccaacatggtgaaactc -catctctactaaaaatacaaaattagctggctgtggtggctcatgctggtaatcccagct -acttgggaggctgaggcaggagaatcacttgaacctgggaggtggaggttgcagtgagcc -gagatcacaccactgcactccagcctggatgacagagcgagactccattaaaaaaatata -tctatatctatagatatctatagatatatatctagatatagatctatgagtatatatcta -tagatatctagatatatatttatagatagatatatctatagatatctatatatttctatc -gatagagatatctatagatatctatcaatatatctatagatttctagagatatgtatcta -gatataaatctatagacatagatatagatatatagatatttaactgccaatgtcctaaac -actttatactcaacacattttttataaaaaaaaatagatatcggtctagatagtatctat -ctagatatcggtctagatagtatctatctagatatcgg--------------------tc -tagatagtatctatctagatatctgcgtagatgtctagatatctatctagatat------ ----------tatctatctaga--------------------------------------- ------------------------------------------------------------- -tatctgtcgctatctagatatctatctaga---tatctgtcgctatctagatatctatct -aga--------------------------------------------------------- -------------tatctgtcgctatctagatatctatctagatatcatctgtcgctatct -agatatctatctagatatcatctgtcgctatctagatatctatctagatatcatctgtcg -ctatctagatatctatctagatatcatctgtcgctatctagatatctatctagatatcat -ctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctaga -tagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatcta -tctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctaga -tatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgcta -tctagatatctagatagtatctgtcgctatctagatatctagatagtatctgtctagata -gctatctagatagtatctgtctagatagctatctagatagtatctgtccagatatctgta -gctatctagattgtatctgtctagatatctgtagatatctagatatctatatctatctgg -atatctatagatatttaactgccgggcaatgtcctaaacccttt ->p:HG002_1_chr20:55943919-55945807 -taaaattagctagcatttcagccaggtgcagtggctcaagcctgtaatcccagcactttg -ggaggccaaggtgggtggatcacttgaggttaggagtttgagaccagcctggccaacatg -gtgaaacctcgcctctactaaaaatacaaaaattagctgggcatgctggcatgtgcctgt -aatcccagctactcaggaggctgaggcaggagaactgcttgagcctgggaggcagaggtt -gcagtgagctgagatggcaccactgcattccagctgggcaacagagagagactctttctt -aaatatatatattttatatatatatagatacacacacacacacacacacacacacacaca -cacacacacacacacatatatatatatatatatatatatatatatatatatatatatata -tatgcatgcatgccagatgcagtggctcacgcctgtaatcccagcactttgagaggccaa -ggtgggcagatcatctgaggtcaggagttccagaccagcctagccaacatggtgaaactc -catctctactaaaaatacaaaattagctggctgtggtggctcatgctggtaattccagct -acttgggaggctgaggcaggagaatcacatgaacctgggaggtggaggttgcagtgagcc -gagatcacaccactgcactccagcctggatgacagagcgagactccattaaaaaaatata -tctatatctatagatatctatagatatatatctagatatagatctatgagtatatatcta -tagatatctagatatatatttatagatagatatatctatagatatctatatatttctatc -gatagagatatctatagatatctatcaatatatctatagatttctagagatatgtatcta -gatataaatctatagacatagatatagatatatagatatttaactgccaatgtcctaaac -actttatactcaacacattttttataaaaaaaaatagatatcggtctagatagtatctat -ctagatatcggtctagatagtatctatctagatatcgg--------------------tc -tagatagtatctatctagatatctgcgtagatgtctagatatctatctagatat------ ----------tatctatctaga--------------------------------------- ------------------------------------------------------------- -tatctgtcgctatctagatatctatctaga---tatctgtcgctatctagatatctatct -aga--------------------------------------------------------- -------------tatctgtcgctatctagatatctatctagatatcatctgtcgctatct -agatatctatctagatatcatctgtcgctatctagatatctatctagatatcatctgtcg -ctatctagatatctatctagatatcatctgtcgctatctagatatctatctagatatcat -ctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctaga -tagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatcta -tctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctaga -tatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgcta -tctagatatctagatagtatctgtcgctatctagatatctagatagtatctgtctagata -gctatctagatagtatctgtctagatagctatctagatagtatctgtccagatatctgta -gctatctagattgtatctgtctagatatctgtagatatctagatatctatatctatctgg -atatctatagatatttaactgccgggcaatgtcctaaacccttt ->p:HG002_2_chr20:55943919-55945807 -taaaattagctagcatttcagccaggtgcagtggctcaagcctgtaatcccagcactttg -ggaggccaaggtgggtggatcacttgaggttaggagtttgagaccagcctggccaacatg -gtgaaacctcgcctctactaaaaatacaaaaattagctgggcatgctggcatgtgcctgt -aatcccagctactcaggaggctgaggcaggagaactgcttgagcctgggaggcagaggtt -gcagtgagctgagatggcaccactgcattccagctgggcaacagagagagactctttctt -aaatatatatattttatatatatatagatacacacacacacacacacacacacac----- ------------------------------atatatatatatatatatatatatatatata -tatgcatgcatgccagatgcagtggctcacgcctgtaatcccagcactttgagaggccaa -ggtgggcagatcatctgaggtcaggagttccagaccagcctagccaacatggtgaaactc -catctctactaaaaatacaaaattagctggctgtggtggctcatgctggtaatcccagct -acttgggaggctgaggcaggagaatcacttgaacctgggaggtggaggttgcagtgagcc -gagatcacaccactgcactccagcctggatgacagagcgagactccattaaaaaaatata -tctatatctatagatatctatagatatatatctagatatagatctatgagtatatatcta -tagatatctagatatatatttatagatagatatatctatagatatctatatatttctatc -gatagagatatctatagatatctatcaatatatctatagatttctagagatatgtatcta -gatataaatctatagacatagatatagatatatagatatttaactgccaatgtcctaaac -actttatactcaacacattttttataaaaaaaaatagatatcggtctagatagtatctat -ctagatatcggtctagatagtatctatctagatatctgtgtagatgtctagatatctatc -tagatattatctatctagatatct--gtcgctatctagatatctatctagatatctgtcg -ctatctagatatctatctagatatctgtcgctatctagatatctatctagatagtatctg -tcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatag -tatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatct -agatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatat -ctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatct -agatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcg -ctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtat -ctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctaga -tagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatcta -tctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctaga -tatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgcta -tctagatatctagatagtatctgtcgctatctagatatctagatagtatctgtctagata -gctatctagatagtatctgtctagatagctatctagatagtatctgtccagatatctgta -gctatctagattgtatctgtctagatatctgtagatatctagatatctatatctatctgg -atatctatagatatttaactgccgggcaatgtcctaaacccttt ->ref_chr20:55943919-55945807 -taaaattagctagcatttcagccaggtgcagtggctcaagcctgtaatcccagcactttg -ggaggccaaggtgggtggatcacttgaggttaggagtttgagaccagcctggccaacatg -gtgaaacctcgcctctactaaaaatacaaaaattagctgggcatgctggcatgtgcctgt -aatcccagctactcaggaggctgaggcaggagaactgcttgagcctgggaggcagaggtt -gcagtgagctgagatggcaccactgcattccagctgggcaacagagagagactctttctt -aaatatatatattttatatatatatagatacacacacacacacacacacacacac----- ------------------------------atatatatatatatatatatatatatatata -tatgcatgcatgccagatgcagtggctcacgcctgtaatcccagcactttgagaggccaa -ggtgggcagatcatctgaggtcaggagttccagaccagcctagccaacatggtgaaactc -catctctactaaaaatacaaaattagctggctgtggtggctcatgctggtaatcccagct -acttgggaggctgaggcaggagaatcacttgaacctgggaggtggaggttgcagtgagcc -gagatcacaccactgcactccagcctggatgacagagcgagactccattaaaaaaatata -tctatatctatagatatctatagatatatatctagatatagatctatgagtatatatcta -tagatatctagatatatatttatagatagatatatctatagatatctatatatttctatc -gatagagatatctatagatatctatcaatatatctatagatttctagagatatgtatcta -gatataaatctatagacatagatatagatatatagatatttaactgccaatgtcctaaac -actttatactcaacacattttttataaaaaaaaatagatatcggtctagatagtatctat -ctagatatcggtctagatagtatctatctagatatctgtgtagatgtctagatatctatc -tagatattatctatctagatatct--gtcgctatctagatatctatctagatatctgtcg -ctatctagatatctatctaga--------------------------------------- ------------------------------------------------------------- -tatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatct -agatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatat -ctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatct -agatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcg -ctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtat -ctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctaga -tagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatcta -tctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctaga -tatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgcta -tctagatatctagatagtatctgtcgctatctagatatctagatagtatctgtctagata -gctatctagatagtatctgtctagatagctatctagatagtatctgtccagatatctgta -gctatctagattgtatctgtctagatatctgtagatatctagatatctatatctatctgg -atatctatagatatttaactgccgggcaatgtcctaaacccttt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_082a2851433961fb945bb0581d40050c.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_082a2851433961fb945bb0581d40050c.msa deleted file mode 100644 index 01896f65..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_082a2851433961fb945bb0581d40050c.msa +++ /dev/null @@ -1,165 +0,0 @@ ->syndip_1_chr20:38123590-38124705 -gctttgtgatctcaggcctgtcctgtaacctctctgggcctcagaaacctctctctctct -ctatatatatatatataataatatataataataatatataatatgtataataataatata -taatatttataataataatatatataatatgtatatataatatacatatacctattatat -ataatatacctattatatataatatacatatacctattatatataatatacctattatat -ataagatacctattatatataatatacatatacctattatatatataatatacctattat -atatatataatatacctattatatataatatacctattatatatataatatacctattat -atatataatatacctattatatatataatatacctattatatataatatacctattatat -ataaaatatacctattatatataatatacctattatatacattatatataatatacctat -tatatgcattatatataatatacctattatatgcattatatataatatacctattatatg -cattatatataatatacctattatatgcattatatataatatacctattatatgcattat -ataatatattatatataatatgcatattatatgtattatatattatatattatatatata -atatacatattatatgtattatatattatatattatatatataatatacatattatatgt -attatatattatatataatatacatattatatattatatattatatacatattatatatt -atatattatatacatattatatattatatacatat-tatatattatatattatatacata -ttatacattatatatatctaaaatatataatacacattatatattatataatacacatta -tatataatatataatacacat-tatatattatatataatacac--attatatattatata -ta-atacacattatatat-----------------------tatataatacacattatat -attatatataatacacattatatattatatataatacacattatatattatatata-ata -cacattatatattatataatacacattatatattatatataatacacattatatatataa -tacacattatatattatatataatacataatacacat------tatatattatatataat -acacattatatataatatataacacacattatatataatatataacacacattatatatt -atatataatacacattatatattatatataatacacatatattatatataatacacatta -tatattatatataatacacatatattatatataatacacattatatattatatataatac -acattatatataatatataatacacattatatataatacttattatatattatacataat -atacatattatatataatacataatatacgtatattatataatatacatattatatataa -tacataatatacgtatattatataatatacatattatatatattatactatatataatac -tcatatatatacatattatatatacatattatatataatactcatattatatgtacatat -tatacatacatattatatataatacacatatatacatattatatataatacacacacaca -ttatatatgtcttatatataatatacatattatatatgtattatattattatagatataa -tatacatattatatctatatataaaatatatatgtagagagagagagacagggtctcatt -ttgtctcccaggctggagtgcagtggtgcaatcttggctcactacaacctccacctccca -ggctcaagggatcctccagcttcagcccc ->syndip_2_chr20:38123590-38124705 -gctttgtgatctcaggcctgtcctgtaacctctctgggcctcagaaacctctctctctct -ctatatatatatatataataatatataataataatatataatatgtataataataatata -taatatttataataataatatatataatatgtatatataatatacatatacctattatat -ataatatacctattatatataatatacatatacctattatatataatatacctattatat -ataagatacctattatatataatatacatatacctattatatatataatatacctattat -atatatataatatacctattatatataatatacctattatatatataatatacctattat -atatataatatacctattatatatataatatacctattatatataatatacctattatat -ataaaatatacctattatatataatatacctattatata--------------------- -------cattatatataatatacctattatatgcattatatataatatacctattatatg -cattatatataatatacctattatatgcattatatataatatacctattatatgcattat -ataatatattatatataatatgcatattatatgtattatatattatatattatatatata -atatacatattatatgtattatatattatatattatatatataatatacatattatatgt -attatatattatatataatatacatattatatattatatattatatacatattatatatt -atatattatatacatattatatattatatacatat-tatatattatatattatatacata -ttatacattatatatatctaaaatatataatacacattatatattatataatacacatta -tatataatatataatacacat-tatatattatatataatacac--attatatattatata -ta-atacacattatatattatataatacacattatatattatatataatacacattatat -attatatataatacacattatatattatatataatacacattatatattatatata-ata -cacattatatattatataatacacattatatattatatataatacacattatatatataa -tacacattatatattatatataatacataatacacat------tatatattatatataat -acacattatatataatatataacacacattatatataatatataacacacattatatatt -atatataatacacattatatattatatataatacacatatattatatataatacacatta -tatattatatataatacacatatattatatataatacacattatatattatatataatac -acattatatataatatataatacacattatatataatacttattatatattatacataat -atacatattatatataatacataatatacgtatattatataatatacatattatatataa -tacataatatacgtatattatataatatacatattatatatattatactatatataatac -tcatatatatacatattatatatacatattatatataatactcatattatatgtacatat -tatacatacatattatatataatacacatatatacatattatatataatacacacacaca -ttatatatgtcttatatataatatacatattatatatgtattatattattatagatataa -tatacatattatatctatatataaaatatatatgtagagagagagagacagggtctcatt -ttgtctcccaggctggagtgcagtggtgcaatcttggctcactacaacctccacctccca -ggctcaagggatcctccagcttcagcccc ->p:HG002_1_chr20:38123590-38124705 -gctttgtgatctcaggcctgtcctgtaacctctctgggcctcagaaacctctctctctct -ctatatatatatatataataatatataataataatatataatatgtataataataatata -taatatttataataataatatatataatatgtatatataatatacatatacctattatat -ataatatacctattatatataatatacatatacctattatatataatatacctattatat -ataagatacctattatatataatatacatatacctattatatatataatatacctattat -atatatataatatacctattatatataatatacctattatatatataatatacctattat -atatataatatacctattatatatataatatacctattatatataatatacctattatat -ataaaatatacctattatatataatatacctattatata--------------------- -------cattatatataatatacctattatatgcattatatataatatacctattatatg -cattatatataatatacctattatatgcattatatataatatacctattatatgcattat -ataatatattatatataatatgcatattatatgtattatatattatatattatatatata -atatacatattatatgtattatatattatatattatatatataatatacatattatatgt -attatatattatatataatatacatattatatattatatattatatacatattatatatt -atatattatatacatattatatattatatacatat-tatatattatatattatatacata -ttatacattatatatatctaaaatatataatacacattatatattatataatacacatta -tatataatatataatacacat-tatatattatatataatacac--attatatattatata -ta-atacacattatatattatataatacacattatatattatatataatacacattatat -attatatataatacacattatatattatatataatacacattatatattatatata-ata -cacattatatattatataatacacattatatattatatataatacacattatatatataa -tacacattatatattatatataatacataatacacat------tatatattatatataat -acacattatatataatatataacacacattatatataatatataacacacattatatatt -atatataatacacattatatattatatataatacacatatattatatataatacacatta -tatattatatataatacacatatattatatataatacacattatatattatatataatac -acattatatataatatataatacacattatatataatacttattatatattatacataat -atacatattatatataatacataatatacgtatattatataatatacatattatatataa -tacataatatacgtatattatataatatacatattatatatattatactatatataatac -tcatatatatacatattatatatacatattatatataatactcatattatatgtacatat -tatacatacatattatatataatacacatatatacatattatatataatacacacacaca -ttatatatgtcttatatataatatacatattatatatgtattatattattatagatataa -tatacatattatatctatatataaaatatatatgtagagagagagagacagggtctcatt -ttgtctcccaggctggagtgcagtggtgcaatcttggctcactacaacctccacctccca -ggctcaagggatcctccagcttcagcccc ->p:HG002_2_chr20:38123590-38124705 -gctttgtgatctcaggcctgtcctgtaacctctctgggcctcagaaacctctctctctct -ctatatatatatatataataatatataataataatatataatatgtataataataatata -taatatttataataataatatatataatatgtatatataatatacatatacctattatat -ataatatacctattatatataatatacatatacctattatatataatatacctattatat -ataagatacctattatatataatatacatatacctattatatatataatatacctattat -atatatataatatacctattatatataatatacctattatatatataatatacctattat -atatataatatacctattatatatataatatacctattatatataatatacctattatat -ataaaatatacctattatatataatatacctattatatacattatatataatatacctat -tatatgcattatatataatatacctattatatgcattatatataatatacctattatatg -cattatatataatatacctattatatgcattatatataatatacctattatatgcattat -ataatatattatatataatatgcatattatatgtattatatattatatattatatatata -atatacatattatatgtattatatattatatattatatatataatatacatattatatgt -attatatattatatataatatacatattatatattatatattatatacatattatatatt -atatattatatacatattatatattatatacatat-tatatattatatattatatacata -ttatacattatatatatctaaaatatataatacacattatatattatataatacacatta -tatataatatataatacacat-tatatattatatataatacac--attatatattatata -ta-atacacattatatat-----------------------tatataatacacattatat -attatatataatacacattatatattatatataatacacattatatattatatata-ata -cacattatatattatataatacacattatatattatatataatacacattatatatataa -tacacattatatattatatataatacataatacacat------tatatattatatataat -acacattatatataatatataacacacattatatataatatataacacacattatatatt -atatataatacacattatatattatatataatacacatatattatatataatacacatta -tatattatatataatacacatatattatatataatacacattatatattatatataatac -acattatatataatatataatacacattatatataatacttattatatattatacataat -atacatattatatataatacataatatacgtatattatataatatacatattatatataa -tacataatatacgtatattatataatatacatattatatatattatactatatataatac -tcatatatatacatattatatatacatattatatataatactcatattatatgtacatat -tatacatacatattatatataatacacatatatacatattatatataatacacacacaca -ttatatatgtcttatatataatatacatattatatatgtattatattattatagatataa -tatacatattatatctatatataaaatatatatgtagagagagagagacagggtctcatt -ttgtctcccaggctggagtgcagtggtgcaatcttggctcactacaacctccacctccca -ggctcaagggatcctccagcttcagcccc ->ref_chr20:38123590-38124705 -gctttgtgatctcaggcctgtcctgtaacctctctgggcc-------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------tcagaaacctctctctctctctatatatatatatatataataatatataataata -atatataatatgtataataataatatataatatttataata------ataatatatataa -tatgt-atatataatatacatatacctattatatataatatacctattatatataatata -cataaacctattatatat-----aatatac---ctattatatataagatacctattatat -ataatata----------cctattatatataagatacctattatatataatatacatata -cctattatata-tataatatacctattatata-tatataatatacctattatatatataa -tatacctattata-tatataatatacctattatatatataatatacctattatatataat -acacattatatataatatataacacacattatatataatatataacacacattatatatt -atatataatacacattatatattatatataatacacatatattatatataatacacatta -tatattatatataatacacatatattatatataatacacattatatattatatataatac -acattatatataatatataatacacattatatataatacttattatatattatacataat -atacatattatatataatacataatatacgtatattatataatatacatattatatataa -tacataatatacgtatattatataatatacatattatatatattatactatatataatac -tcatatatatacatattatatatacatattatatataatactcatattatatgtacatat -tatacatacatattatatataatacacatatatacatattatatataatacacacacaca -ttatatatgtcttatatataatatacatattatatatgtattatattattatagatataa -tatacatattatatctatatataaaatatatatgtagagagagagagacagggtctcatt -ttgtctcccaggctggagtgcagtggtgcaatcttggctcactacaacctccacctccca -ggctcaagggatcctccagcttcagcccc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_09e5224f3ed49d0a0d63118c15970e8f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_09e5224f3ed49d0a0d63118c15970e8f.msa deleted file mode 100644 index dd108ec0..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_09e5224f3ed49d0a0d63118c15970e8f.msa +++ /dev/null @@ -1,45 +0,0 @@ ->syndip_1_chr20:50775546-50775932 -tttctcattctgtctctccaaagatttccatatatatatatatatatatatatatatata -tatatatatataaatataaatatattctatatattcatatatatatattctatatattca -tatatataaatatattctatatattcatatataaatatattccatatatataaatatatt -ccatatatt---tatatataaatatatatcatatatttatatataaatatatatcatata -tttatatataaatatatatcatatatttatatat-aatatatatcatatatttatatata -aatatatatcatatatttatatataaatatatatcatatatttatatataatatatatca -tata-ttatatataaatatatatcatatatttatatataaatatatatcatatattaata -tatatcatatatttatatattaatatatatcatatatttatatat ->syndip_2_chr20:50775546-50775932 -tttctcattctgtctctccaaagatttccatatatatatatatatatatatatatatata -tatatatatataaatataaatatattctatatattcatatatatatattctatatattca -tatatataaatatattctatatattcatatatataaatatattctatatattcatata-t -aaatatattccatatatataaatatattccatatatttatatataaatatatatcatata -tttatatataaatatatatcatatatttatatataaatatatatcatatatttatatat- -aatatatatcatatatttatatataaatatatatcatatatttatatataatatatatca -tata-ttatatataaatatatatcatatatttatatataaatatatatcatatattaata -tatatcatatatttatatattaatatatatcatatatttatatat ->p:HG002_1_chr20:50775546-50775932 -tttctcattctgtctctccaaagatttccatatatatatatatatatatatatatatata -tatatatatataaatataaatatattctatatattcatatatatatattctatatattca -tatatataaatatattctatatattcatatataaatatatattctatatattcatata-t -aaatatattccatatatataaatatattccatatatttatatataaatatatatcatatc -catatatataaatatattccatatatttatatataaatatatatcatatatttatatata -aatatatatcatatatttatatataaatatatatcatatatttatatataatatatatca -tatatttatatataaatatatatcatatatttatatataaatatatatcatatattaata -tatatcatatatttatatattaatatatatcatatatttatatat ->p:HG002_2_chr20:50775546-50775932 -tttctcattctgtctctccaaagatttccatatatatatatatatatatatatatatata -tatatatatataaatataaatatattctatatattcatatatatatattctatatattca -tatatataaatatattctatatattcatatataaatatattccatatatataaatatatt -ccatatatt---tatatataaatatatatcatatatttatatataaatatatatcatata -tttatatataaatatatatcatatatttatatat-aatatatatcatatatttatatata -aatatatatcatatatttatatataaatatatatcatatatttatatataatatatatca -tata-ttatatataaatatatatcatatatttatatataaatatatatcatatattaata -tatatcatatatttatatattaatatatatcatatatttatatat ->ref_chr20:50775546-50775932 -tttctcattctgtctctccaaagatttccatatatatatatatatatatatatatatata -tatatatatataaatataaatatattctatatattcatatatatatattctatatattca -tatatataaatatattctatatattcatatataaatatattccatatatataaatatatt -ccatatatt---tatatataaatatatatcatatatttatatataaatatatatcatata -tttatatataaatatatatcatatatttatatat-aatatatatcatatatttatatata -aatatatatcatatatttatatataaatatatatcatatattaatatatatcatatat-- ------ttatatattaatatatatcatatatttatatat---------------------- ---------------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_0a842177b0a019f7a4fb813c41b08d1e.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_0a842177b0a019f7a4fb813c41b08d1e.msa deleted file mode 100644 index d4cd5f85..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_0a842177b0a019f7a4fb813c41b08d1e.msa +++ /dev/null @@ -1,170 +0,0 @@ ->syndip_1_chr20:63491857-63492490 -gatggggaggtggatggatagatggatggatggatggatggatggatggatggatggggg -gatagatggatggatggatggatggacggacggatggggagg--------tggatggatg -gatggatggatggatggatggatggatgaggagatgaacggatggatgagatggatggat -ggatgatggagggaaggatggctgggtggggagatggatggatagagaggtggatgggtg -gatggggagatggatggatggatggatggatggggaagtggatggatggggaggtggatg -gatggataggtggatgggtggatggacagaaggatgaatgggtagggagatggatggatg -gatggatggggagggatggatggatggatggatggatgggtggatggatagaaggatgga -tgggtggggaggtgggtgggtgg----gtggatggatggagagatggatagatggata-- ---gatggatggatggatggatggatggagagaaggatggatgggtggggaggtgggtggg -tgggtggatgggtggatggatggatgggtggggaggtgggcgggtggatggatggatgga -tgcagaggtgggtggatggatggatggagagaaggatggatgggtggggaggtgggtggg -tggatggatggatgagtggggaggtgggtgggtgggtggatggatggatggatggatgca -tggatggatgga------------------------------------------------ ------------------------------------------------------------- --------tggagaggtgggtggacggatggatggattgggaggtgggtagatgggtggat -ggacagaaggatggatgggtggggaggtgggtgggtgggtggatggatggatggggaggt -ggatggatggatggttagatggggaggtgggtggatgggtggatggacagaaggatggat -gggtagggaggtaggtgagtggatggatggatggggagatggatggatggatagagagaa -ggatggatgggtgggacaatggatggatggatggatagaaggatggacgggtggggagat -ggatggatggatggatggatggatggatggatggacagaaggatgtatgggtgggtaggt -gggtggatagatggatggatggatggatggataaatggatggatggaaggatggatggat -aggtaggtgggtggatggatggatggatggatgtacagaaggatggatgggtgggtaggt -gggtgagtggatgaatggatggatggatagatagaaggatggatgggtgggtcaatagat -ggatggatagagagaaggatggatgggtggggagatggatggatggatggatggatggat -ggatggatggatggatagagagaaggatggatggttgagaca----atggatggatggat -ggatggagagatggatggatggacggatggacagaaggatggatgggtggggaggtggat -ggatggattgaaggatggatgggtgggga----catggatggatggatggatggatggat -ggatggatggacagaaggatgta--------tgggtggggaggtgggtggatagatggat -ggatggggaaatggatggatggaaggatggatggatagggaggtgggtggatggatggat -ggatggatgtacagaaggatggatgggtggggaggtgggtgagtggatgaatggatggat -ggatagatagaaggatggatgggtgggacaatagatggatggatagagagaaggatggat -gggtggggagatagatggatggatggatggatggatggatagagagaaggatggatggtt -gagacaatggatggatggatggatggatggagagatggatggatggatgga ->syndip_2_chr20:63491857-63492490 -gatggggaggtggatggatagatggatggatggatggatggatggatggatggatggggg -gatagatggatggatggatggatggacggacggatggggaggtggatggatggatggatg -gatggatggatggatggatggatggatgaggagatgaacggatggatgagatggatggat -ggatgatggagggaaggatggctgggtggggagatggatggatagagaggtggatgggtg -gatggggagatggatggatggatggatggatggggaagtggatggatggggaggtggatg -gatggataggtggatgggtggatggacagaaggatgaatgggtagggagatggatggatg -gatggatgcggagggatggatggatggatggatggatgggtggatggatagaaggatgga -tgggtggggaggtgggtgggtgggtgcgtggatggatggagagatggatagatggataga -tggatggatggatggatggatggatggagagaaggatggatgggtggggaggtgggtggg -tgggtggatgggtggatggatggatgggtggggaggtgggcgggtggatggatggatgga -tgcagaggtgggtggatggatggatggagagaaggatggatgggtggggaggtgggtggg -tggatggatggatgagtggggaggtgggtgggtggatggatggatggatggatgcatgga -tggatggatggagaggtgggtggatgggtggatggacagaaggatggatgggtggggagg -tgggtgagtgggtggatggatgaatggggaggtggatggatggatggatggatgaaggat -ggatgggtggggaggtgggtggacggatggatggattgggaggtgggtagatgggtggat -ggacagaaggatggatgggtggggaggtgggtgggtgggtggatggatggatggggaggt -ggatggatggatggttagatggggaggtgggtggatgggtggatggacagaaggatggat -gggtagggaggtaggtgagtggatggatggatggggagatggatggatggatagagagaa -ggatggatgggtgggacaatggatggatggatggatagaaggatggacgggtgggga--- --gatggatggatggatggatggatggatggatggacagaaggatgtatgggtggggaggt -gggtggatagatggatggatggatggatggggaaatggatggatggaaggatggatggat -agggaggtgggtggatggatggatggatggatgtacagaaggatggatgggtggggaggt -gggtgagtggatgaatggatggatggatagatagaaggatggatgggtgggacaatagat -ggatggatagagagaaggatggatgggtgggga--------gatggatggatggatggat -ggatggatggatggatagagagaaggatggatggttgagacaatggatggatggatggat -ggatggagagatggatggatggatggatggacagaaggatggatgggtggggaggtggat -ggatggattgaaggatggacgggtggggagatggatggatggatggatggatggatggat -ggatggatggacagaaggatgtatgggtgggtaggtgggtggatagatggatggatggat -ggatggataaatggatggatggaaggatggatggataggtaggtgggtggatggatggat -ggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggatgaatggatggat -ggatagatagaaggatggatgggtgggtcaatagatggatggatagagagaaggatggat -gggtggg----tagatggatggatggatggatggatggatagagagaaggatggatggtt -gagacaatggatggatggatggatggatggagagatggatggatggatgga ->p:HG002_1_chr20:63491857-63492490 -gatggggaggtggatggatagatggatggatggatggatggatggatggatggatggggg -gatagatggatggatggatggatggacggacggatggggaggtggatggatggatggatg -gatggatggatggatggatggatggatgaggagatgaacggatggatgagatggatggat -ggatgatggagggaaggatggctgggtggggagatggatggatagagaggtggatgggtg -gatggggagatggatggatggatggatggatggggaagtggatggatggggaggtggatg -gatggataggtggatgggtggatggacagaaggatgaatgggtagggagatggatggatg -gatggatgcggagggatggatggatggatggatggatgggtggatggatagaaggatgga -tgggtggggaggtgggtgggtgggtgcgtggatggatggagagatggatagatggataga -tggatggatggatggatggatggatggagagaaggatggatgggtggggaggtgggtggg -tgggtggatgggtggatggatggatgggtggggaggtgggcgggtggatggatggatgga -tgcagaggtgggtggatggatggatggagagaaggatggatgggtggggaggtgggtggg -tggatggatggatgagtggggaggtgggtgggtggatggatggatggatggatgcatgga -tggatggatggagaggtgggtggatgggtggatggacagaaggatggatgggtggggagg -tgggtgagtgggtggatggatgaatggggaggtggatggatggatggatggatgaaggat -ggatgggtggggaggtgggtggacggatggatggattgggaggtgggtagatgggtggat -ggacagaaggatggatgggtggggaggtgggtgggtgggtggatggatggatggggaggt -ggatggatggatggttagatggggaggtgggtggatgggtggatggacagaaggatggat -gggtagggaggtaggtgagtggatggatggatggggagatggatggatggatagagagaa -ggatggatgggtgggacaatggatggatggatggatagaaggatggacgggtgggga--- --gatggatggatggatggatggatggatggatggacagaaggatgtatgggtggggaggt -gggtggatagatggatggatggatggatggggaaatggatggatggaaggatggatggat -agggaggtgggtggatggatggatggatggatgtacagaaggatggatgggtggggaggt -gggtgagtggatgaatggatggatggatagatagaaggatggatgggtgggacaatagat -ggatggatagagagaaggatggatgggtgggga--------gatggatggatggatggat -ggatggatggatggatagagagaaggatggatggttgagacaatggatggatggatggat -ggatggagagatggatggatggatggatggacagaaggatggatgggtggggaggtggat -ggatggattgaaggatggacgggtggggagatggatggatggatggatggatggatggat -ggatggatggacagaaggatgtatgggtgggtaggtgggtggatagatggatggatggat -ggatggataaatggatggatggaaggatggatggataggtaggtgggtggatggatggat -ggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggatgaatggatggat -ggatagatagaaggatggatgggtgggtcaatagatggatggatagagagaaggatggat -gggtggg----tagatggatggatggatggatggatggatagagagaaggatggatggtt -gagacaatggatggatggatggatggatggagagatggatggatggatgga ->p:HG002_2_chr20:63491857-63492490 -gatggggaggtggatggatagatggatggatggatggatggatggatggatggatggggg -gatagatggatggatggatggatggacggacggatggggaggtggatggatggatggatg -gatggatggatggatggatggatggatgaggagatgaacggatggatgagatggatggat -ggatgatggagggaaggatggctgggtggggagatggatggatagagaggtggatgggtg -gatggggagatggatggatggatggatggatggggaagtggatggatggggaggtggatg -gatggatgtatgggtgggtggatggacagaaggatgaatgggtagggagatggatggatg -gatggatggggagggatggatggatggatggatggatgggtggatggatagaaggatgga -tgggtggggaggtgggtgggtgg----gtggatggatggagagatggatagatggata-- ---gatggatggatggatggatggatggagagaaggatggatgggtggggaggtgggtggg -tgggtggatgggtggatggatggatgggtggggaggtgggcgggtggatggatggatgga -tgcagaggtgggtggatggatggatggagagaaggatggatgggtggggaggtgggtggg -tggatggatggatgagtggggaggtgggtgggtgggtggatggatggatggatggatgca -tggatggatgga------------------------------------------------ ------------------------------------------------------------- --------tggagaggtgggtggacggatggatggattgggaggtgggtagatgggtggat -ggacagaaggatggatgggtggggaggtgggtgggtgggtggatggatggatggggaggt -ggatggatggatggttagatggggaggtgggtggatgggtggatggacagaaggatggat -gggtagggaggtaggtgagtggatggatggatggggagatggatggatggatagagagaa -ggatggatgggtgggacaatggatggatggatggatagaaggatggacgggtggggagat -ggatggatggatggatggatggatggatggatggacagaaggatgtatgggtggggaggt -gggtggatagatggatggatggatggatggggaaatggatggatggaaggatggatggat -agggaggtgggtggatggatggatggatggatgtacagaaggatggatgggtggggaggt -gggtgagtggatgaatggatggatggatagatagaaggatggatgggtgggacaatagat -ggatggatagagagaaggatggatgggtggggagatggatggatggatggatggatggat -ggatggatggatggatagagagaaggatggatggttgagaca----atggatggatggat -ggatggagagatggatggatggacggatggacagaaggatggatgggtggggaggtggat -ggatggattgaaggatggatgggtgggga----catggatggatggatggatggatggat -ggatggatggacagaaggatgta--------taggtgggtggatagatggatggatggat -ggatggataaatggatggatggaaggatggatggataggtaggtgggtggatggatggat -ggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggatgaatggatggat -ggatagatagaaggatggatgggtgggtcaatagatggatggatagagagaaggatggat -gggtggg----tagatggatggatggatggatggatggatagagagaaggatggatggtt -gagacaatggatggatggatggatggatggagagatggatggatggatgga ->ref_chr20:63491857-63492490 -gatggggaggtggatggatagatggatggatggatggatggatggatggatggatggggg -gatagatggatggatggatggatggacggacggatggggaggtggatggatggatggatg -gatggatggatggatggatggatggatgaggagatgaacggatggatgagatggatggat -ggatgatggagggaaggatggctgggtggggagatggatggatagagaggtggatgggtg -gatggggagatggatggatggatggatggatggggaagtggatggatggggaggtggatg -gatggatgtatgggtggg------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------taggtgggtggatagatggatggatggat -ggatggataaatggatggatggaaggatggatggataggtaggtgggtggatggatggat -ggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggatgaatggatggat -ggatagatagaaggatggatgggtgggtcaatagatggatggatagagagaaggatggat -gggtggg----tagatggatggatggatggatggatggatagagagaaggatggatggtt -gagacaatggatggatggatggatggatggagagatggatggatggatgga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_0b060e62331ab50c5edfcb210d920370.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_0b060e62331ab50c5edfcb210d920370.msa deleted file mode 100644 index 491a0298..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_0b060e62331ab50c5edfcb210d920370.msa +++ /dev/null @@ -1,70 +0,0 @@ ->syndip_1_chr20:63559205-63559929 -ttccctcccagtcctggcaccttgcaggtggagagggctcttcaggaaggcatagttggc -ctcctgcagacgcgcacctggccggcaggcacgagggtctgctgagcctcgcagaagtcc -aggaggctacgccagagggggcagcagcgcagaaggaggtggtctcctgtgagggtggga -gtcagatgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgggag------- ------------------------------------------------------------- -------------------------------------------------------ggagtc -agggtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggag-gag -tcagggtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtgggaggag -tcagggtcagatgggagtcagtcagagtcaggtgggag-gagtcagggtcaggtgggagg -agtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggag -gagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtcaggcaggagtcg -gcagctccctagcccagccctggcctcacctgtgttcccaccctggaagagcccagcccc -gccctcaccg ->syndip_2_chr20:63559205-63559929 -ttccctcccagtcctggcaccttgcaggtggagagggctcttcaggaaggcatagttggc -ctcctgcagacgcgcacctggccggcaggcacgagggtctgctgagcctcgcagaagtcc -aggaggctacgccagagggggcagcagcgcagaaggaggtggtctcctgtgagggtggga -gtcagatgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgggag------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------gagtcagggtcaggtgggagtcagtcagggtcaggtgggagg -agtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggag -gagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtcaggcaggagtcg -gcagctccctagcccagccctggcctcacctgtgttcccaccctggaagagcccagcccc -gccctcaccg ->p:HG002_1_chr20:63559205-63559929 -ttccctcccagtcctggcaccttgcaggtggagagggctcttcaggaaggcatagttggc -ctcctgcagacgcgcacctggccggcaggcacgagggtctgctgagcctcgcagaagtcc -aggaggctacgccagagggggcagcagcgcagaaggaggtggtctcctgtgagggtggga -gtcagatgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgggag------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------gagtcagggtcaggtgggagtcagtcagggtcaggtgggagg -agtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggag -gagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtcaggcaggagtcg -gcagctccctagcccagccctggcctcacctgtgttcccaccctggaagagcccagcccc -gccctcaccg ->p:HG002_2_chr20:63559205-63559929 -ttccctcccagtcctggcaccttgcaggtggagagggctcttcaggaaggcatagttggc -ctcctgcagacgcgcacctggccggcaggcacgagggtctgctgagcctcgcagaagtcc -aggaggctacgccagagggggcagcagcgcagaaggaggtggtctcctgtgagggtggga -gtcagatgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgggag------- ------------------------------------------------------------- -------------------------------------------------------ggagtc -agggtcaggtgggaggagtcagggtcaggtgggag-gagtcagggtcagatgggagtcag -tcagagtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggt---cggag -tcagggtcaggtgggag-gagtcagggtcaggtgggagtcagtcagggtcaggtgggagg -agtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggag -gagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtcaggcaggagtcg -gcagctccctagcccagccctggcctcacctgtgttcccaccctggaagagcccagcccc -gccctcaccg ->ref_chr20:63559205-63559929 -ttccctcccagtcctggcaccttgcaggtggagagggctcttcaggaaggcatagttggc -ctcctgcagacgcgcacctggccggcaggcacgagggtctgctgagcctcgcagaagtcc -aggaggctacgccagagggggcagcagcgcagaaggaggtggtctcctgtgagggtggga -gtcagatgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgggaggagtcag -ggtcaggtgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgggaggagtca -gggtcagatgggagtcagtcagagtcaggtgggaggagtcagggtcaggtgggaggagtc -agggtcaggtgggaggagtcagggtcaggtgggag-gagtcagggtcagatgggagtcag -tcagagtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggt---cggag -tcagggtcaggtgggag-gagtcagggtcaggtgggagtcagtcagggtcaggtgggagg -agtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggag -gagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtcaggcaggagtcg -gcagctccctagcccagccctggcctcacctgtgttcccaccctggaagagcccagcccc -gccctcaccg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_0cb2ac2b9539805c6a980d5bb94043de.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_0cb2ac2b9539805c6a980d5bb94043de.msa deleted file mode 100644 index 8b62a9ea..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_0cb2ac2b9539805c6a980d5bb94043de.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:34235750-34236213 -actccagcctgtgtgacagagtgagactctgagaaagaagaaagaaagaaagaaagaaag -aaagaaagaaagaaagaaagaaagaaagaaggaaggaaggaaggaaggaaggaaggaagg -aaggaaggaagggaaggaaggaaggaaggaaggaagcgggagggagggaagaaggaagga -aggaggagggagggaagaatgaaggaaggaaggaaggagggaaggaaggaaggaagcggg -agggagggaagaaggaaggaaggaaggaaggagggagggagggaagaaggaaggaggagg -gagggagggaagcaggaaagaaggaaggaaggagaaagagagaa--agagagagaagaag -aaagagaaagaaacagaaaaggaaggaaggagagagagaaagaaagagaaagagaaggaa -ggaaggagaaagaaaggaaaaggaaaggaaaggagtggaaaggaaaggagaggaaaggag -aaaggagggagggagggaaaagaaagaaagaaagaaaaggctaaacctgactatgatatt -gaattta ->syndip_2_chr20:34235750-34236213 -actccagcctgtgtgacagagtgagactctgagaaagaagaaagaaagaaagaaagaaag -aaagaaagaaagaaagaaagaaagaaagaaggaaggaaggaaggaaggaaggaaggaagg -aaggaaggaagggaaggaaggaaggaaggaaggaagcgggagggagggaagaaggaagga -aggaggagggagggaagaatgaaggaaggaaggaaggagggaaggaaggaaggaagcggg -agggagggaagaaggaaggaaggaaggaaggagggagggagggaagaaggaaggaggagg -gagggagggaagcaggaaagaaggaaggaaggagaaagagagaa--agagagagaagaag -aaagagaaagaaacagaaaaggaaggaaggagagagagaaagaaagagaaagagaaggaa -ggaaggagaaagaaaggaaaaggaaaggaaaggagtggaaaggaaaggagaggaaaggag -aaaggagggagggagggaaaagaaagaaagaaagaaaaggctaaacctgactatgatatt -gaattta ->p:HG002_1_chr20:34235750-34236213 -actccagcctgtgtgacagagtgagactctgagaaagaagaaagaaagaaagaaagaaag -aaagaaagaaagaaagaaagaaagaaagaaggaaggaaggaaggaaggaaggaaggaagg -aaggaaggaagggaaggaaggaaggaaggaaggaagcgggagggagggaagaaggaagga -aggaggagggagggaagaatgaaggaaggaaggaaggagggaaggaaggaaggaagcggg -agggagggaagaaggaaggaaggaaggaaggagggagggagggaagaaggaaggaggagg -gagggagggaagcaggaaagaaggaaggaaggagaaagagagaa--agagagagaagaag -aaagagaaagaaacagaaaaggaaggaaggagagagagaaagaaagagaaagagaaggaa -ggaaggagaaagaaaggaaaaggaaaggaaaggagtggaaaggaaaggagaggaaaggag -aaaggagggagggagggaaaagaaagaaagaaagaaaaggctaaacctgactatgatatt -gaattta ->p:HG002_2_chr20:34235750-34236213 -actccagcctgtgtgacagagtgagactctgagaaagaagaaagaaagaaagaaagaaag -aaagaaagaaagaaagaaagaaagaaagaaggaaggaaggaaggaaggaaggaaggaagg -aaggaaggaagggaaggaaggaaggaaggaaggaagcgggagggagggaagaaggaagga -aggaggagggagggaagaatgaaggaaggaaggaaggagggaaggaaggaaggaagcggg -agggagggaagaaggaaggaaggaaggaaggagggagggagggaagaaggaaggaggagg -gagggagggaagcaggaaagaaggaaggaaggagaaagagagaa--agagagagaagaag -aaagagaaagaaacagaaaaggaaggaaggagagagagaaagaaagagaaagagaaggaa -ggaaggagaaagaaaggaaaaggaaaggaaaggagtggaaaggaaaggagaggaaaggag -aaaggagggagggagggaaaagaaagaaagaaagaaaaggctaaacctgactatgatatt -gaattta ->ref_chr20:34235750-34236213 -actccagcctgtgtgacagagtgagactctgagaaagaagaaagaaagaaagaaagaaag -aaagaaagaaagaaagaaagaaagaaagaaagaaggaaggaaggaaggaaggaaggaaag -gaaggaaggaaggaaggaaggaaggaagga------------------------------ --------------------------aaggaaggaaggaaggaaggaaggaaggaagcggg -agggagggaagaaggaaggaaggaaggaaggagggagggagggaaga------------- --------------aggaaagaaggaaggaaggagaaagagagaaagagagagagaagaag -aaagagaaagaaacagaaaaggaaggaaggagagagagaaagaaagagaaagagaaggaa -ggaaggaaggagaaag--aaaggaaaggaaaggagtggaaaggaaaggagaggaaaggag -aaaggagggagggagggaaaagaaagaaagaaagaaaaggctaaacctgactatgatatt -gaattta diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_0ce802f2b6832e0ec9729163f8b6e1f1.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_0ce802f2b6832e0ec9729163f8b6e1f1.msa deleted file mode 100644 index 2f23f3c5..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_0ce802f2b6832e0ec9729163f8b6e1f1.msa +++ /dev/null @@ -1,45 +0,0 @@ ->syndip_1_chr20:49834109-49834558 -cgtggtggtgcacgcttgtaatattagcttgtctctctctctctctctctctctctctct -ctctctctctctctc------------tatatatatatatatatacacacacacacacac -tatgtatatacacacactgtatatacgcactatatgcactatatatacacacagtatatg -tatatacacacactatatatacagtgtgtatatatatatatactgtgtgtatatatatat -atactgtata------------------------------tatatatatatatactgtgt -atatatatatactg---------------------------------------------t -gtatatatatatatatactgtatatatacacacacacactatatatatgccatatataat -atctggtggccagttgtgtgaaatacattcat ->syndip_2_chr20:49834109-49834558 -cgtggtggtgcacgcttgtaatattagcttgtctctctctctctctctctctctctctct -ctctctctctctctctctctctctatatatatatatatatatatatatacacacacacac -tatgtatatacacacactgtatatacgcactatatgcactatatatacacacagtatatg -tatatacacacactatatatacagtgtgtatatatatatatactgtgtatatatatatat -actgtatatatatatatactgtgtatatatatatatactgtatatatatatatactgtgt -atatatatatactgtatatatatactgtatatatatatatatactgtatatatatatact -gtgtatatatatatatactgtatatatacacacacacactatatatatgccatatataat -atctggtggccagttgtgtgaaatacattcat ->p:HG002_1_chr20:49834109-49834558 -cgtggtggtgcacgcttgtaatattagcttgtctctctctctctctctctctctctctct -ctctctctctctctctctctctctatatatatatatatatatatatatacacacacacac -tatgtatatacacacactgtatatacgcactatatgcactatatatacacacagtatatg -tatatacacacactatatatacagtgtgtatatatatatatactgtgtatatatatatat -actgtatatatatatatactgtgtatatatatatatactgtatatatatatatactgtgt -atatatatatactgtatatatatactgtatatatatatatatactgtatatatatatact -gtgtatatatatatatactgtatatatacacacacacactatatatatgccatatataat -atctggtggccagttgtgtgaaatacattcat ->p:HG002_2_chr20:49834109-49834558 -cgtggtggtgcacgcttgtaatattagcttgtctctctctctctctctctctctctctct -ctctctctctctctc------------tatatatatatatatatacacacacacacacac -tatgtatatacacacactgtatatacgcactatatgcactatatatacacacagtatatg -tatatacacacactatatatacagtgtgtatatatatatatactgtgtgtatatatatat -atactgtata------------------------------tatatatatatatactgtgt -atatatatatactg---------------------------------------------t -gtatatatatatatatactgtatatatacacacacacactatatatatgccatatataat -atctggtggccagttgtgtgaaatacattcat ->ref_chr20:49834109-49834558 -cgtggtggtgcacgcttgtaatattagcttg--tctctctctctctctctctctctctct -ctctctctctctctctctctatatatatatatatatatatatatatatacacacacacac -tatgtatatacacacactgtatatacgcactatatgcactatatatacacacagtatatg -tatatacacacactatatatacagtgtgtatatatatatatactgtgtatatatatatat -actgtatatatatatatactgtgtatatatatatatactgtgtatatatatatactgtgt -atatatatatactgtatatatatactgtatatatatatatatactgtatatatatatact -gtgtatatatatatatactgtatatatacacacacacactatatatatgccatatataat -atctggtggccagttgtgtgaaatacattcat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_0cfdee8d034b48611d374ae4635eb28d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_0cfdee8d034b48611d374ae4635eb28d.msa deleted file mode 100644 index d1ce715b..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_0cfdee8d034b48611d374ae4635eb28d.msa +++ /dev/null @@ -1,70 +0,0 @@ ->syndip_1_chr20:63535674-63536245 -gcccagcatggagcccctggggtccaccccctccacttccgcacacctggaagcactgcc -ccacctgcccctccaaccacctggcctcccgcccccccctcacctggcctcccgccccct -cctcacctggcctcccgccccctcctcacctggcctcccgcccccccctcacctggcctc -ccaccccgtcctcacctggcctcccgcacccccctcacctggcctcccgcccccccctca -tctggcctcccgccccctcctcacctggcctcccgccccctcctctcctggcctcccgcc -ccccccctcacctggcctcccgccccctcctcacctggcctcccgccccctcctcacctg -gcctcccgccccccccctcacctggcctcccgccccctcctcacctggcctcccgccccc -cccctcacctggcctcccgccccctcctcacctggcctcccgcccccccctcacctggcc -tcccaccccgtcctcacctggcctcccgcacccccctcacctggcctcccgcccccccct -cacctggcctcccgccccctcctctcctggcctcccgccccctcctctcctggcctcccg -tcccctcctctcctggtctcccgccccccccacctggcctcccgccccccctcacctggc -ctccagccccccccacctggcctcccgct-ccccccccacctggcctcccaccccctcct -cacctggcctcctccccacttctcacctgggcgagttctcaggactcagggtctttgcac ->syndip_2_chr20:63535674-63536245 -g----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------cccagcatggagcccctggggtccaccccctccacttcc -gcacacctggaagcactgccccacctgcccctccaac-------cacctggcctcccgcc -ccccccctcacctggcctcccgccccctcctcacctggcctcccgccccctcctcacctg -gcctcccgccccccccctcacctggcctcccgccccctcctcacctggcctcccg-cccc -ctcctcacctggcctcccgcccccccctcacctggcctcccaccccgtcctcacctggcc -tcccgcacccccctcacctggcctcccgcccccccctcacctggcctcccgccccctcct -cacctggcctcccgccccctcctctcctggcctcccgccccctcctctcctggcctcccg -tcccctcctctcctggtctcccgccccccccacctggcctcccgccccccctcacctggc -ctccagccccccccacctagcctcccgctcccccccccacctggcctcccaccccctcct -cacctggcctcctccccacttctcacctgggcgagttctcaggactcagggtctttgcac ->p:HG002_1_chr20:63535674-63536245 -g----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------cccagcatggagcccctggggtccaccccctccacttcc -gcacacctggaagcactgccccacctgcccctccaac-------cacctggcctcccgcc -ccccccctcacctggcctcccgccccctcctcacctggcctcccgccccctcctcacctg -gcctcccgccccccccctcacctggcctcccgccccctcctcacctggcctcccg-cccc -ctcctcacctggcctcccgcccccccctcacctggcctcccaccccgtcctcacctggcc -tcccgcacccccctcacctggcctcccgcccccccctcacctggcctcccgccccctcct -cacctggcctcccgccccctcctctcctggcctcccgccccctcctctcctggcctcccg -tcccctcctctcctggtctcccgccccccccacctggcctcccgccccccctcacctggc -ctccagccccccccacctagcctcccgctcccccccccacctggcctcccaccccctcct -cacctggcctcctccccacttctcacctgggcgagttctcaggactcagggtctttgcac ->p:HG002_2_chr20:63535674-63536245 -gcccagcatggagcccctggggtccaccccctccacttccgcacacctggaagcactgcc -ccacctgcccctccaaccacctggcctcccgcccccccctcacctggcctcccgccccct -cctcacctggcctcccgccccctcctcacctggcctcccgcccccccctcacctggcctc -ccaccccgtcctcacctggcctcccgcacccccctcacctggcctcccgcccccccctca -tctggcctcccgccccctcctcacctggcctcccgccccctcctctcctggcctcccgcc -ccccccctcacctggcctcccgccccctcctcacctggcctcccgccccctcctcacctg -gcctcccgccccccccctcacctggcctcccgccccctcctcacctggcctcccgccccc -cccctcacctggcctcccgccccctcctcacctggcctcccgcccccccctcacctggcc -tcccaccccgtcctcacctggcctcccgcacccccctcacctggcctcccgcccccccct -cacctggcctcccgccccctcctctcctggcctcccgccccctcctctcctggcctcccg -tcccctcctctcctggtctcccgccccccccacctggcctcccgccccccctcacctggc -ctccagccccccccacctggcctcccgct-ccccccccacctggcctcccaccccctcct -cacctggcctcctccccacttctcacctgggcgagttctcaggactcagggtctttgcac ->ref_chr20:63535674-63536245 -g----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------cccagcatggagcccctggggtccaccccctccacttcc -gcacacctggaagcactgccccacctgcccctccaac-------cacctggcctcccgcc -ccccccctcacctggcctcccgccccctcctcacctggcctcccgccccctcctcacctg -gcctcccgccccccccctcacctggcctcccgccccctcctcacctggcctcccg-cccc -ctcctcacctggcctcccgcccccccctcacctggcctcccaccccgtcctcacctggcc -tcccgcacccccctcacctggcctcccgcccccccctcacctggcctcccgccccctcct -cacctggcctcccgccccctcctctcctggcctcccgccccctcctctcctggcctcccg -tcccctcctctcctggtctcccgccccccccacctggcctcccgccccccctcacctggc -ctccagccccccccacctagcctcccgctcccccccccacctggcctcccaccccctcct -cacctggcctcctccccacttctcacctgggcgagttctcaggactcagggtctttgcac diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_0e0c7abb27747bd1ba807c59637cfd86.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_0e0c7abb27747bd1ba807c59637cfd86.msa deleted file mode 100644 index b6bf7859..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_0e0c7abb27747bd1ba807c59637cfd86.msa +++ /dev/null @@ -1,460 +0,0 @@ ->syndip_1_chr20:20354570-20358323 -taaagaagttgaattcataagggtaatgaggggaggaaggggtggtcatactgtgtgaag -ggagatggtcacactgagggaaggtggtcacactgtgagaagggaggtagtcacattgtg -agagaaaaagtgatcacactgtgtgaggggaggtggtcacactgtgagagaaaaagtaat -catactgtgaaagggaggtggtcacgctgagaggggaggtggtcacactgtgtcagggga -ggtggtcacactgtgagagaaaaagtaatcacactgtgaggggatgtggtcacactgaga -ggggaggtggtcagactgtgtcagaggaggtggtcacactgaggggaggtggtcacactg -tgagaggggaggtggtcagactctgtcagaggaggtggtcacactgtgagaggggaggtg -gtcacactgaggggaagtggtcacactgtgagaggggaggtggtcacactgaggggagat -ggtcacactgcaagaggggaggtgatcacactgagggg---------------------- --aggtggtcacactgtgagagggaaggtggtcacactgtgagagggaaggtggtcacact -gtgtgaggggaggtggtcacactgtgaggggaggtggtcacattgtgagagggaaggggg -tcactgtgagaggggagaaggtcacactaaggggaggtagtcacactgtgaggggaggtg -atcacactaaggggaggtggtcacactgtgagaggaggtggtcacactgtgaggggtggt -cacactgtgaggggaggtcacactgaggggaggtagtgacactatgagcagagatggtca -cactgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagcagagatggtc -acactgtgaggggaggtggtcacactgaggggaggtactcacactgtgaggggaggtggt -cacactgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagcagagatgg -tcacactgtgaggggagggggtcacactgtgagggggaaggtggtcacactgtgagaggg -gagaaggtcacactaaggggaggtagtcacactgtgaggggaggtgatcacactaagggg -aggtggtcacactgtgagaggaggtggtcacactgtgaggggaggtcacactgaggggag -gtagtgacactatgagcagagatggtcacactgtgaggggaggtggtcacactgagggga -ggtagtgacactgtgagcagagatggtcacactgtgaggggaggtggtcacactgagggg -aggtagtcacactgtgaggggaggtggtcacactgtgaggggaggtggtcacactgaggg -gaggtagtgacactgtgagcagagatggtcacactgtgaggggagggggtcacactgtga -gggggaaggtggtcacactgtgagaggggagaaggtcacactaaggggaggtagtcacac -tgtgaggggaggtgatcacactaaggggaggtggtcacactgtgagaggaggtggtcaca -ctgtgaggggaggtcacactgaggggaggtagtgacactatgagcagagatggtcacact -gtgaggggaggtggtcacactgaggggaggtagtgacactgtgagcagagatggtcacac -tgtgaggggaggtggtcacactgaggggaggtagtcacactgtgaggggaggtggtcaca -ctgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagcagagatggtcac -actgtaaggggaggtgatcacactgtgaggggacgtggtcacactgtgaggggaggtggt -cacactgtgagaggggaggtgaccacacaggggaggtggtcacactgaggggaggtagtg -acactgtgagcagaggtggtcacactgtgaggggaggtggtcacactgtgaggggaggtg -gtcacactgagaggaggtggtcacactgaggggaagtggtcacactgagggggggtggtc -acactgaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggaggggtc -atactgcgagtggaggtggtcacactgtgaagggtggtagtcacactgagaggaggtgtt -cacactgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtc -acactgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtca -cactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcac -agtgtgaggggagatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtca -cactgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacac -tgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacact -gaggggaggtggtcaca--ctgaggggaggtggtcatagtgtgaggggaggtggtcacac -tgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacact -gaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactg -gggaggtggtcacactgtgaggggaggtggtcacactgtgaggggaggtggtcacactga -gaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcacactgaggg -gaggtggtcacagtgtgaggggaggtggtcatactgtgagtgaggaggtagtcacac--t -gaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcacac -tgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatactg- ----------------------------------------tgaggggaagtggtcacactg -aggggaggtggtcatagtgtga--ggggaggtggtcacactgaggggaggtggtcacagt -gtgaggggaggtggtcacac--tgaggggaggtggtcacactgaggggaggtggtcacag -tgtgagaggaggtggtcacactgaggggaggtggtcacagtgtgaggggagatggtcaca -ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag -tgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagt -gtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggagatggtcacac -tgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcaca-- ------------------gtgtgaggggaggtggtcacactgaggggaggtggtcacactg -agaggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcacact -gaggggaagtggtcacactgaggggaggtg------------------------------ -------------gtcacactgaggggagggggtcatactgcgagtggaggtagtcacact -gtgaagggtggtagtcacactgagaggaggtggtcacactgaggggaagtggtcacactg -aggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtcatagtgt -gaggggag---------------------------------------------------- --------------------------------------------------gtggtcacact -gaggggaggtggtcacactgaggggaggtggtcacagtgtga--ggggaggtggtcacac -tgaggggaggtggtcacagtgtacggggaggtggtcatac--tgaggggaggtggtcaca -gtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacag -tgtgaggggaggtggtcacactgaggggaggtggtcacactgtgaggggaggtggtcaca -ctgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcaca- -c-tgaggagaggtggtcat-------------------agtgtgaggggaggtggtcaca -c----------------------------------------------------------- -------------------------------------------tgaggggaggtggtcaca -ctgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatag -tgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcacagtg-------------------------------------- -tgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacact -gaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactg -tgaggggaggtggtcacattgaggagaggtggtcatagtgtgaggggaggtggtcacact -gaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactg -aggagaggtggtcatagtgtgcggggaggtggtcacactgaggggaggtggtcacactga -ggggaggtggtcacagtgtgaggggaggtggtcacagtgtgaggggaggtggtcacactg -aggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactga -gggaaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcatagtgtg -aggggaggtggtcacagtgtgaggggaggtggtcacactgaggagaggtggtcatagtgt -gaggggaggtggtcacactgaggggaggtggtcacactgtgaggggaggtgggcacactg -tgaggggtggtagtcacactgagaggaggtggtcacactgaggggaggtggtcacactga -ggggaggtggtcacactgaggggaatggtcatactgtgaggggaggtggtcacactgagg -ggaagtggtcacactgaggggaatggtcatactgtgaggggaggtggtcacactgtgaaa -gaagatgatcacagtatgagaggtcatc ->syndip_2_chr20:20354570-20358323 -taaagaagttgaattcataagggtaatgaggggaggaaggggtggtcatactgtgtgaag -ggagatggtcacactgagggaaggtggtcacactgtgagaagggaggtagtcacattgtg -agagaaaaagtgatcacactgtgtgaggggaggtggtcacactgtgagagaaaaagtaat -catactgtgaaagggaggtggtcacgctgagaggggaggtggtcacactgtgtcagggga -ggtggtcacactgtgagagaaaaagtaatcacactgtgaggggatgtggtcacactgaga -ggggaggtggtcagactgtgtcagaggaggtggtcacactgaggggaggtggtcacactg -tgagaggggaggtggtcagactctgtcagaggaggtggtcacactgtgagaggggaggtg -gtcacactgaggggaagtggtcacactgtgagaggggaggtggtcacactgaggggagat -ggtcacactgcaagaggggaggtgatcacactgaggggaggtggtcacactgtgagaggg -aaggtggtcacactgtgagagggaaggtggtcacactgtgagagggaaggtggtcacact -gtgtgaggggaggtggtcacactgtgaggggaggtggtcacattgtgagagggaaggggg -tcactgtgagaggggagaaggtcacactaaggggaggtagtcacactgtgaggggaggtg -atcacactaaggggaggtggtcacactgtgagaggaggtggtcacactgtgaggggtggt -cacactgtgaggggaggtcacactgaggggaggtagtgacactatgagcagagatggtca -cactgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagcagaga----- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------tggtcacactgtgaggggaggtggtcacactgagggg -aggtactcacactgtgaggggaggtggtcacactgtgaggggaggtggtcacactgaggg -gaggtagtgacactgtgagcagagatggtcacactgtgaggggagggggtcacactgtga -gggggaaggtggtcacactgtgagaggggagaaggtcacactaaggggaggtagtcacac -tgtgaggggaggtgatcacactaaggggaggtggtcacactgtgagaggaggtggtcaca -ctgtgaggggaggtcacactgaggggaggtagtgacactatgagcagagatggtcacact -gtgaggggaggtggtcacactgaggggaggtagtgacactgtgagcagagatggtcacac -tgtgaggggaggtggtcacactgaggggaggtagtcacactgtgaggggaggtggtcaca -ctgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagcagagatggtcac -actgtaaggggaggtgatcacactgtgaggggacgtggtcacactgtgaggggaggtggt -cacactgtgagaggggaggtgaccacacaggggaggtggtcacactgaggggaggtagtg -acactgtgagcagaggtggtcacactgtgaggggaggtggtcacactgtgaggggaggtg -gtcacactgagaggaggtggtcacactgaggggaagtggtcacactgagggggggtggtc -acactgaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggaggggtc -atactgcgagtggaggtggtcacactgtgaagggtggtagtcacactgagaggaggtggt -cacactgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtc -acactgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtca -cactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcac -agtgtgaggggagatggtcacactgaggggaggtggtcacagtg---------------- ----tgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacac -tgtgaggggaggtggtcacactgtgaggaggtggtcacactgaggggaagtggtcacact -gaggggaggtggtcatagtgtgaggggaggtggtcacact----ggggaggtggtcacac -tgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacact -gaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacact- ---------------------ggggaggtggtcacactgtgaggggaggtggtcacactga -gaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcacactgaggg -gaggtggtcatagtgtgaggggaggtggtcacac------tggggaggtggtcacactgt -gaggggaggtggtcacactgtgaggggaggtggtcacac--tgagaggaggtggtcacac -tgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatactgt -gagtgaggaggtagtcacactgaggggaagtggtcacactgaggggaggtggtcacactg -aggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggagggggtcatact -gcgagtggaggtagtcacactgtgaagggtggtagtcacactgagaggaggtggtcaca- --ctgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcaca -ctgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacag -tgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagt -gtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacac -tgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacact -gaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactg -agaggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaagtagtcacact -gaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatactgtg -agtgaggaggtagtcacactgaggggagggggtcatactgcgagtggaggtagtcacact -gtgaagggtggtagtcacactgagaggaggtggtcacactgaggggaagtggtcacactg -aggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtcatagtgt -gaggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactg -aggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggaagtggtcacact -gaggggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcacac -tgaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcaca ---ctgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatac -tgtgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcaca -ctgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacag -tgtgcggggaggtggtcatactgaggggaggtggtcacagtgtgaggggaggtggtcaca -ctgaggggaggtggtcacagtgtgcggggaggtggtcacactgaggggaggtggtcatag -tgtgaggggaggtggtcatactgaggggaggtggtcacactgtgaggggaggtggtcaca -ctgaggagaggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcatag -tgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcacac -tgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtgacact -gaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactg -tgaggggaggtggtcacattgaggagaggtggtcatagtgtgaggggaggtggtcacact -gaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactg -aggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactga -ggggaggtggtcacagtgtgaggggaggtggtcacagtgtgaggggaggtggtcacactg -aggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactga -gggaaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcatagtgtg -aggggaggtggtcacagtgtgaggggaggtggtcacactgaggagaggtggtcatagtgt -gaggggaggtggtcacactgaggggaggtggtcacactgtgaggggaggtgggcacactg -tgaggggtggtagtcacactgagaggaggtggtcacactgaggggaggtggtcacactga -ggggaagtggtcacactgaggggaatggtcatactgtgaggggaggtggtcacactgagg -ggaagtggtcacactgaggggaatggtcatactgtgaggggaggtggtcacactgtgaaa -gaagatgatcacagtatgagaggtcatc ->p:HG002_1_chr20:20354570-20358323 -taaagaagttgaattcataagggtaatgaggggaggaaggggtggtcatactgtgtgaag -ggagatggtcacactgagggaaggtggtcacactgtgagaagggaggtagtcacattgtg -agagaaaaagtgatcacactgtgtgaggggaggtggtcacactgtgagagaaaaagtaat -catactgtgaaagggaggtggtcacgctgagaggggaggtggtcacactgtgtcagggga -ggtggtcacactgtgagagaaaaagtaatcacactgtgaggggatgtggtcacactgaga -ggggaggtggtcagactgtgtcagaggaggtggtcacactgaggggaggtggtcacactg -tgagaggggaggtggtcagactctgtcagaggaggtggtcacactgtgagaggggaggtg -gtcacactgaggggaagtggtcacactgtgagaggggaggtggtcacactgaggggagat -ggtcacactgcaagaggggaggtgatcacactgaggggaggtggtcacactgtgagaggg -aaggtggtcacactgtgagagggaaggtggtcacactgtgagagggaaggtggtcacact -gtgtgaggggaggtggtcacactgtgaggggaggtggtcacattgtgagagggaaggggg -tcactgtgagaggggagaaggtcacactaaggggaggtagtcacactgtgaggggaggtg -atcacactaaggggaggtggtcacactgtgagaggaggtggtcacactgtgaggggtggt -cacactgtgaggggaggtcacactgaggggaggtagtgacactatgagcagagatggtca -cactgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagcagaga----- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------tggtcacactgtgaggggaggtggtcacactgagggg -aggtactcacactgtgaggggaggtggtcacactgtgaggggaggtggtcacactgaggg -gaggtagtgacactgtgagcagagatggtcacactgtgaggggagggggtcacactgtga -gggggaaggtggtcacactgtgagaggggagaaggtcacactaaggggaggtagtcacac -tgtgaggggaggtgatcacactaaggggaggtggtcacactgtgagaggaggtggtcaca -ctgtgaggggaggtcacactgaggggaggtagtgacactatgagcagagatggtcacact -gtgaggggaggtggtcacactgaggggaggtagtgacactgtgagcagagatggtcacac -tgtgaggggaggtggtcacactgaggggaggtagtcacactgtgaggggaggtggtcaca -ctgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagcagagatggtcac -actgtaaggggaggtgatcacactgtgaggggacgtggtcacactgtgaggggaggtggt -cacactgtgagaggggaggtgaccacacaggggaggtggtcacactgaggggaggtagtg -acactgtgagcagaggtggtcacactgtgaggggaggtggtcacactgtgaggggaggtg -gtcacactgagaggaggtggtcacactgaggggaagtggtcacactgagggggggtggtc -acactgaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggaggggtc -atactgcgagtggaggtggtcacactgtgaagggtggtagtcacactgagaggaggtggt -cacactgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtc -acactgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtca -cactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcac -agtgtgaggggagatggtcacactgaggggaggtggtcacagtg---------------- ----tgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacac -tgtgaggggaggtggtcacactgtgaggaggtggtcacactgaggggaagtggtcacact -gaggggaggtggtcatagtgtgaggggaggtggtcacact----ggggaggtggtcacac -tgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacact -gaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacact- ---------------------ggggaggtggtcacactgtgaggggaggtggtcacactga -gaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcacactgaggg -gaggtggtcatagtgtgaggggaggtggtcacac------tggggaggtggtcacactgt -gaggggaggtggtcacactgtgaggggaggtggtcacac--tgagaggaggtggtcacac -tgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatactgt -gagtgaggaggtagtcacactgaggggaagtggtcacactgaggggaggtggtcacactg -aggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggagggggtcatact -gcgagtggaggtagtcacactgtgaagggtggtagtcacactgagaggaggtggtcaca- --ctgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcaca -ctgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacag -tgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagt -gtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacac -tgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacact -gaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactg -agaggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaagtagtcacact -gaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatactgtg -agtgaggaggtagtcacactgaggggagggggtcatactgcgagtggaggtagtcacact -gtgaagggtggtagtcacactgagaggaggtggtcacactgaggggaagtggtcacactg -aggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtcatagtgt -gaggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactg -aggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggaagtggtcacact -gaggggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcacac -tgaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcaca ---ctgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatac -tgtgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcaca -ctgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacag -tgtgcggggaggtggtcatactgaggggaggtggtcacagtgtgaggggaggtggtcaca -ctgaggggaggtggtcacagtgtgcggggaggtggtcacactgaggggaggtggtcatag -tgtgaggggaggtggtcatactgaggggaggtggtcacactgtgaggggaggtggtcaca -ctgaggagaggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcatag -tgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcacac -tgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtgacact -gaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactg -tgaggggaggtggtcacattgaggagaggtggtcatagtgtgaggggaggtggtcacact -gaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactg -aggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactga -ggggaggtggtcacagtgtgaggggaggtggtcacagtgtgaggggaggtggtcacactg -aggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactga -gggaaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcatagtgtg -aggggaggtggtcacagtgtgaggggaggtggtcacactgaggagaggtggtcatagtgt -gaggggaggtggtcacactgaggggaggtggtcacactgtgaggggaggtgggcacactg -tgaggggtggtagtcacactgagaggaggtggtcacactgaggggaggtggtcacactga -ggggaagtggtcacactgaggggaatggtcatactgtgaggggaggtggtcacactgagg -ggaagtggtcacactgaggggaatggtcatactgtgaggggaggtggtcacactgtgaaa -gaagatgatcacagtatgagaggtcatc ->p:HG002_2_chr20:20354570-20358323 -taaagaagttgaattcataagggtaatgaggggaggaaggggtggtcatactgtgtgaag -ggagatggtcacactgagggaaggtggtcacactgtgagaagggaggtagtcacattgtg -agagaaaaagtgatcacactgtgtgaggggaggtggtcacactgtgagagaaaaagtaat -catactgtgaaagggaggtggtcacgctgagaggggaggtggtcacactgtgtcagggga -ggtggtcacactgtgagagaaaaagtaatcacactgtgaggggatgtggtcacactgaga -ggggaggtggtcagactgtgtcagaggaggtggtcacactgaggggaggtggtcacactg -tgagaggggaggtggtcagactctgtcagaggaggtggtcacactgtgagaggggaggtg -gtcacactgaggggaagtggtcacactgtgagaggggaggtggtcacactgaggggagat -ggtcacactgcaagaggggaggtgatcacactgagggg---------------------- --aggtggtcacactgtgagagggaaggtggtcacactgtgagagggaaggtggtcacact -gtgtgaggggaggtggtcacactgtgaggggaggtggtcacattgtgagagggaaggggg -tcactgtgagaggggagaaggtcacactaaggggaggtagtcacactgtgaggggaggtg -atcacactaaggggaggtggtcacactgtgagaggaggtggtcacactgtgaggggtggt -cacactgtgaggggaggtcacactgaggggaggtagtgacactatgagcagagatggtca -cactgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagcagagatggtc -acactgtgaggggaggtggtcacactgaggggaggtactcacactgtgaggggaggtggt -cacactgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagcagagatgg -tcacactgtgaggggagggggtcacactgtgagggggaaggtggtcacactgtgagaggg -gagaaggtcacactaaggggaggtagtcacactgtgaggggaggtgatcacactaagggg -aggtggtcacactgtgagaggaggtggtcacactgtgaggggaggtcacactgaggggag -gtagtgacactatgagcagagatggtcacactgtgaggggaggtggtcacactgagggga -ggtagtgacactgtgagcagagatggtcacactgtgaggggaggtggtcacactgagggg -aggtagtcacactgtgaggggaggtggtcacactgtgaggggaggtggtcacactgaggg -gaggtagtgacactgtgagcagagatggtcacactgtgaggggagggggtcacactgtga -gggggaaggtggtcacactgtgagaggggagaaggtcacactaaggggaggtagtcacac -tgtgaggggaggtgatcacactaaggggaggtggtcacactgtgagaggaggtggtcaca -ctgtgaggggaggtcacactgaggggaggtagtgacactatgagcagagatggtcacact -gtgaggggaggtggtcacactgaggggaggtagtgacactgtgagcagagatggtcacac -tgtgaggggaggtggtcacactgaggggaggtagtcacactgtgaggggaggtggtcaca -ctgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagcagagatggtcac -actgtaaggggaggtgatcacactgtgaggggacgtggtcacactgtgaggggaggtggt -cacactgtgagaggggaggtgaccacacaggggaggtggtcacactgaggggaggtagtg -acactgtgagcagaggtggtcacactgtgaggggaggtggtcacactgtgaggggaggtg -gtcacactgagaggaggtggtcacactgaggggaagtggtcacactgagggggggtggtc -acactgaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggaggggtc -atactgcgagtggaggtggtcacactgtgaagggtggtagtcacactgagaggaggtgtt -cacactgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtc -acactgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtca -cactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcac -agtgtgaggggagatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtca -cactgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacac -tgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacact -gaggggaggtggtcaca--ctgaggggaggtggtcatagtgtgaggggaggtggtcacac -tgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacact -gaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactg -gggaggtggtcacactgtgaggggaggtggtcacactgtgaggggaggtggtcacactga -gaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcacactgaggg -gaggtggtcacagtgtgaggggaggtggtcatactgtgagtgaggaggtagtcacac--t -gaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcacac -tgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatactg- ----------------------------------------tgaggggaagtggtcacactg -aggggaggtggtcatagtgtga--ggggaggtggtcacactgaggggaggtggtcacagt -gtgaggggaggtggtcacac--tgaggggaggtggtcacactgaggggaggtggtcacag -tgtgagaggaggtggtcacactgaggggaggtggtcacagtgtgaggggagatggtcaca -ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag -tgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagt -gtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggagatggtcacac -tgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcaca-- ------------------gtgtgaggggaggtggtcacactgaggggaggtggtcacactg -agaggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcacact -gaggggaagtggtcacactgaggggaggtg------------------------------ -------------gtcacactgaggggagggggtcatactgcgagtggaggtagtcacact -gtgaagggtggtagtcacactgagaggaggtggtcacactgaggggaagtggtcacactg -aggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtcatagtgt -gaggggag---------------------------------------------------- --------------------------------------------------gtggtcacact -gaggggaggtggtcacactgaggggaggtggtcacagtgtga--ggggaggtggtcacac -tgaggggaggtggtcacagtgtacggggaggtggtcatac--tgaggggaggtggtcaca -gtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacag -tgtgaggggaggtggtcacactgaggggaggtggtcacactgtgaggggaggtggtcaca -ctgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcaca- -c-tgaggagaggtggtcat-------------------agtgtgaggggaggtggtcaca -c----------------------------------------------------------- -------------------------------------------tgaggggaggtggtcaca -ctgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatag -tgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcacagtg-------------------------------------- -tgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacact -gaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactg -tgaggggaggtggtcacattgaggagaggtggtcatagtgtgaggggaggtggtcacact -gaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactg -aggagaggtggtcatagtgtgcggggaggtggtcacactgaggggaggtggtcacactga -ggggaggtggtcacagtgtgaggggaggtggtcacagtgtgaggggaggtggtcacactg -aggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactga -gggaaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcatagtgtg -aggggaggtggtcacagtgtgaggggaggtggtcacactgaggagaggtggtcatagtgt -gaggggaggtggtcacactgaggggaggtggtcacactgtgaggggaggtgggcacactg -tgaggggtggtagtcacactgagaggaggtggtcacactgaggggaggtggtcacactga -ggggaggtggtcacactgaggggaatggtcatactgtgaggggaggtggtcacactgagg -ggaagtggtcacactgaggggaatggtcatactgtgaggggaggtggtcacactgtgaaa -gaagatgatcacagtatgagaggtcatc ->ref_chr20:20354570-20358323 -taaagaagttgaattcataagggtaatgaggggaggaaggggtggtcatactgtgtgaag -ggagatagtcacactgagggaaggtggtcacactgtgagaagggaggtagtcacattgtg -agagaaaaagtgatcacactgtgtgaggggaggtggtcacactgtgagagaaaaagtaat -catactgtgaaagggaggtggtcacgctgagaggggaggtggtcacactgtgtcagggga -ggtggtcacactgtgagagaaaaagtaatcacactgtgaggggatgtggtcacactgaga -ggggaggtggtcagactgtgtcagaggaggtggtcacactgagg---------------- -------------------------------ggaggtggtcacactgtgagaggggaggtg -gtcacactgaggggaagtggtcacactgtgagaggggaggtggtcacactgaggggagat -ggtcacactgcaagaggggaggtgatcacactgagggg---------------------- --aggtggtcacactgtgagagggaaggtggtcacactgtgagagggaaggtggtcacact -gtgtgaggggaggtggtcacactgtgaggggaggtggtcacattgtgagagggaaggggg -tcactgtgagaggggagaaggtcacactaaggggaggtagtcacactgtgaggggaggtg -atcacactaaggggaggtggtcacactgtgagaggaggtggtcacactgtgaggggtggt -cacactgtgaggggaggtcacactgaggggaggtagtgacactatgagcagagatggtca -cactgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagcagagatggtc -acactgtgaggggaggtggtcacactgaggggagg------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------tggtcacactgtgaggggaggtggtcacactgagggg -aggtggtcacactgtgaggggaggtggtcacactgtgaggggaggtggtcacactgaggg -gaggtagtgacactgtgagcagagatggtcacactgtgaggggagggggtcacactgtga -gggggaaggtggtcacactgtgagaggggagaaggtcacactaaggggaggtagtcacac -tgtgaggggaggtgatcacactaaggggaggtggtcacactgtgagaggaggtggtcaca -ctgtgaggggaggtcacactgaggggaggtagtgacactatgagcagagatggtcacact -gtgaggggaggtggtcacactgaggggaggtagtgacactgtgagcagagatggtcacac -tgtgaggggaggtggtcacactgaggggaggtagtcacactgtgaggggaggtggtcaca -ctgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagcagagatggtcac -actgtaaggggaggtgatcacactgtgaggggac---gtcacactgtgaggggaggtggt -cacactgtgagaggggaggtgaccacacaggggaggtggtcacactgaggggaggtagtg -acactgtgagcagagatggtcacactgtgaggggaggtggtcacac--tgaggggaggta -gtcacactgagaggaggtggtcacactgaggggaagtggtcacactgagggggggtggtc -acactgaggggaggtggtcatactgtgagtgaggagctagtcacactgaggggaggggtc -atactgcgagtggaggtagtcacactgtgaagggtggtagtcacactgagaggaggtggt -cacactgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtc -acactgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtca -cactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcac -agtgtgaggggagatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtca -cactgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacac -tgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacact -gaggggaggtggtcatagtgtgaggggaggtggtcacact----ggggaggtggtcacac -tgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacact -gaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacact- ---------------------ggggaggtggtcacactgtgaggggaggtggtcacactga -gaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcacactgaggg -gaggtggtcatagtgtgaggggaggtggtcacac------tggggaggtggtcacactgt -gaggggaggtggtcacactgtgaggggaggtggtcacac--tgagaggaggtggtcacac -tgaggggaagtggtcacactgagaggaggtggtcacactgaggggaggtggtcatactgt -gagtgaggaggtagtcacactgaggggaagtggtcacactgaggggaggtggtcacactg -aggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggagggggtcatact -gcgagtggaggtagtcacactgtgaagggtggtagtcacactgagaggaggtggtcaca- --ctgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcaca -ctgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacag -tgtgaggggaggtggtcacactgaggggaggtggtcaca--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------gtgtgcggggaggtggtcatactgaggggaggtggtcacactg -aggggaggtggtcacactgaggggaggtggtcatactgtgagt----------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------gaggaggtagtcacac -tgaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcaca ---ctgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatac -tgtgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcaca -ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag -tgtgcggggaggtggtcat----------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------actga -ggggaggtggtcacagtgtgaggggaggtggtcacagtgtgaggggaggtggtcacactg -aggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactga -gggaaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcatagtgtg -aggggaggtggtcacagtgtgaggggaggtggtcacactgaggagaggtggtcatagtgt -gaggggaggtggtcacactgaggggaggtggtcacactgtgaggggaggtgggcacactg -tgaggggtggtagtcacactgagaggaggtggtcacactgaggggaggtggtcacactga -ggggaagtggtcacactgaggggaatggtcatactgtgaggggaggtggtcacactgagg -ggaagtggtcacactgaggggaatggtcatactgtgaggggaggtggtcacactgtgaaa -gaagatgatcacagtatgagaggtcatc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_1191bb91085ac462fc6dbdd9ec0c272d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_1191bb91085ac462fc6dbdd9ec0c272d.msa deleted file mode 100644 index 2c436027..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_1191bb91085ac462fc6dbdd9ec0c272d.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:23560729-23561308 -gaccactgccttaacaaatcattgtggctactattatttcaaagagttttgtcctaaaat -cttcatacagaagatataagagatttgcaaattaccgttatagtattagagtattctgaa -tgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttcagcattc -ctttctctttctttctttctttctttctttctttccttccttccttccttccttccttcc -ttccttccttccttccttccttc------------------------------------- ------------------------------------------------------------- -----------------------ctttctttctttctttctttctttctttctttctttct -ttctttctttcttctttctttctttttcttttacagagtcttactcttgttgcccaggct -gtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgcattcaag -aaattctcctgcctcagcctccagagtagctgggattacaggcacctgccaa ->syndip_2_chr20:23560729-23561308 -gaccactgccttaacaaatcattgtggctactattatttcaaagagttttgtcctaaaat -cttcatacagaagatataagagatttgcaaattaccgttatagtattagagtattctgaa -tgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttcagcattc -ctttctctttctttctttctttctttctttctttctttctttctttctttccttctttcc -ttccttccttccttccttccttccttccttccttccttccttccttccttccttctttcc -ttctttccttctttccttctttccttctttccttctttccttctttccttctttctttct -ttctttccttctttccttctttctttctttctttctttctttctttctttctttctttct -ttctttctttcttctttctttctttttcttttacagagtcttactcttgttgcccaggct -gtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgcattcaag -aaattctcctgcctcagcctccagagtagctgggattacaggcacctgccaa ->p:HG002_1_chr20:23560729-23561308 -gaccactgccttaacaaatcattgtggctactattatttcaaagagttttgtcctaaaat -cttcatacagaagatataagagatttgcaaattaccgttatagtattagagtattctgaa -tgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttcagcattc -ctttctctttctttctttctttctttctttctttctttctttctttctttccttctttcc -ttccttccttccttccttccttccttccttccttccttccttccttctttccttctttcc -ttctttccttctttccttctttccttctttccttctttccttctttccttctttctttct -ttctttctttctttccttctttctttctttctttctttctttctttctttctttctttct -ttctttctttcttctttctttctttttcttttacagagtcttactcttgttgcccaggct -gtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgcattcaag -aaattctcctgcctcagcctccagagtagctgggattacaggcacctgccaa ->p:HG002_2_chr20:23560729-23561308 -gaccactgccttaacaaatcattgtggctactattatttcaaagagttttgtcctaaaat -cttcatacagaagatataagagatttgcaaattaccgttatagtattagagtattctgaa -tgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttcagcattc -ctttctctttctttctttctttctttctttctttctttctttctttctttccttctttcc -ttccttccttccttccttccttc------------------------------------- ------------------------------------------------------------- -----------------------ctttctttctttctttctttctttctttctttctttct -ttctttctttcttctttctttctttttcttttacagagtcttactcttgttgcccaggct -gtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgcattcaag -aaattctcctgcctcagcctccagagtagctgggattacaggcacctgccaa ->ref_chr20:23560729-23561308 -gaccactgccttaacaaatcattgtggctactattatttcaaagagttttgtcctaaaat -cttcatacagaagatataagagatttgcaaattaccgttatagtattagagtattctgaa -tgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttcagcattc -ctttctctttctttctttctttctttctttctttctttctttctttctttccttctttcc -ttccttccttccttccttccttccttccttccttccttccttccttccttccttctttcc -ttctttccttctttccttctttccttctttccttctttccttctttcc------------ -ttctttccttctttccttctttctttctttctttctttctttctttctttctttctttct -ttctttctttcttctttctttctttttcttttacagagtcttactcttgttgcccaggct -gtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgcattcaag -aaattctcctgcctcagcctccagagtagctgggattacaggcacctgccaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_119e5b6348bc355476c33c9f3cc7ec8c.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_119e5b6348bc355476c33c9f3cc7ec8c.msa deleted file mode 100644 index fd16f1d4..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_119e5b6348bc355476c33c9f3cc7ec8c.msa +++ /dev/null @@ -1,160 +0,0 @@ ->syndip_1_chr20:62349412-62350132 -cagcaactgcaaggacaatggactctcccaagcacctggagaggtgaagagacagtcaaa -tcatttctccaaagtgctgagagatgcagctatcaaccacgaatcctacagtcagctcaa -ctatcattcaagagggaggacaaaacagccgttttcagacaattccggatagactgtcat -ggaatagaaaaactacagggtgcatttcaggaaggaggaagcagcaacccaggggatggg -gatggggatggggatggggatggtgggggtgatgggggtgatgatggtgatggtgggggt -gatgatggtgatggtgatggtgatggtgggggtggtgatggtgggggtgggggtggtgat -ggtgggggtgggggtgatgatggtgatggtgggggtgatgacggtggggctgggggtgat -gatggtgggggtgatgacggtgatgatgggggtggaggggtgatgacggtgatgatgggg -gtgggggggtgatgacggtgatgtgggggtgatgacggtgggggtgggggtgatgacggt -gat---------------------ggtgggggtgatgacggtgggggtgggggtgatgac -ggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgat -gatggtgatggtgggggtgatgatggtgggggtgggggtgatgatggtgagggtgatgat -ggtgggggtaatgacggtggggtgggggtgatgacggtgggggtgggggtgatgacggtg -atggtgggggtgatgacgatgatggtgggggtgatgacggtgatggcggtgggggtgatg -acggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtg -atgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggg -gtgatgacggtgggggtgggggtgatgacggtgatggtagaggtgatgatggtgggggtg -atggtgggggtgggggtggg---------ggtgggggtgatgatggtgatggtgggggtg -atgatggtgagggtgatgatggtgggggtgatggtgggggtggg---------------- -----------------------------------------ggtgggggtgggggtgatga -cggtgat----------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----ggtgggggtgatgatggtgggagtgggctggtagtgggggtgatggtttgggtggg -agtaaggtgatggtggaggtaaagaggcagaaaattgctggctgatgacatggagccccc -ttccctggaggagaggtggggtggcgggtaaagggtgcagggagaacatgggcaggctaa -tgttttgggacactggtgggtgaccaggtcctggtaacagaggctgtggttccatgaaag -attcccagtcacccctgcttgcacctgcagggagagctgagctcagtccacacccaggtg -cggtgagtca ->syndip_2_chr20:62349412-62350132 -cagcaactgcaaggacaatggactctcccaagcacctggagaggtgaagagacagtcaaa -tcatttctccaaagtgctgagagatgcagctatcaaccacgaatcctacagtcagctcaa -ctatcattcaagagggaggacaaaacagccgttttcagacaattccggatagactgtcat -ggaatagaaaaactacagggtgcatttcaggaaggaggaagcagcaacccaggggatggg -gatggggatggggatggggatggtgggggtgatgggggtgatgatggtgatggtgggggt -gatgatggtgatggtga---------------tggtgatggtgatggtgggggtggtgat -ggtgggggtgggggtgatgatggtgatggtgggggtgatgacggtggggctgggggtgat -gatggtgggggtgatgacggtgatgatgggggtggaggggtgatgacggtgatgatgggg -gtgggggggtgatgacggtgatgtgggggtgatgacggtgggggtgggggtgatgacggt -gatggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgac -ggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgat -gatggtgatggtgggggtgatgatggtgggggtgggggtgatgatggtgagggtgatgat -ggtgggggtaatgacggtggggtgggggtgatgacggtgggggtgggggtgatgacggtg -atggtgggggtgatgacgatgatggtgggggtgatgacggtgatggcggtgggggtgatg -acggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtg -atgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggg -gtgatgacggtgggggtgggggtgatgacggtgatggtagaggtgatgatggtgggggtg -ggggtgggggtgggggtgagggtgatgatggtgggggtgatgatggtgatggtgggggtg -atgatggtgagggtgatgatggtgggggtgatggtgggggtgggggtgggggtaatgacg -gtggggtgggggtaatgacggtgggggtgggggtgatgacggtgggggtgggggtgatga -cggtgatggtgggggtgatgacgatgatggtgggggtgatgacggtgatggcggtggggg -tgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgg -gggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatgg -tagaggtgatgatggtgggggtgatggtgggggtgggggtgggggtgggggtgatgatgg -tgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtgggggtggggg -tgggggtgggggtgatgatggtgggagtgggctggtagtgggggtgatggtttgggtggg -agtaaggtgatggtggaggtaaagaggcagaaaattgctggctgatgacatggagccccc -ttccctggaggagaggtggggtggcgggtaaagggtgcagggagaacatgggcaggctaa -tgttttgggacactggtgggtgaccaggtcctggtaacagaggctgtggttccatgaaag -attcccagtcacccctgcttgcacctgcagggagagctgagctcagtccacacccaggtg -cggtgagtca ->p:HG002_1_chr20:62349412-62350132 -cagcaactgcaaggacaatggactctcccaagcacctggagaggtgaagagacagtcaaa -tcatttctccaaagtgctgagagatgcagctatcaaccacgaatcctacagtcagctcaa -ctatcattcaagagggaggacaaaacagccgttttcagacaattccggatagactgtcat -ggaatagaaaaactacagggtgcatttcaggaaggaggaagcagcaacccaggggatggg -gatggggatggggatggggatggtgggggtgatgggggtgatgatggtgatggtgggggt -gatgatggtgatggtga---------------tggtgatggtgatggtgggggtggtgat -ggtgggggtgggggtgatgatggtgatggtgggggtgatgacggtggggctgggggtgat -gatggtgggggtgatgacggtgatgatgggggtggaggggtgatgacggtgatgatgggg -gtgggggggtgatgacggtgatgtgggggtgatgacggtgggggtgggggtgatgacggt -gatggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgac -ggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgat -gatggtgatggtgggggtgatgatggtgggggtgggggtgatgatggtgagggtgatgat -ggtgggggtaatgacggtggggtgggggtgatgacggtgggggtgggggtgatgacggtg -atggtgggggtgatgacgatgatggtgggggtgatgacggtgatggcggtgggggtgatg -acggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtg -atgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggg -gtgatgacggtgggggtgggggtgatgacggtgatggtagaggtgatgatggtgggggtg -ggggtgggggtgggggtgagggtgatgatggtgggggtgatgatggtgatggtgggggtg -atgatggtgagggtgatgatggtgggggtgatggtgggggtgggggtgggggtaatgacg -gtggggtgggggtaatgacggtgggggtgggggtgatgacggtgggggtgggggtgatga -cggtgatggtgggggtgatgacgatgatggtgggggtgatgacggtgatggcggtggggg -tgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgg -gggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatgg -tagaggtgatgatggtgggggtgatggtgggggtgggggtgggggtgggggtgatgatgg -tgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtgggggtggggg -tgggggtgggggtgatgatggtgggagtgggctggtagtgggggtgatggtttgggtggg -agtaaggtgatggtggaggtaaagaggcagaaaattgctggctgatgacatggagccccc -ttccctggaggagaggtggggtggcgggtaaagggtgcagggagaacatgggcaggctaa -tgttttgggacactggtgggtgaccaggtcctggtaacagaggctgtggttccatgaaag -attcccagtcacccctgcttgcacctgcagggagagctgagctcagtccacacccaggtg -cggtgagtca ->p:HG002_2_chr20:62349412-62350132 -cagcaactgcaaggacaatggactctcccaagcacctggagaggtgaagagacagtcaaa -tcatttctccaaagtgctgagagatgcagctatcaaccacgaatcctacagtcagctcaa -ctatcattcaagagggaggacaaaacagccgttttcagacaattccggatagactgtcat -ggaatagaaaaactacagggtgcatttcaggaaggaggaagcagcaacccaggggatggg -gatggggatggggatggggatggtgggggtgatgggggtgatgatggtgatggtgggggt -gatgatggtgatggtgatggtgatggtgggggtggtgatggtgggggtgggggtggtgat -ggtgggggtgggggtgatgatggtgatggtgggggtgatgacggtggggctgggggtgat -gatggtgggggtgatgacggtgatgatgggggtggaggggtgatgacggtgatgatgggg -gtgggggggtgatgacggtgatgtgggggtgatgacggtgggggtgggggtgatgacggt -gat---------------------ggtgggggtgatgacggtgggggtgggggtgatgac -ggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgat -gatggtgatggtgggggtgatgatggtgggggtgggggtgatgatggtgagggtgatgat -ggtgggggtaatgacggtggggtgggggtgatgacggtgggggtgggggtgatgacggtg -atggtgggggtgatgacgatgatggtgggggtgatgacggtgatggcggtgggggtgatg -acggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtg -atgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggg -gtgatgacggtgggggtgggggtgatgacggtgatggtagaggtgatgatggtgggggtg -atggtgggggtgggggtggg---------ggtgggggtgatgatggtgatggtgggggtg -atgatggtgagggtgatgatggtgggggtgatggtgggggtggg---------------- -----------------------------------------ggtgggggtgggggtgatga -cggtgat----------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----ggtgggggtgatgatggtgggagtgggctggtagtgggggtgatggtttgggtggg -agtaaggtgatggtggaggtaaagaggcagaaaattgctggctgatgacatggagccccc -ttccctggaggagaggtggggtggcgggtaaagggtgcagggagaacatgggcaggctaa -tgttttgggacactggtgggtgaccaggtcctggtaacagaggctgtggttccatgaaag -attcccagtcacccctgcttgcacctgcagggagagctgagctcagtccacacccaggtg -cggtgagtca ->ref_chr20:62349412-62350132 -cagcaactgcaaggacaatggactctcccaagcacctggagaggtgaagagacagtcaaa -tcatttctccaaagtgctgagagatgcagctatcaaccacgaatcctacagtcagctcaa -ctatcattcaagagggaggacaaaacagccgttttcagacaattccggatagactgtcat -ggaatagaaaaactacagggtgcatttcaggaaggaggaagcagcaaccca------ggg -gatggggatggggatggggatggtgggggtgatgggggtgatgatggtgatggt---gat -ggtgatggtgatggtgatggtgatggtgggggtggtgat--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------gggtgggggtgatgacggtgggagtgggggtgatgacggtg -atggtgggggtgatgacggtgat------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------ggtgggggtgatga -cggtgat----------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----ggtgggggtgatgatggtgggagtgggctggtagtgggggtgatggtttgggtggg -agtaaggtgatggtggaggtaaagaggcagaaaattgctggctgatgacatggagccccc -ttccctggaggagaggtggggtggcgggtaaagggtgcagggagaacatgggcaggctaa -tgttttgggacactggtgggtgaccaggtcctggtaacagaggctgtggttccatgaaag -attcccagtcacccctgcttgcacctgcagggagagctgagctcagtccacacccaggtg -cggtgagtca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_128fb036b042795e9a505408662c68b2.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_128fb036b042795e9a505408662c68b2.msa deleted file mode 100644 index aeb4fa87..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_128fb036b042795e9a505408662c68b2.msa +++ /dev/null @@ -1,80 +0,0 @@ ->syndip_1_chr20:2240925-2241726 -cacttggaaaatgtagtcatcttctcaaagttttctttttctttctttctttttcctttc -tttctttctttttctttctttctctctctctccttccttccttctttccttccctccctc -ccttccttttttcttctttctttcattttctttctttctctctttcttctttctcttcct -ttcttc------------------------------------------------------ -------tttcttttcctccttcctcccttctttccttcccttccttcttccctccctccc -tctttgtttctttctttctctccctc---------------------------------- --cttccctccctccctttctttctcctt-----------ttcttccttccctccctgcct -gtctccctctttctttctcttttttcttttccttccttccgtctttttcctcccttcttt -cctccctcctccctccctccctcctccctctttttctttctttctttcttttttctttct -ctcttc-ttttttttttttttttttaagagatagggtctgttgcccaggctggagtgcag -tggcatgatcatggttcactgcagccttgaactcctgggctcaggtgatcctcctacctc -agcctcctaagtagctgggactataggtgcatgccatcacacccagctaattttttaaaa -gaaattttgtaaagacaggggtcttgctatgttccccaggctggtctcaaactcctgggc -tcaagtgatcctccagcctcagtatcccaaagtgctgggattataggtgtgagtcactgc -agccagctcaaata ->syndip_2_chr20:2240925-2241726 -cacttggaaaatgtagtcatcttctcaaagttttctt-------------------tttc -tttctttctttttctttctttctctctctctccttccttccttctttccttccctccctc -ccttccttttttcttcttcctttcattttctttctttctctctttcttctttctcttcct -ttcttctttcttttcctccttcctcccttctttccttcccttccttcttccctccctccc -tctttgtttctttctttctctccctccttccctccctccctttcttccttctttccttat -ccctcccttctttccttccttccctttgtttctctttctttctttctttctctctctctt -ccttccttccctccctccctccctccttcctcccttctttccttccctccctgcctctct -gtctccctctttctttctcttttttcttttccttccttccgtctttttcctcccttcttt -cctccctcctccctccctccctcctccctctttttctttctttctttcttttttctctct -ctcttctttttttttttttttttttaagagatagggtctgttgcccaggctggagtgcag -tggcatgatcatggttcactgcagccttgaactcctgggctcaggtgatcctcctacctc -agcctcctaagtagctgggactataggtgcatgccatcacacccagctaattttttaaaa -gaaattttgtaaagacaggggtcttgctatgttccccaggctggtctcaaactcctgggc -tcaagtgatcctccagcctcagtatcccaaagtgctgggattataggtgtgagtcactgc -agccagctcaaata ->p:HG002_1_chr20:2240925-2241726 -cacttggaaaatgtagtcatcttctcaaagttttctt-------------------tttc -tttctttctttttctttctttctctctctctccttccttccttctttccttccctccctc -ccttccttttttcttcttcctttcattttctttctttctctctttcttctttctcttcct -ttcttctttcttttcctccttcctcccttctttccttcccttccttcttccctccctccc -tctttgtttctttctttctctccctccttccctccctccctttcttccttctttccttat -ccctcccttctttccttccttccctttgtttctctttctttctttctttctctctctctt -ccttccttccctccctccctccctccttcctcccttctttccttccctccctgcctctct -gtctccctctttctttctcttttttcttttccttccttccgtctttttcctcccttcttt -cctccctcctccctccctccctcctccctctttttctttctttctttcttttttctctct -ctcttctttttttttttttttttttaagagatagggtctgttgcccaggctggagtgcag -tggcatgatcatggttcactgcagccttgaactcctgggctcaggtgatcctcctacctc -agcctcctaagtagctgggactataggtgcatgccatcacacccagctaattttttaaaa -gaaattttgtaaagacaggggtcttgctatgttccccaggctagtctcaaactcctgggc -tcaagtgatcctccagcctcagtatcccaaagtgctgggattataggtgtgagtcactgc -agccagctcaaata ->p:HG002_2_chr20:2240925-2241726 -cacttggaaaatgtagtcatcttctcaaagttttctttttctttctttctttttcctttc -tttctttctttttctttctttctctctctctccttccttccttctttccttccctccctc -ccttccttttttcttctttctttcattttctttctttctctctttcttctttctcttcct -ttcttc------------------------------------------------------ -------tttcttttcctccttcctcccttctttccttcccttccttcttccctccctccc -tctttgtttctttctttctctccctc---------------------------------- --cttccctccctccctttctttctcctt-----------ttcttccttccctccctgcct -gtctccctctttctttctcttttttcttttccttccttccgtctttttcctcccttcttt -cctccctcctccctccctccctcctccctctttttctttctttctttcttttttctttct -ctcttc-ttttttttttttttttttaagagatagggtctgttgcccaggctggagtgcag -tggcatgatcatggttcactgcagccttgaactcctgggctcaggtgatcctcctacctc -agcctcctaagtagctgggactataggtgcatgccatcacacccagctaattttttaaaa -gaaattttgtaaagacaggggtcttgctatgttccccaggctggtctcaaactcctgggc -tcaagtgatcctccagcctcagtatcccaaagtgctgggattataggtgtgagtcactgc -agccagctcaaata ->ref_chr20:2240925-2241726 -cacttggaaaatgtagtcatcttctcaaagttttctttttctttctttctttttcctttc -tttctttctttttctttctttctctctctctccttccttccttctttccttccctccctc -ccttccttttttcttctttctttcattttctttctttctctctttcttctttctcttcct -ttcttt---------------ccttccgtccctcccttccttccttttttcttcttcctt -tcat--tttctttctttctctctttcttctttctcttcctttcttctttcttttcctcct -tcctcccttctttccttcccttcctt---------------------------------- --cttccctccctccctctttgtttctttctttctctccctccttccctccctccctttct -gtctccctctttctttctcttttttcttttccttccttccgtctttttcctcccttcttt -cctccctcctccctccctccctcctccctctttttctttctttctttcttttttctttct -ctcttctttttttttttttttttttaagagatagggtctgttgcccaggctggagtgcag -tggcatgatcatggttcactgcagccttgaactcctgggctcaggtgatcctcctacctc -agcctcctaagtagctgggactataggtgcatgccatcacacccagctaattttttaaaa -gaaattttgtaaagacaggggtcttgctatgttccccaggctggtctcaaactcctgggc -tcaagtgatcctccagcctcagtatcccaaagtgctgggattataggtgtgagtcactgc -agccagctcaaata diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_12dd4c35160846476740112f03a5afbd.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_12dd4c35160846476740112f03a5afbd.msa deleted file mode 100644 index 60affcb0..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_12dd4c35160846476740112f03a5afbd.msa +++ /dev/null @@ -1,215 +0,0 @@ ->syndip_1_chr20:56280331-56282123 -agtgtatctacagatgggacaatctaagatggttacaacattactacatagtatcgcaaa -tagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatcaaaaaggtaa -catccatatacagatataatatctataacatatatagatatatggatataacatccatat -atagatatatctatatatctatctatagctac---------------------------- -------------------------------------atctacagatatctatagctacat -ctacagatatctatagctacatctacagatatctacagatatctacagctacatctacag -atatctatagatatctatagctatatctacagatatctatcgatagatatatctatcgat -agatatatccacatagatatctagatatatatggatatatctatagatatctatctggat -atatctatcgatagatatatagatatatatagataaagctatatagatatatatagataa -acctatatagatacatagatatatagagagaaacctatatacatatatagatatatagag -agaaacctatatagatatatagatatatagagagaaacctatatagatgtatagataaac -ctatatagatatatagataaacctatgtagatatatagatatatatagataaatctatat -agatatataaaatagataaatctatatagatatatatacataaatctatatagatatata -tacataaatctatatatatacataaatctatatatacataaatctatatagatatatata -cataaatctatatagatatatatacataaatctatatagatatatatacataaatctata -tagatatatatacataaatctatatagatatatacataaatctatatagatatatataca -taaatctatatagatatatatacataaatctatatagatatatatacataaatctatata -gatacatatagataaatctatacagatatatagatacatatagataaatctatacagata -tatagatacatatagataaatctatacagatatatagatacatatagataaatctataca -gatatatagatacatatagataaatctatacagatatatagatacatatagataaatcta -tacagatatatagatacatatagataaatctatacagatatatagatacatatagataca -tctatacagatatatagatacatatagatacatctatacagatatatagatacatataga -tacatctatacagatatattgatacatatagatacatctatatagatatatagat--ata -tagatacatctatatagatatatagatatatagatacatctatatagatatattgataca -t--atagatacatctatatagattagatatatatagatacatctatatagattagatata -tatagatacatctatatagattagatatatatagatacatctatatatagatatatagat -atatatagatacatctatatatagacatatagatatatatagatacatctatatatagat -atatagatgtatatagatacatctatatatagatatatagatgtatatagatacatctat -atatagatatatagatgtatatagatacatctatatatagatatatagatgtatatagat -acatctatatatagatatatagatgtatatagatacatctatat--atagatatatagat -gtatatagatacatctatatatagatatatagatgtatatagatacatctatatatagat -atatagatgtatatagatacatctatatatagatatatagatgtatatagatacatctat -atatagatatatagatgtatatagatacatagatatatatagatacatttatgtatatat -atatgtatatatagatatatagatatatatagatacatctacacagagagatatatagaa -acatctacacagggagatatatagatacatctacatagagagatatatagatacatctac -atagagagatatatagatacatctacatagagagatatatagatacatctacatagagag -atatatagatacatctacacagagagatatatagaaacatctacacagggagatatatag -atacatctacacagagagatatatagatacatctacatagagagatatatagatacatct -acatagagagatatatagatacatctacatagagagatatatagatacatctacatagag -agatatatagatacatctacatagagatatatatagatacatctacatagagatatatat -agatacatctatatagagatatatctacctatacttcctgtgagttgtgtttctctggag -aactaa ->syndip_2_chr20:56280331-56282123 -agtgtatctacagatgggacaatctaagatggttacaacattactacatagtatcgcaaa -tagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatcaaaaaggtaa -catccatatacagatataatatctataacatatatagatatatggatataacatccatat -atagatatatctatatatctatctatagctacatctacagatatctatagctacatctac -agatatctacagatatctatagctacatctacagatatctacagatatctatagctacat -ctacagatatctatagctacatctacagatatctacagatatctacagctacatctacag -atatctatagatatctatagctatatctacagatatctatcgatagatatatctatcgat -agatatatccacatagatatctagatatatatggatatatctatagatatctatctggat -atatctatcgatagatatatagatatatatagataaagctatatagatatatatagataa -acctatatagatacatagatatatagagagaaacctatatacatatatagatatatagag -agaaacctatatagatatatagatatatagagagaaacctatatagatgtatagataaac -ctatatagatatatagataaacctatgtagatatatagatatatatagataaatctatat -agatatataaaatag------------------------ataaatctatatagatatata -tacataaatctatatagatatatatacataaatctatatatatacataaatctatatata -cataaatctatatagatatatatacataaatctatatagatatatatacataaatctata -tagatatatatacataaatctatatagatatatatacataaatctatatagatatataca -taaatctatatagatatatatacataaatctatatagatatatatacataaatctatata -ga------------------------tatatagatacatatagataaatctatacagata -tatagatacatatagataaatctatacagatatatagatacatatagataaatctataca -gatatatagatacatatagataaatctatacagatatatagatacatatagataaatcta -tacagatatatagatacatatagataaatctatacagatatatagatacatatagataaa -tctatacagatatatagatacatatagatacatctatacagatatatagatacatataga -tacatctatacagatatatagatacatatagatacatctatacagatatattgatacata -tagatacatctatatagatatatagatatatagatacatctata---------------- ------------------------------------------------------------- ----------------------tagatatatatagatacatctatatatagacatatagat -atatatagatacatctatatatagacatatagatatatatagatacatctatatatagat -atatagatatatatagatacatctacacagag------agatatatagaaacatctacac -agggagatatatagatacatctacacagagagatatatagatacatctacatagagagat -atatagatacatctatatagagagatatatagatacatctacatagagagatatatagat -acatctacatagagagatatatagatacatctacatagagagatatatagatacatctac -atagagatatatatagatacatctacatagagata--------tatatagatacatctat -atagagatatat------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------ctacctatacttcctgtgagttgtgtttctctggag -aactaa ->p:HG002_1_chr20:56280331-56282123 -agtgtatctacagatgggacaatctaagatggttacaacattactacatagtatcgcaaa -tagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatcaaaaaggtaa -catccatatacagatataatatctataacatatatagatatatggatataacatccatat -atagatatatctatatatctatctatagctacatctacagatatctatagctacatctac -agatatctacagatatctatagctacatctacagatatctacagatatctatagctacat -ctacagatatctatagctacatctacagatatctacagatatctacagctacatctacag -atatctatagatatctatagctatatctacagatatctatcgatagatatatctatcgat -agatatatccacatagatatctagatatatatggatatatctatagatatctatctggat -atatctatcgatagatatatagatatatatagataaagctatatagatatatatagataa -acctatatagatacatagatatatagagagaaacctatatacatatatagatatatagag -agaaacctatatagatatatagatatatagagagaaacctatatagatgtatagataaac -ctatatagatatatagataaacctatgtagatatatagatatatatagataaatctatat -agatatataaaatagataaatctatatagatatatatacataaatctatatagatatata -tacataaatctatatagatatatatacataaatctatatatatacataaatctatatata -cataaatctatatagatatatatacataaatctatatagatatatatacataaatctata -tagatatatatacataaatctatatagatatatatacataaatctatatagatatataca -taaatctatatagatatatatacataaatctatatagatatatata--------tatata -gatatatatacataaatc--------tatatagatacatatagataaatctatacagata -tatagatacatatagataaatctatacagatatatagatacatatagataaatctataca -gatatatagatacatatagataaatctatacagatatatagatacatatagataaatcta -tacagatatatagatacatatagataaatctatacagatatatagatacatatagataaa -tctatacagatatatagatacatatagatacatctatacagatatatagatacatataga -tacatctatacagatatatagatacatatagatacatctatacagatatattgatacata -tagatacatctatatagatatatagatatatagatacatctata---------------- ------------------------------------------------------------- ----------------------tagatatatagatata----tagatacatctatatagat -atatatagatacatctatatatagacatatagatatatatagatacatctatatatagat -atatagatatatatagatacatctacacagag------agatatatagaaacatctacac -agggagatatatagatacatctacacagagagatatatagatacatctac---------- -----------------atagagagatatatagatacatctacatagagagatatatagat -acatctacatagagagatatatagatacatctacatagagagatatatagatacatctac -atagagatatatatagatacatctacatagagata--------tatatagatacatctat -atagagatatat------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------ctacctatacttcctgtgagttgtgtttctctggag -aactaa ->p:HG002_2_chr20:56280331-56282123 -agtgtatctacagatgggacaatctaagatggttacaacattactacatagtatcgcaaa -tagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatcaaaaaggtaa -catccatatacagatataatatctataacatatatagatatatggatataacatccatat -atagatatatctatatatctatctatagctac---------------------------- -------------------------------------atctacagatatctatagctacat -ctacagatatctatagctacatctacagatatctacagatatctacagctacatctacag -atatctatagatatctatagctatatctacagatatctatcgatagatatatctatcgat -agatatatccacatagatatctagatatatatggatatatctatagatatctatctggat -atatctatcgatagatatatagatatatatagataaagctatatagatatatatagataa -acctatatagatacatagatatatagagagaaacctatatacatatatagatatatagag -agaaacctatatagatatatagatatatagagagaaacctatatagatgtatagataaac -ctatatagatatatagataaacctatgtagatatatagatatatatagataaatctatat -agatatataaaatagataaatctatatagatatatatacataaatctatatagatatata -tacataaatctatatagatatatatacataaatctatatatatacataaatctatatata -cataaatctatatagatatatatacataaatctatatagatatatatacataaatctata -tagatatatatacataaatctatatagatatatatacataaatctatatagatatataca -taaatctatatagatatatatacataaatctatatagatatatatacataaatctatata -gatatatatacataaatctatacagatatatagatacatatagataaatctatacagata -tatagatacatatagataaatctatacagatatatagatacatatagataaatctataca -gatatatagatacatatagataaatctatacagatatatagatacatatagataaatcta -tacagatatatagatacatatagataaatctatacagatatatagatacatatagataaa -tctatacagatatatagatacatatagatacatctatacagatatatagatacatataga -tacatctatacagatatatagatacatatagatacatctatacagatatattgatacata -tagatacatctatatagatatatagatatatagatacatctatatagatatatagatata -tagatacatacatctatatagattagatatatatagatacatctatatagattagatata -tatagatacatctatatagattagatatatatagatacatctatatatagatatatagat -atatatagatacatctatatatagatatatagatatatatagatacatctatatatagat -atatagatgtatatagatacatctatatatagatatatagatgtatatagatacatctat -atatagatatatagatgtatatagatacatctatatatagatatatagatgtatatagat -acatctatatatagatatatagatgtatatagatacatctatat--atagatatatagat -gtatatagatacatctatatatagatatatagatgtatatagatacatctatatatagat -atatagatgtatatagatacatctatatatagatatatagatgtatatagatacatctat -atatagatatatagatgtatatagatacatagatatatatagatacatttatgtatatat -atatgtatatatagatatatagatatatatagatacatctacacagagagatatatagaa -acatctacacagggagatatatagatacatctacatagagagctatatagatatatatag -atacatctatatatagacatatagatatatatagatacatctatatatagatatatagat -atatatagatacatctacacagagagatatatagaaacatctacacagggagatatatag -atacatctacacagagagatatatagatacatctacatagagagatatatagatacatct -acatagagagatatatagatacatctacatagagagatatatagatacatctacatagag -agatatatagatacatctacatagagatatatatagatacatctacatagagatatatat -agatacatctatatagagatatatctacctatacttcctgtgagttgtgtttctctggag -aactaa ->ref_chr20:56280331-56282123 -agtgtatctacagatgggacaatctaagatggttacaacattactacatagtatcgcaaa -tagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatcaaaaaggtaa -catccatatacagatataatatctataacatatatagatatatggatataacatccatat -atagatatatctatatatctatctatagctac---------------------------- -----atctacagatatctatagctacatctacagatatctacagatatctatagctacat -ctacagatatctatagctacatctacagatatctacagatatctacagctacatctacag -atatctatagatatctatagctatatctacagatatctatcgatagatatatctatcgat -agatatatccacatagatatctagatatatatggatatatctatagatatctatctggat -atatctatcgatagatatatagatatatatagataaagctatatagatatatatagataa -acctatatagatacatagatatatagagagaaacctatatacatatatagatatatagag -agaaacctatatagatatatagatatatagagagaaacctatatagatgtatagataaac -ctatatagatatatagataaacctatgtagatatatagatatatatagataaatctatat -agatatataaaatagataaatctatatagatatatatacataaatctatatagatatata -tacataaatctatatagatatatatacataaatctatatatatacataaatctatatata -cataaatctatatagatatatatacataaatctatatagatatatatacataaatctata -tagatatatatacataaatctatatagatatatatacataaatctatatagatatataca -taaatctatatagatatatatacataaatctatatagatatatatacataaatctatata -gatatatatacataaatc--------tatatagatacatatagataaatctatacagata -tatagatacatatagataaatctatacagatatatagatacatatagataaatctataca -gatatatagatacatatagataaatctatacagatatatagatacatatagataaatcta -tacagatatatagatacatatagataaatctatacagatatatagatacatatagataaa -tctatacagatatatagatacatatagatacatctatacagatatatagatacatataga -tacatctatacagatatatagatacatatagatacatctatacagatatattgatacata -tagatacatctatatagatatatagatatatagatacatctata---------------- ------------------------------------------------------------- ----------------------tagatatatagatata----tagatacatctatatagat -atatatagatacatctatatatagacatatagatatatatagatacatctatatatagat -atatagatatatatagatacatctacacagag------agatatatagaaacatctacac -agggagatatatagatacatctacacagagagatatatagatacatctac---------- -----------------atagagagatatatagatacatctacatagagagatatatagat -acatctacatagagagatatatagatacatctacatagagagatatatagatacatctac -atagagatatatatagatacatctacatagagata--------tatatagatacatctat -atagagatatat------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------ctacctatacttcctgtgagttgtgtttctctggag -aactaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_14b6806a49917dbd5955b9d083e9e812.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_14b6806a49917dbd5955b9d083e9e812.msa deleted file mode 100644 index ec3bc81e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_14b6806a49917dbd5955b9d083e9e812.msa +++ /dev/null @@ -1,65 +0,0 @@ ->syndip_1_chr20:57948798-57949490 -agacttggcccactgctgtgccctgcacagatggacagatggttggaa----ggatggat -ggatggatggatggatggatggatggggttggatggatggatggatggatggatggatag -tggatagatggatgaatagtggatggataaatggattaatggatggatgaatggatgatg -gatggatgaatgagatggatggatt----------------gatggatggatggatggat -ggatggatggaagaatggatgatggatggatga--------------------gatggat -ggatggatggatggaagaatggatgatggatggatga--------gatggatggatggat -ggggggttggatggatggatgg-------------------------------------- -----------------atggatggatggatagtggatagatggatgaatagtggatggat -aaatggattaatggatggatgaatggatgatggatggatgaatgagatggatggatt--- ----------gatggatggatggatggatggaagaatggatgatggatggatgaatgagat -gggtggattgatggatggatggatggatggatggatggatggatggatggatggcagatg -gatggatccatctatgtcaggcctgcatgacacctgg ->syndip_2_chr20:57948798-57949490 -agacttggcccactgctgtgccctgcacagatggacagatggttggaaggatggatggat -ggatggatggatggatggatggatggggttggatggatggatggatggatggatggatag -tggatagatggatgaatagtggatggataaatggattaatggatggatgaatggatgatg -gatggatgaatgagatggatggattgatggatggatggatggatggatggatggatggat -ggatggatggaagaatggatgatggatggatgagatggatggatggatggatggatggat -ggatggatggatggaagaatggatgatggatggatgagatggatggatggatggatggat -ggggggttggatggatggatggatggatggatggatagtggatagatggatgaatagtga -atggataaatggattaatggatggatggatagtggatagatggatgaatagtggatggat -aaatggattaatggatggatgaatggatgatggatggatgaatgagatggatggattgat -ggatggatggatggatggatggatggatggaagaatggatgatggatggatgaatgagat -gggtggatt----gatggatggatggatggatggatggatggatggatggatggcagatg -gatggatccatctatgtcaggcctgcatgacacctgg ->p:HG002_1_chr20:57948798-57949490 -agacttggcccactgctgtgccctgcacagatggacagatggttggaaggatggatggat -ggatggatggatggatggatggatggggttggatggatggatggatggatggatggatag -tggatagatggatgaatagtggatggataaatggattaatggatggatgaatggatgatg -gatggatgaatgagatggatggattgatggatggatggatggatggatggatggatggat -ggatggatggaagaatggatgatggatggatgagatggatggatggatggatggatggat -ggatggatggatggaagaatggatgatggatggatgagatggatggatggatggatggat -ggggggttggatggatggatggatggatggatggatagtggatagatggatgaatagtga -atggataaatggattaatggatggatggatagtggatagatggatgaatagtggatggat -aaatggattaatggatggatgaatggatgatggatggatgaatgagatggatggattgat -ggatggatggatggatggatggatggatggaagaatggatgatggatggatgaatgagat -gggtggatt----gatggatggatggatggatggatggatggatggatggatggcagatg -gatggatccatctatgtcaggcctgcatgacacctgg ->p:HG002_2_chr20:57948798-57949490 -agacttggcccactgctgtgccctgcacagatggacagatggttggaa----ggatggat -ggatggatggatggatggatggatggggttggatggatggatggatggatggatggatag -tggatagatggatgaatagtggatggataaatggattaatggatggatgaatggatgatg -gatggatgaatgagatggatggatt----------------gatggatggatggatggat -ggatggatggaagaatggatgatggatggatga--------------------gatggat -ggatggatggatggaagaatggatgatggatggatga--------gatggatggatggat -ggggggttggatggatggatgg-------------------------------------- -----------------atggatggatggatagtggatagatggatgaatagtggatggat -aaatggattaatggatggatgaatggatgatggatggatgaatgagatggatggatt--- ----------gatggatggatggatggatggaagaatggatgatggatggatgaatgagat -gggtggattgatggatggatggatggatggatggatggatggatggatggatggcagatg -gatggatccatctatgtcaggcctgcatgacacctgg ->ref_chr20:57948798-57949490 -agacttggcccactgctgtgccctgcacagatggacagatggttggaaggatggatggat -ggatggatggatggatggatggatggggttggatggatggatggatggatggatggatag -tggatagatggatgaatagtggatggataaatggattaatggatggatgaatggatgatg -gatggatgaatgagatggatggattgatggatggatggatggatggatggatggatggat -ggatggatggaagaatggatgatggatggatgagatggatggatggatggatggatggat -ggatggatggatggaagaatggatgatggatggatgagatggatggatggatggatggat -ggggggttggatggatggatggatggatggatggatagtggatagatggatgaatagtga -atggataaatggattaatggatggatggatagtggatagatggatgaatagtggatggat -aaatggattaatggatggatgaatggatgatggatggatgaatgagatggatggattgat -ggatggatggatggatggatggatggatggaagaatggatgatggatggatgaatgagat -gggtggatt----gatggatggatggatggatggatggatggatggatggatggcagatg -gatggatccatctatgtcaggcctgcatgacacctgg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_14defb5c005fb476e5f665c1f6a8bb78.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_14defb5c005fb476e5f665c1f6a8bb78.msa deleted file mode 100644 index 6ff76737..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_14defb5c005fb476e5f665c1f6a8bb78.msa +++ /dev/null @@ -1,95 +0,0 @@ ->syndip_1_chr20:63221299-63221931 -ctgcaggcctcagctccctccctgcttttccaggagttgaaacagggcctctcctaactc -cactttgccaagagcctcttctcccactgcagagaactgtcatctgcctgtaagtaccag -tgccaggtgctctggggccgatgtctccgttagccccaaggtggaggctcagggagcaga -tgtgagcgtgccttgctcatcgcagtagcttcggac------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----tgcagggattgcagggactgcagggactgcagggattgcagggactgcagggactgc -agggactgcagggattgcagggattgcagggactgcagggactgcattgctcttgcagca -ccacccgcctccgtggacaccttcagcagtgagacaatgcaggctctgctacaagaggtg -cttactgggctctgctctggtgaggagaggcctcgcctggcagccagacagagtcccagc -agggcaagatgaaaattcggggccctcgttcaaaca ->syndip_2_chr20:63221299-63221931 -ctgcaggcctcagctccctccctgcttttccaggagttgaaacagggcctctcctaactc -cactttgccaagagcctcttctcccactgcagagaactgtcatctgcctgtaagtaccag -tgccaggtgctctggggccgatgtctccgttagccccaaggtggaggctcagggagcaga -tgtgagcgtgccttgctcatcgcagtagcttcggactgcagggattgcagggactgcagg -gattgcagggattgcagggagtgcagggactgcagggactgcagggattgcagggactgc -agggactgcagggactgcagggactgcagggactgcagggactgcagggattgcagggac -tgcagggactgcagggattgcagggattgcagggattgcagggactgcagggattgcagg -gactgcagggactgcagggactgcagggactgcagggactgcagggattgcagggattgc -agggattgcagggactgcagggattgcagggactgcagggactgcagggattgcagggac -tgcagggactgcagggactgcagggattgcagggattgcagggattgcagggattgcagg -gattgcagggactgcagggactgcagggactgcagggactgcagggattgcagggattgc -agggattgcagggattgcagggactgcagggactgcagggattgcagggattgcagggat -tgcagggattgcagggattgcagggattgcagggactgcagggactgcagggactgcagg -gattgcagggattgcagggattgcagggattgcagggactgcagggactgcagggattgc -agggattgcagggattgcagggattgcagggactgcagggactgcattgctcttgcagca -ccacccgcctccgtggacaccttcagcagtgagacaatgcaggctctgctacaagaggtg -cttactgggctctgctctggtgaggagaggcctcgcctggcagccagacagagtcccagc -agggcaagatgaaaattcggggccctcgttcaaaca ->p:HG002_1_chr20:63221299-63221931 -ctgcaggcctcagctccctccctgcttttccaggagttgaaacagggcctctcctaactc -cactttgccaagagcctcttctcccactgcagagaactgtcatctgcctgtaagtaccag -tgccaggtgctctggggccgatgtctccgttagccccaaggtggaggctcagggagcaga -tgtgagcgtgccttgctcatcgcagtagcttcggactgcagggattgcagggactgcagg -gattgcagggattgcagggattgcagggactgcagggattgcagggactgcagggactgc -agggactgcagggactgcagggactgcagggattgcagggattgcagggattgcagggac -tgcagggactgcagggattgcagggattgcagggactgcagggactgcagggattgcagg -gactgcagggactgcagggactgcagggactgcagggactgcagggactgcagggattgc -agggattgcagggattgcagggattgcagggactgcagggactgcagggactgcagggac -tgcagggactgcagggactgcagggattgcagggattgcagggattgcagggattgcagg -gattgcagggactgcagggactgcagggactgcagggactgcagggattgcagggattgc -agggattgcagggattgcagggactgcagggactgcagggattgcagggattgcagggat -tgcagggattgcagggattgcagggattgcagggactgcagggactgcagggactgcagg -gattgcagggattgcagggactgcagggactgcagggattgcagggactgcagggactgc -agggactgcagggattgcagggattgcagggactgcagggactgcattgctcttgcagca -ccacccgcctccgtggacaccttcagcagtgagacaatgcaggctctgctacaagaggtg -cttactgggctctgctctggtgaggagaggcctcgcctggcagccagacagagtcccagc -agggcaagatgaaaattcggggccctcgttcaaaca ->p:HG002_2_chr20:63221299-63221931 -ctgcaggcctcagctccctccctgcttttccaggagttgaaacagggcctctcctaactc -cactttgccaagagcctcttctcccactgcagagaactgtcatctgcctgtaagtaccag -tgccaggtgctctggggccgatgtctccgttagccccaaggtggaggctcagggagcaga -tgtgagcgtgccttgctcatcgcagtagcttcggac------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----tgcagggattgcagggactgcagggactgcagggattgcagggactgcagggactgc -agggactgcagggattgcagggattgcagggactgcagggactgcattgctcttgcagca -ccacccgcctccgtggacaccttcagcagtgagacaatgcaggctctgctacaagaggtg -cttactgggctctgctctggtgaggagaggcctcgcctggcagccagacagagtcccagc -agggcaagatgaaaattcggggccctcgttcaaaca ->ref_chr20:63221299-63221931 -ctgcaggcctcagctccctccctgcttttccaggagttgaaacagggcctctcctaactc -cactttgccaagagcctcttctcccactgcagagaactgtcatctgcctgtaagtaccag -tgccaggtgctctggggccgatgtctccgttagccccaaggtggaggctcagggagcaga -tgtgagcgtgccttgctcatcgcagtagcttcggactgcagggattgcagggactgcagg -gattgcagggattgcagggattgcagggactgcagggattgcagggactgcagggactgc -agggactgcagggactgcagggactgcagggattgcagggattgcagggattgcagggac ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----tgcagggattgcagggactgcagggactgcagggattgcagggactgcagggactgc -agggactgcagggattgcagggattgcagggactgcagggactgcattgctcttgcagca -ccacccgcctccgtggacaccttcagcagtgagacaatgcaggctctgctacaagaggtg -cttactgggctctgctctggtgaggagaggcctcgcctggcagccagacagagtcccagc -agggcaagatgaaaattcggggccctcgttcaaaca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_157340f8623d37786583821b8bd25147.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_157340f8623d37786583821b8bd25147.msa deleted file mode 100644 index fa589a59..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_157340f8623d37786583821b8bd25147.msa +++ /dev/null @@ -1,160 +0,0 @@ ->syndip_1_chr20:61100821-61102505 -ctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatcctgtgccac -atctggagagacccctgtgagggcagagagctacctcctcttcttcctgtgtcacacctg -gagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggaga -gaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacctggggagacc -ctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccggagagaccccaa -gagagggcagacagccacctcctctacttcctgtgtcacacctggagagaccccgagtga -gggcggatggccacgtcttctacttcctgtgtcacacctggagagaccccgagtgagggc -agatggccacatcctctacttcctgtgtcacacctggggagaccctgagtgagggcaga- --------------------------------------------------------cagcc -atgtcctctacgtcctgtgccacatccggagagaccccaagagagggcagacagccacct -cctctacttcctgtgtcacacct------------------------------------- --------------------ggagagactccaagtgaggagagacggccacatcttctact -tcctgtgtcacacctggagagacctcgagtgagggcagatggccacatcctctaattcct -gtgtcatacctggagagaccccgagtgagggcagatggccacctcctctacttcctgtgt -cacacctggagagaccccaagtgagggcagactgccacctcctctacttcctgtgtcaca -cctagagagaccccgagtgaggacagccagccatgtcctctacttcctgtgccacatccg -gagagatcccgagtgagggcagacagccatgtcctctacttcctgtgtcacacctggaga -gaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacctggagagacc -ccgagtgagggcagacggccacctcctctacttcctgtgtcacacctggagagaccccga -gtgagggcagacggccacatcctctaattcctgtgtcatgcctggagagaccccgagtga -gggcatatggccacatcctctaattcctatgtcacacctggagagaccccgagtgagggt -ggatggccacatcctctaattcctgtgtcatacctggagagaccccgagtgagggcagat -ggccacctcctctacttcctgtgtcacacctggagagaccccgagtgagggcagatggcc -acctcctctacttcctgtgtcacacctggagagaccccaagtgagggcagacagccatgt -cctctacgtcctgtgccacatccggagagaccccga-tgagggcagacagctaccccctc -tacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccacctcttctact -tcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcctctacttcct -gtgtcacacctggagagaccccgagtgagggcagacggccacatcctctatttcctgtgt -cacacctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcaca -catggagagaccccgagtgagggcagaaggccacatcctctacttcctgtgtcacaccta -gagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcacacc ->syndip_2_chr20:61100821-61102505 -ctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatcctgtgccac -atctggagagacccctgtgagggcagagagctacctcctcttcttcctgtgtcacacctg -gagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggaga -gaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacctggggagacc -ctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccggagagaccccaa -gagagggcagacagccacctcctctacttcctgtgtcacacctggagagactccaagtga -ggagagacggccacatcttctacttcctgtgtcacacctggagagacctcgagtgagggc -agatggccacatcctctaattcctgtgtcacacctggagagaccccaagtgagggcagac -tgccacctcctctacttcctgtgtcacacctagagagaccccgagtgaggacagccagcc -atgtcctctacttcctgtgccacatccggagagatcccgagtgagggcagacagccatgt -cctctacttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctc -taattcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaat -tcctgtgtcatgcctggagagaccccgagtgagggcatatggccacatcctctaattcct -atgtcacacctggagagaccccgagtgagggtggatggccacatcctctaattcctgtgt -catacctggagagaccccgagtgagggcagatggccacctcctctacttcctgtgtcaca -cctggagagaccccaagtgagggcagacagccatgtcctctacgtcctgtgccacatccg -gagagaccccga-tgagggcagacagctaccccctctacttcctgtgtcacacctgcaga -gaccccaagtgagggcagatggccacctcttctacttcctgtgtcacacctggagaggcc -ccgagtgagggcagacggccacctcctctacttcctgtgtcacacctggagagaccccga -gtgagggcagacggccacatcctctatttcctgtgtcacacctggagagaccccgagtga -gggcagacggccacatcctctaattcctgtgtcacacatggagagaccccgagtgaaggc -agaaggccacatcctctacttcctgtgtcacacctagagagaccccgagtgagggcggat -ggccacatcctctaattcctatgtcacacctggagagaccccgagtgagggtggatggcc -acatcctctaattcctgtgtcatacctggagagaccccgagtgagggcagatggccacct -cctctacttcctgtgtcacacctggagagaccccaagtgagggcagacagccatgtcctc -tacgtcctgtgccacatccggagagaccccga-tgagggcagacagctaccccctctact -tcctgtgtcacacctgcagagaccccaagtgagggcagatggccacctcttctacttcct -gtgtcacacctggagaggccccgagtgagggcagacggccacctcctctacttcctgtgt -cacacctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcaca -catggagagaccctgagtgagggcagaaggccacatcctctacttcctgtgtcacaccta -gagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcacacc ->p:HG002_1_chr20:61100821-61102505 -ctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatcctgtgccac -atctggagagacccctgtgagggcagagagctacctcctcttcttcctgtgtcacacctg -gagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggaga -gaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacctggggagacc -ctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccggagagaccccaa -gagagggcagacagccacctcctctacttcctgtgtcacacctggagagaccccgagtga -gggcggatggccacgtcttctacttcctgtgtcacacctggagagaccccgagtgagggc -agatggccacatcctctaattcctgtgtcacacctggagaaaccccaagtgagggcagac -tgccacctcctctacttcctgtgtcacacctagagagaccccgagtgaggacagccagcc -atgtcctctacttcctgtgccacatccggagagatcccgagtgagggcagacagccatgt -cctctacttcctgtgtcacacctggggagaccctgagtgagggcagacagccatgtcctc -tacgtcctgtgccacatccggagagaccccaagagagggcagacagccacctcctctact -tcctgtgtcacacctggagagactccaagtgaggagagacggccacatcttctacttcct -gtgtcacacctggagagacctcgagtgagggcagatggccacatcctctaattcctgtgt -cacacctggagagaccccaagtgagggcagactgccacctcctctacttcctgtgtcaca -cctagagagaccccgagtgaggacagccagccatgtcctctacttcctgtgccacatccg -gagagatcccgagtgagggcagacagccatgtcctctacttcctgtgtcacacctggaga -gaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacctggagagacc -ccgagtgagggcagacggccacctcctctacttcctgtgtcacacctggagagaccccga -gtgagggcagacggccacatcctctaattcctgtgtcatgcctggagagaccccgagtga -gggcatatggccacatcctctaattcctatgtcacacctggagagaccccgagtgagggt -ggatggccacatcctctaattcctgtgtcatacctggagagaccccgagtgagggcagat -ggccacctcctctacttcctgtgtcacacctggagagaccccgagtgagggcagatggcc -acctcctctacttcctgtgtcacacctggagagaccccaagtgagggcagacagccatgt -cctctacgtcctgtgccacatccggagagaccccga-tgagggcagacagctaccccctc -tacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccacctcttctact -tcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcctctacttcct -gtgtcacacctggagagaccccgagtgagggcagacggccacatcctctatttcctgtgt -cacacctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcaca -catggagagaccccgagtgagggcagaaggccacatcctctacttcctgtgtcacaccta -gagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcacacc ->p:HG002_2_chr20:61100821-61102505 -ctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatcctgtgccac -atctggagagacccctgtgagggcagagagctacctcctcttcttcctgtgtcacacctg -gagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggaga -gaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacctggggagacc -ctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccggagagaccccaa -gagagggcagacagccacctcctctacttcctgtgtcacacctggagagaccccgagtga -gggcggatggccacgtcttctacttcctgtgtcacacctggagagaccccgagtgagggc -agatggccacatcctctacttcctgtgtcacacctggggagaccctgagtgagggcaga- --------------------------------------------------------cagcc -atgtcctctacgtcctgtgccacatccggagagaccccaagagagggcagacagccacct -cctctacttcctgtgtcacacct------------------------------------- --------------------ggagagactccaagtgaggagagacggccacatcttctact -tcctgtgtcacacctggagagaccccgagtgagggtggatggccacatcctctaattcct -gtgtcatacctggagagacctcgagtgagggcagatggccacatcctctaattcctgtgt -cacacctggagagaccccaagtgagggcagactgccacctcctctacttcctgtgtcaca -cctagagagaccccgagtgaggacagccagccatgtcctctacttcctgtgccacatccg -gagagatcccgagtgagggcagacagccatgtcctctacttcctgtgtcacacctggaga -gaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacctggagagacc -ccgagtgagggcagacggccacctcctctacttcctgtgtcacacctggagagaccccga -gtgagggcagacggccacatcctctaattcctgtgtcatgcctggagagaccccgagtga -gggcatatggccacatcctctaattcctatgtcacacctggagagaccccgagtgagggt -ggatggccacatcctctaattcctgtgtcatacctggagagaccccgagtgagggcagat -ggccacctcctctacttcctgtgtcacacctggagagaccccgagtgagggcagatggcc -acctcctctacttcctgtgtcacacctggagagaccccaagtgagggcagacagccatgt -cctctacgtcctgtgccacatccggagagaccccga-tgagggcagacagctaccccctc -tacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccacctcttctact -tcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcctctacttcct -gtgtcacacctggagagaccccgagtgagggcagacggccacatcctctatttcctgtgt -cacacctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcaca -catggagagaccccgagtgagggcagaaggccacatcctctacttcctgtgtcacaccta -gagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcacacc ->ref_chr20:61100821-61102505 -ctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatcctgtgccac -atctggagagacccctgtgagggcagagagctacctcctcttcttcctgtgtcacacctg -gagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggaga -gaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacctggggagacc -ctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccggagagaccccaa -gagagggcagacagccacctcctctacttcctgtgtcacacctggagagaccccgagtga -gggcggatggccacgtcttctacttcctgtgtcacacctggagagaccccgagtgagggc -agatggccacatcctctacttcctgtgtcacacctggggagaccctgagtgagggcaga- --------------------------------------------------------cagcc -atgtcctctacgtcctgtgccacatccggagagaccccaagagagggcagacagccacct -cctctacttcctgtgtcacacct------------------------------------- --------------------ggagagactccaagtgaggagagacggccacatcttctact -tcctgtgtcac------------------------------------------------- --------acctggagagacctcgagtgagggcagatggccacatcctctaattcctgtgt -cacacctggagagaccccaagtgagggcagactgccacctcctctacttcctgtgtcaca -cctagagagaccccgagtgaggacagccagccatgtcctctacttcctgtgccacatccg -gagagatcccgagtgagggcagacagccatgtcctctacttcctgtgtcacacctggaga -gaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacctggagagacc -ccgagtgagggcagacggccacctcctctacttcctgtgtcacacctggagagaccccga -gtgagggcagacggccacatcctctaattcctgtgtcatgcctggagagaccccgagtga -gggcatatggccacatcctctaattcctatgtcacacctggagagaccccgagtgagggt -ggatggccacatcctctaattcctgtgtcatacctggagagaccccgagtgagggcagat -ggccacctcctctacttcctgtgtcacacctggagagaccccgagtgagggcagatggcc -acctcctctacttcctgtgtcacacctggagagaccccaagtgagggcagacagccatgt -cctctacgtcctgtgccacatccggagagaccccga-tgagggcagacagctaccccctc -tacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccacctcttctact -tcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcctctacttcct -gtgtcacacctggagagaccccgagtgagggcagacggccacatcctctatttcctgtgt -cacacctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcaca -catggagagaccccgagtgagggcagaaggccacatcctctacttcctgtgtcacaccta -gagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcacacc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_1a54f2fb6fa56b5e227e9d8ec45fa8f7.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_1a54f2fb6fa56b5e227e9d8ec45fa8f7.msa deleted file mode 100644 index ded6f29c..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_1a54f2fb6fa56b5e227e9d8ec45fa8f7.msa +++ /dev/null @@ -1,445 +0,0 @@ ->syndip_1_chr20:64173209-64176729 -tgaggcaaggcccatgggtcagcctggccaatttccctcccctcctgagcaccgtgggag -ggtcaggcctcaagcagccctcggaggcagcagtcacagacagaggtgggctgttggaca -ggtgcggctgatagagtgggtgtcttttgtgggcttctccccagcctgtggcctggccta -gtcagtagagatggtcaggggagcaggagggagcccataccccagtgcctgtagttgtgt -ccatttcccctccctgacttctcctcctgcagcatccttccctttagttgtgtccatttc -ccctccctgacttctcctcctgcagcatctttcc---tagttgtgtccatttcccctccc -tgacttctcctcctgcagcatctttccttgtagttgtgtccatttcccctccctggcttc -tcctcctgcagcatctttcctagttgtgtccatttcccctccctgacttctcctcctgca -gcatccttccctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatctttccttgt -agttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtg -tccattccccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggct -t--------------------------------------------------------ctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcca -tttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagtt -gtgtccatttcccctccctggcttctcctgtagcatctttcc------------------ ---------------------------------tagttgtgtccatttcccctccctggct -tctc-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------ctgcagcatctttccctgt -agttgtgtccatttcccctccctggcttctcctgtagcaactttcctagttgtgtccatt -tcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggc -ttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgca -gcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcc---tagttgt -gtccatttcccctccctggcttctcctgtagcatctttcc---tagttgtgtccattccc -cctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggc -tt---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------ctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggc -ttctcctgtagcatctttcc---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------t -agttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatt -tcccctccctggctt---ctcctgcagcatctttccctg--------------------- ------------------------------------------------------------- --------------tagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt -gtccatttcccctccctggcttctcctgtagcatctttcc---tagttgtgtccatttcc -cctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggc -ttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgta -gcatctttccctgtagttgtgtccatttcccctccctggcgtctcctcctgcagcatctt -tcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt -gtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatt -ccccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttcccctc -cctggcttctcctcctgcagcatctttccctgtagttgtgtccattccccctccctggct -tctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctcctgcagc -atctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccct -gtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgt -ccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccc -tccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggctt -ctcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctcctcc -tgcagcatctttccctgtagttgtgtccatttcccctccctggcttctgcagcatctttc -cctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgt -ccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccc -tccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggctt -ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagc -atctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccct -gtagttgtgttcatttcccctccctggcttctcctgcagcatctttccctgtagttgtgt -ccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccc -tccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctgg--- ------------------------------------------------------------- -----------------------------------------------cttctcctgcagca -tctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtc -catttcccctccctggcttctcctcttctagcatctttcctgctccctggtagcctcttg -ggagccacctatttctggaggtccccactctgggttccttgtcctgggtgtggggcgaat -gtgctggactggggtcacagcattgaaccccacttggagctgaggatgttctcgccccag -aaggaaaagctgtgtgtgtctgcgtggagcagtgtggagtggtttccttggtgccgcctg -ggttccgggcacccggcctgggtgt ->syndip_2_chr20:64173209-64176729 -tgaggcaaggcccatgggtcagcctggccaatttccctcccctcctgagcaccgtgggag -ggtcaggcctcaagcagccctcggaggcagcagtcacagacagaggtgggctgttggaca -ggtgcggctgatagagtgggtgtcttttgtgggcttctccccagcctgtggcctggccta -gtcagtagagatggtcaggggagcaggagggagcccataccccagtgcctgtagttgtgt -ccatttcccctccctgacttctcctcctgcagcatccttccctttagttgtgtccatttc -ccctccctgacttctcctcctgcagcatctttcc---tagttgtgtccatttcccctccc -tgacttctcctcctgcagcatctttccttgtagttgtgtccatttcccctccctggcttc -tcctcctgcagcatctttcctagttgtgtccatttcccctccctgacttctcctcctgca -gcatccttccctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatctttccttgt -agttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtg -tccattccccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggct -tctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatc -tttccctgtagttgtgtccatttcccctccctggcttct--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagtt -gtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatttccc -ctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggct -tctc-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------ctgcagcatctttccctgt -agttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatt -tcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggc -ttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgca -gcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctacagcatctttccctgtagttgt -gtccatttcccctccctggcttctcctgtagcatctttcc---tagttgtgtccatttcc -cctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggc -tt---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------ctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggc -ttctcctgtagcatctttcc---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------tagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt -gtccatttcccctccctggcttctcctgtagcatctttcc---tagttgtgtccatttcc -cctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggc -ttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgta -gcatctttccctgtagttgtgtccatttcccctccctggcgtctcctcctgcagcatctt -tcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt -gtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatt -ccccctccctggcttctc------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------ctcctgcagcatctttccctgtagttgtgt -ccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccc -tccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctgg--- ------------------------------------------------------------- -----------------------------------------------cttctcctgcagca -tctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtc -catttcccctccctggcttctcctcttctagcatctttcctgctccctggtagcctcttg -ggagccacctatttctggaggtccccactctgggttccttgtcctgggtgtggggcgaat -gtgctggactggggtcacagcattgaaccccacttggagctgaggatgttctcgccccag -aaggaaaagctgtgtgtgtctgcgtggagcagtgtggagtggtttccttggtgccgcctg -ggttccgggcacccggcctgggtgt ->p:HG002_1_chr20:64173209-64176729 -tgaggcaaggcccatgggtcagcctggccaatttccctcccctcctgagcaccgtgggag -ggtcaggactcaagcagccctcggaggcagcagtcacagacagaggtgggctgttggaca -ggtgcggctgatagagtgggtgtcttttgtgggcttctccccagcctgtggcctggccta -gtcagtagagatggtcaggggagcaggagggagcccataccccagtgcctgtagttgtgt -ccatttcccctccctgacttctcctcctgcagcatccttccctttagttgtgtccatttc -ccctccctgacttctcctcctgcagcatctttcc---tagttgtgtccatttcccctccc -tgacttctcctcctgcagcatctttccttgtagttgtgtccatttcccctccctggcttc -tcctcctgcagcatctttcctagttgtgtccatttcccctccctgacttctcctcctgca -gcatccttccctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatctttccttgt -agttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtg -tccattccccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggct -tctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatc -tttccctgtagttgtgtccatttcccctccctggcttct--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagtt -gtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatttccc -ctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggct -tctc-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------ctgcagcatctttccctgt -agttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatt -tcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggc -ttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgca -gcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctacagcatctttccctgtagttgt -gtccatttcccctccctggcttctcctgtagcatctttcc---tagttgtgtccatttcc -cctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggc -tt---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------ctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggc -ttctcctgtagcatctttcc---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------tagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt -gtccatttcccctccctggcttctcctgtagcatctttcc---tagttgtgtccatttcc -cctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggc -ttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgta -gcatctttccctgtagttgtgtccatttcccctccctggcgtctcctcctgcagcatctt -tcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt -gtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatt -ccccctccctggcttctc------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------ctcctgcagcatctttccctgtagttgtgt -ccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccc -tccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctgg--- ------------------------------------------------------------- -----------------------------------------------cttctcctgcagca -tctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtc -catttcccctccctggcttctcctcttctagcatctttcctgctccctggtagcctcttg -ggagccacctatttctggaggtccccactctgggttccttgtcctgggtgtggggcgaat -gtgctggactggggtcacagcattgaaccccacttggagctgaggatgttctcgccccag -aaggaaaagctgtgtgtgtctgcgtggagcagtgtggagtggtttccttggtgccgcctg -ggttccgggcacccggcctgggtgt ->p:HG002_2_chr20:64173209-64176729 -tgaggcaaggcccatgggtcagcctggccaatttccctcccctcctgagcaccgtgggag -ggtcaggactcaagcagccctcggaggcagcagtcacagacagaggtgggctgttggaca -ggtgcggctgatagagtgggtgtcttttgtgggcttctccccagcctgtggcctggccta -gtcagtagagatggtcaggggagcaggagggagcccataccccagtgcctgtagttgtgt -ccatttcccctccctgacttctcctcctgcagcatccttccctttagttgtgtccatttc -ccctccctgacttctcctcctgcagcatctttcc---tagttgtgtccatttcccctccc -tgacttctcctcctgcagcatctttccttgtagttgtgtccatttcccctccctggcttc -tcctcctgcagcatctttcctagttgtgtccatttcccctccctgacttctcctcctgca -gcatccttccctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatctttccttgt -agttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtg -tccattccccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggct -t--------------------------------------------------------ctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcca -tttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagtt -gtgtccatttcccctccctggcttctcctgtagcatctttcc------------------ ---------------------------------tagttgtgtccatttcccctccctggct -tctc-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------ctgcagcatctttccctgt -agttgtgtccatttcccctccctggcttctcctgtagcaactttcctagttgtgtccatt -tcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggc -ttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgca -gcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcc---tagttgt -gtccatttcccctccctggcttctcctgtagcatctttcc---tagttgtgtccattccc -cctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggc -tt---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------ctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggc -ttctcctgtagcatctttcc---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------t -agttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatt -tcccctccctggctt---ctcctgcagcatctttccctg--------------------- ------------------------------------------------------------- --------------tagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt -gtccatttcccctccctggcttctcctgtagcatctttcc---tagttgtgtccatttcc -cctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggc -ttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgta -gcatctttccctgtagttgtgtccatttcccctccctggcgtctcctcctgcagcatctt -tcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt -gtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatt -ccccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttcccctc -cctggcttctcctcctgcagcatctttccctgtagttgtgtccattccccctccctggct -tctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctcctgcagc -atctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccct -gtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgt -ccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccc -tccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggctt -ctcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctcctcc -tgcagcatctttccctgtagttgtgtccatttcccctccctggcttctgcagcatctttc -cctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgt -ccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccc -tccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggctt -ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagc -atctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccct -gtagttgtgttcatttcccctccctggcttctcctgcagcatctttccctgtagttgtgt -ccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccc -tccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctgg--- ------------------------------------------------------------- -----------------------------------------------cttctcctgcagca -tctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtc -catttcccctccctggcttctcctcttctagcatctttcctgctccctggtagcctcttg -ggagccacctatttctggaggtccccactctgggttccttgtcctgggtgtggggcgaat -gtgctggactggggtcacagcattgaaccccacttggagctgaggatgttctcgccccag -aaggaaaagctgtgtgtgtctgcgtggagcagtgtggagtggtttccttggtgccgcctg -ggttccgggcacccggcctgggtgt ->ref_chr20:64173209-64176729 -tgaggcaaggcccatgggtcagcctggccaatttccctcccctcctgagcaccgtgggag -ggtcaggcctcaagcagccctcggaggcagcagtcacagacagaggtgggctgttggaca -ggtgcggctgatagagtgggtgtcttttgtgggcttctccccagcctgtggcctggccta -gtcagtagagatggtcaggggagcaggagggagcccataccccagtgcctgtagttgtgt -ccatttcccctccctgacttctcctcctgcagcatccttccctttagttgtgtccatttc -ccctccctgacttctcctcctgcagcatccttccctttagttgtgtccatttcccctccc -tgacttctcctcctgcagcatctttcc--------------------------------- ------------------------------------------------------------- --------------tagttgtgtccatttcccctccctgacttctcctcctgcagcatctt -tccttgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccttgt -agttgtgtccatttcccctccctgacttctcctcctgcagcatccttccctgtagttgtg -tccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggct -t--------------------------------------------------------ctc -ctgcagcatctttccctg------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------tagttgtgtccatttcccctccctggct -tctcctgtagcatctttccctgtagttgtgtccattccccctccctggcttctcctgtag -catctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgt -agttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatt -tcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccattccccctc -cctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcct -gtagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt -gtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcc -cctccctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccctgac -ttctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcgtctcct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcat -ctttcctagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgt -agttgtgtccattccccctccctggcttctcctgtagcatctttcctagttgtgtccatt -tcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggc -ttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgca -gcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt -gtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcc -cctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggc -ttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgta -gcatctttccctgtagttgtgtccattccccctccctggcgtctcctcctgcagcatctt -tccctgtagttgtgtccattccccctccctggcttctcctgcagcatctttccctgtagt -tgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggc -ttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgta -gcatctttccctgtagttgtgtccattccccctccctgacttctcctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcgtctcctcctgcagcatctttccctgt -agttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatt -tcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccattccccctc -cctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcct -gtagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt -gtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcc -cctccctggcttctcctgcagcatctttcc---tagttgtgtccatttcccctccctggc -ttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgta -gcatctttccctgtagttgtgtccattccccctccctggcgtctc--------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------ctcctgcagcatctttccctgtagttgtgt -ccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccc -tccctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccctggcgt -ctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctcc -tgcagcatctttccctgtagttgtgtccattccccctccctggcttctcctcctgcagca -tctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtc -catttcccctccctggcttctcctcttctagcatctttcctgctccctggtagcctcttg -ggagccacctatttctggaggtccccactctgggttccttgtcctgggtgtggggcgaat -gtgctggactggggtcacagcattgaaccccacttggagctgaggatgttctcgccccag -aaggaaaagctgtgtgtgtctgcgtggagcagtgtggagtggtttccttggtgccgcctg -ggttccgggcacccggcctgggtgt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_1d7c9e595e1b2ef479098d45351d36d3.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_1d7c9e595e1b2ef479098d45351d36d3.msa deleted file mode 100644 index e2dd4670..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_1d7c9e595e1b2ef479098d45351d36d3.msa +++ /dev/null @@ -1,50 +0,0 @@ ->syndip_1_chr20:63559315-63559819 -gcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggtctcctgt -gagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgg -gag--------------------ggagtcagggtcaggtgggaggagtcagggtcagatg -ggagtcagtcagagtcaggtgggag-gagtcagggtcaggtgggaggagtcagggtcagg -tgggag--------------------gagtcagggtcaggtgggaggagtcagggtcaga -tgggagtcagtcagagtcaggtgggag-gagtcagggtcaggtggga------------- -----ggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcagg -tgggaggagtcagggtcaggtgggag---------------------------------- ---------------------------- ->syndip_2_chr20:63559315-63559819 -gcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggtctcctgt -gagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgg -gaggagtcagggtcaggtgggagtcagtcagggtcaggtgggaggagtcagggtcaggtg -ggag-gagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcagggtcagg -tgggag------------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------- ->p:HG002_1_chr20:63559315-63559819 -gcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggtctcctgt -gagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgg -gaggagtcagggtcaggtgggagtcagtcagggtcaggtgggaggagtcagggtcaggtg -ggag-gagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcagggtcagg -tgggag------------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------- ->p:HG002_2_chr20:63559315-63559819 -gcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggtctcctgt -gagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgg -gaggg--------------------agtcagggtcaggtgggaggagtcagggtcaggtg -ggag-gagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcagggtcagg -tgggag--------------------gagtcagggtcaggt---cggagtcagggtcagg -tgggag-gagtcagggtcaggtgggagtcagtcagggtcaggtggga------------- -----ggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcagg -tgggaggagtcagggtcaggtgggag---------------------------------- ---------------------------- ->ref_chr20:63559315-63559819 -gcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggtctcctgt -gagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgg -gaggagtcagggtcaggtgggagtcagtcagggtcaggtgggaggagtcagggtcaggtg -ggag-gagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcagggtcagg -tgggaggagtcagggtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaga -tgggagtcagtcagagtcaggtgggag-gagtcagggtcaggtgggaggagtcagggtca -ggtcggagtcagggtcaggtgggaggagtcagggtcaggtgggagtcagtcagggtcagg -tgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcag -gtgggaggagtcagggtcaggtgggag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_1fd9443159fe4a505bcb8e7dcad03085.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_1fd9443159fe4a505bcb8e7dcad03085.msa deleted file mode 100644 index 9cb61c5e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_1fd9443159fe4a505bcb8e7dcad03085.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:57110212-57110785 -agcaggcttcgctatgcacgcataatagcgacagcgcaaacagcagcagcagcagcagcc -tcagctggctcggcggggcttggctcagcgtgtgcggggtgctgagctaagtcttcccaa -acggcgtgtgcggggtgctgcgctgtcttccagatccgcttgtgcagggcgctgtgctgt -cttctggttcggcgtgtgcggggcgctgtgctaagtcttccggctgggcgtgtgcggggc -gctgtgctaagtcttccggctgggcgtgtgcggggc------------------------ ------------------------------------------------------------- -----------------------gctgtgctaagtcttccggctgggcgtgtgcggggcgc -tgtgctgtcttccggttcggcgtgtgcggggcgttatgctaagtcttccggctgggcgtg -tgcggggcgctgtgctgtcttccggttcggcgtgtgcggggcgctgtgctaagtcttccg -gctgcattcgcactctttccctccgactcaacca ->syndip_2_chr20:57110212-57110785 -agcaggcttcgctatgcacgcataatagcgacagcgcaaacagcagcagcagcagcagcc -tcagctggctcggcggggcttggctcagcgtgtgcggggtgctgagctaagtcttcccaa -acggcgtgtgcggggtgctgcgctgtcttccagatccgcttgtgcagggcgctgtgctgt -cttctggttc------------------------------------ggcgtgtgcggggc -gctgtgctaagtcttccggctgggcgtgtgcggggc------------------------ ------------------------------------------------------------- -----------------------gctgtgctaagtcttccggctgggcgtgtgcggggcgc -tgtgctgtcttccggttcggcgtgtgcggggcgttatgctaagtcttccggctgggcgtg -tgcggggcgctgtgctgtcttccggttcggcgtgtgcggggcgctgtgctaagtcttccg -gctgcattcgcactctttccctccgactcaacca ->p:HG002_1_chr20:57110212-57110785 -agcaggcttcgctatgcacgcataatagcgacagcgcaaacagcagcagcagcagcagcc -tcagctggctcggcggggcttggctcagcgtgtgcggggtgctgagctaagtcttcccaa -acggcgtgtgcggggtgctgcgctgtcttccagatccgcttgtgcagggcgctgtgctgt -cttctggttc------------------------------------ggcgtgtgcggggc -gctgtgctaagtcttccggctgggcgtgtgcggggc------------------------ ------------------------------------------------------------- -----------------------gctgtgctaagtcttccggctgggcgtgtgcggggcgc -tgtgctgtcttccggttcggcgtgtgcggggcgttatgctaagtcttccggctgggcgtg -tgcggggcgctgtgctgtcttccggttcggcgtgtgcggggcgctgtgctaagtcttccg -gctgcattcgcactctttccctccgactcaacca ->p:HG002_2_chr20:57110212-57110785 -agcaggcttcgctatgcacgcataatagcgacagcgcaaacagcagcagcagcagcagcc -tcagctggctcggcggggcttggctcagcgtgtgcggggtgctgagctaagtcttcccaa -acggcgtgtgcggggtgctgcgctgtcttccagatccgcttgtgcagggcgctgtgctgt -cttctggttcggcgtgtgcggggcgctgtgctaagtcttccggctgggcgtgtgcggggc -gctgtgctaagtcttccggctgggcgtgtgcggggc------------------------ ------------------------------------------------------------- -----------------------gctgtgctaagtcttccggctgggcgtgtgcggggcgc -tgtgctgtcttccggttcggcgtgtgcggggcgttatgctaagtcttccggctgggcgtg -tgcggggcgctgtgctgtcttccggttcggcgtgtgcggggcgctgtgctaagtcttccg -gctgcattcgcactctttccctccgactcaacca ->ref_chr20:57110212-57110785 -agcaggcttcgctatgcacgcataatagcgacagcgcaaacagcagcagcagcagcagcc -tcagctggctcggcggggcttggctcagcgtgtgcggggtgctgagctaagtcttcccaa -acggcgtgtgcggggtgctgcgctgtcttccagatccgcttgtgcagggcgctgtgctgt -cttctggttcggcgtgtgcggggcgctgtgctaagtcttccggctgggcgtgtgcggggc -gctgtgctaagtcttccggctgggcgtgtgcggggcgctgtgctaagtcttccggctggg -cgtgtgcggggcgctgtgctgtcttccggttcggcgtgtgcggggcgctgtgctaagtct -tccggctgggcgtgtgcggggtgctgtgctaagtcttccggctgggcgtgtgcggggcgc -tgtgctgtcttccggttcggcgtgtgcggggcgttatgctaagtcttccggctgggcgtg -tgcggggcgctgtgctgtcttccggttcggcgtgtgcggggcgctgtgctaagtcttccg -gctgcattcgcactctttccctccgactcaacca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_200255f584324918b25a1c0884b51ea0.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_200255f584324918b25a1c0884b51ea0.msa deleted file mode 100644 index b8d85fdb..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_200255f584324918b25a1c0884b51ea0.msa +++ /dev/null @@ -1,365 +0,0 @@ ->syndip_1_chr20:63167387-63167627 -gatttggagtcactcacggttcccaccagcactcagccccatctcagcccccatctcagc -ccccaccgcagcctcacctcagtgcccacctcagccccctcctcagcccccacctccgcc -cccacctcagcccct------------------------cctcagcccccacctcagccc -cctcctcagcccccacctcc-----------------------gcccccacctccgcccc -cacctctgcccct-------------cctcagcccccacctcagccccctcctcagcccc -cacctccgcccccacctccgcccccacctctgcccct----------------------- ---------------cctcagcccccacctcagccccctcctcagcccccacctccgcccc -cacctccgcccccacctctgcccctcctcagcccccacctcagccccctcctcag----- -------cccccacctccgccccctcctcagcccccacctctgcccct------------c -ctcagcccccacctcagccccctcctcagcccccacctccgcccccacctccgcccccac -ctccgcccctcctccgcccccacctcagcccccacctcc--------------------- ---gccccctcctcagcccccacctctgcccctcctcagcccccacctcagcccccacctc -agcccccacctc------------------------------------------------ -------------------------------------------------ccccctcctcag -cccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctccg -cccct------------cctcagcccccacctccgcccccacctcagcccccacctcagc -ccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacctccgc -ccccacctcagcccccacctctgcccctcctcagcccccacctccgccccctcctcagcc -cccacctctg------------------------------------cccctcctcagccc -ccacctcagcccccacctcagcccccacctcc-cccctcctcagcccccacctcagcccc -cacctcagccccctcctcagcccccacctcagcccccacctcagcccccacctccgcccc -tcctcagcccccacctcagcccccacctccgcccctcctcagcccccacctcag------ ------------------------------------------------------------- -----------------------------ccccctcctcagcccccacctccgcccccacc -tccgcccccacctctgcccctcctcagcccccacctcagccccctcctcagcccccacct -ccgcccccacctccgcccccacctccgcccctcctccgcccccacctcagcccccacctc -cgccccct----------------------------------cctcagcccccacctctg -cccctcctcagcccccacctcagcccccacctcagcccccacct---------------- ----------cccccctcctcagcccccacctcagcccccacctccgcccctcctcagccc -ccacctccgccccca--------------------------------------------- ---------------cctcagcccccacctcagcccccacctccgcccccacctcagcccc -cacctccgcccccacctcagcccccacctcc-----------gcccccacctcagccccc -acctctgcccctcctcagcccccacctccgccccctcctcagcccccacctctgcccctc -ctcagcccccacctcagcccccacctcagcccccacct---------------------- ----cccccctcctcagccccca-----------------------------------cct -cagcccccacctcagccccctcctcagcccccacctcagcccccacctcagcccccacct -ccgcccctcctcagccccca-----------------------cctcagcccccacctcc -gcccctcctccgcccccacctcagccccctcctcagcccccacctctgcccctcctcagc -ccccacctcagcccccacctccgcccccacctcagccccctcctcagcccccacctc--- -----------------------------------ccccctcctccgcccccacctcagcc -cccacctcagcccccacctcagcccccacctc---------------------------- ------------------------------------------------------------- --------------------ccccctcctccgcccccacctcagccccca----------- -cctcagcccccacctccgcccccacctcagcccccacctcc------------------- ------------------------------------------------------------- ----------------------------cccctcctcagcccccacctcagcccccacctc -cgccccca-----------cctcagcccccacctcagcccccacctcagcccccacctcc -gcccctcctcagcccccacctccgcccccacctcagcccccacctcagcccccacctccg -ccccca------------------------------------------------------ ----------------cctcagcccccacctccgcccccacctcagcccccacctccgccc -ccacctcagcccccacctccgcccccacctccgcccccacctcc-----------gcccc -cacctcagcccccacctcagcccccacctccgccccca---------------------- -------------------------cctcagcccccacctcagcccccacctcagccccca -cctccgcccctcctcagcccccacctcagcccctcctcagcccccacctcagcccccacc -tcagcccccacctcagcccct-------------------------cctcagcccccacc -tcagccccctcctcagccccctcctcagcccccacctcagcccccacctccgcccccacc -tccgcccccacctcagccccacctcagcccctcctcagcccccacctcagccc------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------cctcagcccccacctcagcccccacctccgcccccacctccgcccccacctc -c----------------------------------------------------------- -------------------------gcccctcctcagcccccacctcagcccccacctcag -cccctcctcagcccccacctcc-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------acccccacctccgtccccacctccgccccc -tcctcagccccctcctcagcccccacctcagcccccacctccgcccccacctcagcccct -cctcagcccccacctctgcccccacctcagaccctcctcagcccctcctcagcccctcct -catcccctcctcagcagctgctggaatgggctaccctcaggagtt ->syndip_2_chr20:63167387-63167627 -gatttggattcactcacggttcccaccagcactcagccccatctcagcccccatctcagc -ccccaccgcagcctcacctcagtgcccacctcagccccctcctcagcccccacctccgcc -cccacctccgccccctcctcagcccctcctccgcccccacctcagcccccacctcagccc -cctcctcagcccccacctccgcccctcctcagcccccacctcagcccccacctcagcccc -cacctccgccccctcctcagcccccacctcagcccccacctcagccccctcctcagcccc -cacctcagcccccacctccgcccccacctcagcccccacctcagccccctcctcagcccc -cacctcagcccccacctcagcccccacctcagccccctcctcagcccccacctcagcccc -cacctccgccccctcctcagcccccacctcccccccacctccgccccctcctcagccccc -acctcccccccacctccgccccctcctcagcccccacctctgcccctcctcaggccccac -ctcagcccccacctcagccccctcctcagcccccacctcagcccccacctcagcccccac -ctccgcccctcctcagcccccacctcagcccccacctccgcccctcctctgcccccacct -cagccccctcctcagcccccacctctgcccctcctcagcccccacctcagcccccacctc -cgcccccacctcagcccccacctcagcccccacctccccccctcctcagcccccacctcc -acccccacctcagcccccacctcagcccccacctccccccctcctcagcccccacctccg -cccccacctcagcccccacctccgcccccacctcagcccccacctcagcccccacctccg -cccctcctcagcccccacctcagcccccacctccgcccccacctccgcccccacctcagc -ccccacctccgccccctcctcagcccccacctcagcccccacctcagcccccacctccac -ccccacctcagcccccacctcagcccccacctcccccccacctccgccccctcctcagcc -cccacctctgcccctcctcaggccccacctcagcccccacctcagccccctcctcagccc -ccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccc -cacctccacccccacctcagcccccacctccgcccccacctcagcccccacctccgcccc -tcctcagcccccacctcagcccccacctccgcccctcctctgcccccacctcagccccct -cctcagcccccacctctgcccctcctcagcccccacctcagcccccacctccgcccccac -ctcagcccccacctcagcccccacctccccccctcctcagcccccacctccacccccacc -tcagcccccacctccgcccctcctcagcccccacctcagcccccacctccacccccacct -cagcccccacctccgcccccacctccgcccctcctcagcccccacctccgcccccacctc -agcccctcctcagcccccacctccgcccctcctcagcccccacctcagcccccacctccg -cccctcctcagcccccacctcagcccccacctccacccccacctcagcccccacctcagc -ccccacctcccccccacctccgccccctcctcagcccccacctctgcccctcctcaggcc -ccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctcagccc -ccacctccgcccctcctcagcccccacctcagcccccacctccacccccacctcagcccc -cacctccgcccccacctcagcccccacctccgcccctcctcagcccccacctcagccccc -acctccgcccctcctctgcccccacctcagccccctcctcagcccccacctctgcccctc -ctcagcccccacctcagcccccacctccgcccccacctcagcccccacctcagcccccac -ctccccccctcctcagcccccacctccacccccacctcagcccccacctccgcccctcct -cagcccccacctcagcccccacctccacccccacctcagcccccacctcagcccccacct -ccgcccctcctcagcccccacctccgcccccacctcagcccctcctcagcccccacctcc -gcccctcctcagcccccacctccgcccccacctcagccccctcctccgcccctcctcagc -ccccacctccacccccacctcagcccccacctcagccccctcctcagcccccacctccgc -ccctcctcagcccccacctcagcccccacctcagcccccacctccgccccctcctcagcc -cccacctcagcccccacctcagccccctcctccacccctcctcagcccccacctccgccc -ccacctcagcccccacctccgcccctcctcagcccccacctccacccccacctcagcccc -cacctccgcccctcctcagcccccacctccgcccccacctcagcccccacctccccccct -cctcagcccccacctccgcccccacctcagcccccacctccgcccctcctcagcccccac -ctccacccccacctcagcccccacctccgcccctcctcagcccccacctccgcccccacc -tcagcccctcctcagcccccacctccgcccctcctcagcccccacctccgcccccacctc -agcccccacctccccccctcctcagcccccacctccgcccccacctcagcccccacctcc -gcccctcctcagcccccacctcagcccccacctccacccccacctcagcccccacctcag -cccccacctccgcccctcctcagcccccacctccgcccccacctcagcccctcctcagcc -cccacctccgcccctcctcagcccccacctccgcccccacctcagcccccacctccgccc -ccacctcagcccccacctccgcccccacctcagcccccacctccgcccctcctcagcccc -cacctcagcccccacctcagaccccacctccgcccccacctccgcccctcctcagccccc -acctcagcccccacctcagcccctcctcagcccccacctccgcccccacctccgccccca -cctccgcccctcctcagcccccacctcagcccctcctcagcccccacctcagcccccacc -tcagccccctcctcagcccccacctcagcccccacctccgcccccacctcagccccctcc -tcagcccccacctcagccccctcctcagcccccacctcagcccccacctccgcccccacc -tccgcccccacctcagccccacctcagcccctcctcagcccccacctcagcccctcctca -gcccccacctcagcccctcctcagcccccacctcagccccctcagcccccacctcagccc -ccacctccgcccccacctccgcccctcctcagcccccacctcagcccccacctcagcccc -tcctcagcccccacctccgcccccacctccgcccccacctcagcccctcctcagccccca -cctcagcccccacctcagccccctcctcagcccccacctccgcccccacctccgccccca -cctcagccccacctcagcccctcctcagcccccacctcagcccctcctcagcccccacct -cagcccctcctcagcccccacctcagcccccacctccgcccccacctccgcccccacctc -cgcccccacctcagcccctcctcagcccccacctcagcccccacctcagccccctcctca -gcccccacctccgcccccacctcagcccctcctcagcccccacctcagcccccacctcag -cccctcctcagcccccacctccgcccccacctccgcccccacctcagcccctcctcagcc -cccacctcagcccccacctcagccccctcctcagcccccacctccgcccccacctccgcc -cccacctcagccccacctcagcccctcctcagcccccacctcagcccctcctcagccccc -tcctcagcccccacctcagcccccacctcagcccccacctccgcccccacctccgccccc -acctcagccccctcctcagccccctcctcagcccccacctcagcccccacctcagcccct -cctcagcccccacctccgcccccacctcaga-----------ccctcctcagcccctcct -catcccctcctcagcagctgctggaatgggctaccctcaggagtt ->p:HG002_1_chr20:63167387-63167627 -gatttggattcactcacggttcccaccagcactcagccccatctcagcccccatctcagc -ccccaccgcagcctcacctcagtgcccacctcagccccctcctcagcccccacctccgcc -cccacctccgccccctcctcagcccctcctccgcccccacctcagcccccacctcagccc -cctcctcagcccccacctccgcccctcctcagcccccacctcagcccccacctcagcccc -cacctccgccccctcctcagcccccacctcagcccccacctcagccccctcctcagcccc -cacctcagcccccacctccgcccccacctcagcccccacctcagccccctcctcagcccc -cacctcagcccccacctcagcccccacctcagccccctcctcagcccccacctcagcccc -cacctccgccccctcctcagcccccacctcccccccacctccgccccctcctcagccccc -acctcccccccacctccgccccctcctcagcccccacctctgcccctcctcaggccccac -ctcagcccccacctcagccccctcctcagcccccacctcagcccccacctcagcccccac -ctccgcccctcctcagcccccacctcagcccccacctccgcccctcctctgcccccacct -cagccccctcctcagcccccacctctgcccctcctcagcccccacctcagcccccacctc -cgcccccacctcagcccccacctcagcccccacctccccccctcctcagcccccacctcc -acccccacctcagcccccacctcagcccccacctccccccctcctcagcccccacctccg -cccccacctcagcccccacctccgcccccacctcagcccccacctcagcccccacctccg -cccctcctcagcccccacctcagcccccacctccgcccccacctccgcccccacctcagc -ccccacctccgccccctcctcagcccccacctcagcccccacctcagcccccacctccac -ccccacctcagcccccacctcagcccccacctcccccccacctccgccccctcctcagcc -cccacctctgcccctcctcaggccccacctcagcccccacctcagccccctcctcagccc -ccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccc -cacctccacccccacctcagcccccacctccgcccccacctcagcccccacctccgcccc -tcctcagcccccacctcagcccccacctccgcccctcctctgcccccacctcagccccct -cctcagcccccacctctgcccctcctcagcccccacctcagcccccacctccgcccccac -ctcagcccccacctcagcccccacctccccccctcctcagcccccacctccacccccacc -tcagcccccacctccgcccctcctcagcccccacctcagcccccacctccacccccacct -cagcccccacctccgcccccacctccgcccctcctcagcccccacctccgcccccacctc -agcccctcctcagcccccacctccgcccctcctcagcccccacctcagcccccacctccg -cccctcctcagcccccacctcagcccccacctccacccccacctcagcccccacctcagc -ccccacctcccccccacctccgccccctcctcagcccccacctctgcccctcctcaggcc -ccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctcagccc -ccacctccgcccctcctcagcccccacctcagcccccacctccacccccacctcagcccc -cacctccgcccccacctcagcccccacctccgcccctcctcagcccccacctcagccccc -acctccgcccctcctctgcccccacctcagccccctcctcagcccccacctctgcccctc -ctcagcccccacctcagcccccacctccgcccccacctcagcccccacctcagcccccac -ctccccccctcctcagcccccacctccacccccacctcagcccccacctccgcccctcct -cagcccccacctcagcccccacctccacccccacctcagcccccacctcagcccccacct -ccgcccctcctcagcccccacctccgcccccacctcagcccctcctcagcccccacctcc -gcccctcctcagcccccacctccgcccccacctcagccccctcctccgcccctcctcagc -ccccacctccacccccacctcagcccccacctcagccccctcctcagcccccacctccgc -ccctcctcagcccccacctcagcccccacctcagcccccacctccgccccctcctcagcc -cccacctcagcccccacctcagccccctcctccacccctcctcagcccccacctccgccc -ccacctcagcccccacctccgcccctcctcagcccccacctccacccccacctcagcccc -cacctccgcccctcctcagcccccacctccgcccccacctcagcccccacctccccccct -cctcagcccccacctccgcccccacctcagcccccacctccgcccctcctcagcccccac -ctccacccccacctcagcccccacctccgcccctcctcagcccccacctccgcccccacc -tcagcccctcctcagcccccacctccgcccctcctcagcccccacctccgcccccacctc -agcccccacctccccccctcctcagcccccacctccgcccccacctcagcccccacctcc -gcccctcctcagcccccacctcagcccccacctccacccccacctcagcccccacctcag -cccccacctccgcccctcctcagcccccacctccgcccccacctcagcccctcctcagcc -cccacctccgcccctcctcagcccccacctccgcccccacctcagcccccacctccgccc -ccacctcagcccccacctccgcccccacctcagcccccacctccgcccctcctcagcccc -cacctcagcccccacctcagaccccacctccgcccccacctccgcccctcctcagccccc -acctcagcccccacctcagcccctcctcagcccccacctccgcccccacctccgccccca -cctccgcccctcctcagcccccacctcagcccctcctcagcccccacctcagcccccacc -tcagccccctcctcagcccccacctcagcccccacctccgcccccacctcagccccctcc -tcagcccccacctcagccccctcctcagcccccacctcagcccccacctccgcccccacc -tccgcccccacctcagccccacctcagcccctcctcagcccccacctcagcccctcctca -gcccccacctcagcccctcctcagcccccacctcagccccctcagcccccacctcagccc -ccacctccgcccccacctccgcccctcctcagcccccacctcagcccccacctcagcccc -tcctcagcccccacctccgcccccacctccgcccccacctcagcccctcctcagccccca -cctcagcccccacctcagccccctcctcagcccccacctccgcccccacctccgccccca -cctcagccccacctcagcccctcctcagcccccacctcagcccctcctcagcccccacct -cagcccctcctcagcccccacctcagcccccacctccgcccccacctccgcccccacctc -cgcccccacctcagcccctcctcagcccccacctcagcccccacctcagccccctcctca -gcccccacctccgcccccacctcagcccctcctcagcccccacctcagcccccacctcag -cccctcctcagcccccacctccgcccccacctccgcccccacctcagcccctcctcagcc -cccacctcagcccccacctcagccccctcctcagcccccacctccgcccccacctccgcc -cccacctcagccccacctcagcccctcctcagcccccacctcagcccctcctcagccccc -tcctcagcccccacctcagcccccacctcagcccccacctccgcccccacctccgccccc -acctcagccccctcctcagccccctcctcagcccccacctcagcccccacctcagcccct -cctcagcccccacctccgcccccacctcaga-----------ccctcctcagcccctcct -catcccctcctcagcagctgctggaatgggctaccctcaggagtt ->p:HG002_2_chr20:63167387-63167627 -gatttggagtcactcacggttcccaccagcactcagccccatctcagcccccatctcagc -ccccaccgcagcctcacctcagtgcccacctcagccccctcctcagcccccacctccgcc -cccacctcagcccct------------------------cctcagcccccacctcagccc -cctcctcagcccccacctcc-----------------------gcccccacctccgcccc -cacctctgcccct-------------cctcagcccccacctcagccccctcctcagcccc -cacctccgcccccacctccgcccccacctctgcccct----------------------- ---------------cctcagcccccacctcagccccctcctcagcccccacctccgcccc -cacctccgcccccacctctgcccctcctcagcccccacctcagccccctcctcag----- -------cccccacctccgccccctcctcagcccccacctctgcccct------------c -ctcagcccccacctcagccccctcctcagcccccacctccgcccccacctccgcccccac -ctccgcccctcctccgcccccacctcagcccccacctcc--------------------- ---gccccctcctcagcccccacctctgcccctcctcagcccccacctcagcccccacctc -agcccccacctc------------------------------------------------ -------------------------------------------------ccccctcctcag -cccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctccg -cccct------------cctcagcccccacctccgcccccacctcagcccccacctcagc -ccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacctccgc -ccccacctcagcccccacctctgcccctcctcagcccccacctccgccccctcctcagcc -cccacctctg------------------------------------cccctcctcagccc -ccacctcagcccccacctcagcccccacctcc-cccctcctcagcccccacctcagcccc -cacctcagccccctcctcagcccccacctcagcccccacctcagcccccacctccgcccc -tcctcagcccccacctcagcccccacctccgcccctcctcagcccccacctcag------ ------------------------------------------------------------- -----------------------------ccccctcctcagcccccacctccgcccccacc -tccgcccccacctctgcccctcctcagcccccacctcagccccctcctcagcccccacct -ccgcccccacctccgcccccacctccgcccctcctccgcccccacctcagcccccacctc -cgccccct----------------------------------cctcagcccccacctctg -cccctcctcagcccccacctcagcccccacctcagcccccacct---------------- ----------cccccctcctcagcccccacctcagcccccacctccgcccctcctcagccc -ccacctccgccccca--------------------------------------------- ---------------cctcagcccccacctcagcccccacctccgcccccacctcagcccc -cacctccgcccccacctcagcccccacctcc-----------gcccccacctcagccccc -acctctgcccctcctcagcccccacctccgccccctcctcagcccccacctctgcccctc -ctcagcccccacctcagcccccacctcagcccccacct---------------------- ----cccccctcctcagccccca-----------------------------------cct -cagcccccacctcagccccctcctcagcccccacctcagcccccacctcagcccccacct -ccgcccctcctcagccccca-----------------------cctcagcccccacctcc -gcccctcctccgcccccacctcagccccctcctcagcccccacctctgcccctcctcagc -ccccacctcagcccccacctccgcccccacctcagccccctcctcagcccccacctc--- -----------------------------------ccccctcctccgcccccacctcagcc -cccacctcagcccccacctcagcccccacctc---------------------------- ------------------------------------------------------------- --------------------ccccctcctccgcccccacctcagccccca----------- -cctcagcccccacctccgcccccacctcagcccccacctcc------------------- ------------------------------------------------------------- ----------------------------cccctcctcagcccccacctcagcccccacctc -cgccccca-----------cctcagcccccacctcagcccccacctcagcccccacctcc -gcccctcctcagcccccacctccgcccccacctcagcccccacctcagcccccacctccg -ccccca------------------------------------------------------ ----------------cctcagcccccacctccgcccccacctcagcccccacctccgccc -ccacctcagcccccacctccgcccccacctccgcccccacctcc-----------gcccc -cacctcagcccccacctcagcccccacctccgccccca---------------------- -------------------------cctcagcccccacctcagcccccacctcagccccca -cctccgcccctcctcagcccccacctcagcccctcctcagcccccacctcagcccccacc -tcagcccccacctcagcccct-------------------------cctcagcccccacc -tcagccccctcctcagccccctcctcagcccccacctcagcccccacctccgcccccacc -tccgcccccacctcagccccacctcagcccctcctcagcccccacctcagccc------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------cctcagcccccacctcagcccccacctccgcccccacctccgcccccacctc -c----------------------------------------------------------- -------------------------gcccctcctcagcccccacctcagcccccacctcag -cccctcctcagcccccacctcc-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------acccccacctccgtccccacctccgccccc -tcctcagccccctcctcagcccccacctcagcccccacctccgcccccacctcagcccct -cctcagcccccacctctgcccccacctcagaccctcctcagcccctcctcagcccctcct -catcccctcctcagcagctgctggaatgggctaccctcaggagtt ->ref_chr20:63167387-63167627 -gatttggagtcactcatggttcccaccagcactcagccccatctcagcccccatctcagc -ccccaccgcagcctcacctcagtgcccacctcagccccctcctcagccccca-------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------cctcagcccccacctccgcccccacctcagcccct -cctcagcccccacctccgcccccacctcaga-----------ccctcctcagcccctcct -catcccctcctcagcagctgctggaatgggctaccctcaggagtt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_22262379b8f485111ebe242896994907.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_22262379b8f485111ebe242896994907.msa deleted file mode 100644 index f0d70212..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_22262379b8f485111ebe242896994907.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:17081016-17081610 -aaaacaacgttgattcagaaatgaagattgggaagaaatatacagagtatgatgctgtgt -aaaattttaaaacaaagaaaatgagactgtgtactttcaatgaatattcttttatgtagt -aaaagtataaaactatggctggtaaaaatgcatgccacattgtggatcatgactacctct -gggtcagaaggaaatgtgatgggtaaaggaatcaactccatgtggaattttattttattt -tattttattttattttattttattttattttattttattttatt---------------- ---------------------------------------------------ttattttatt -ttattacgacaaggtctggctctgtcgcctaggctggagtgcattgtggtaatcttggct -tactgcaacctctgcctcccagactcaaccagtcctcccacctcagcctcccaagtagct -gggactacaagtacgtgccatcacgcctggccaatttttgtattttcagtagagaagggt -ttcaccatgttgcccaggctggtctcgaactcctgggttcaagcaatccaccctt ->syndip_2_chr20:17081016-17081610 -aaaacaacgttgattcagaaatgaagattgggaagaaatatacagagtatgatgctgtgt -aaaattttaaaacaaagaaaatgagactgtgtactttcaatgaatattcttttatgtagt -aaaagtataaaactatggctggtaaaaatgcatgccacattgtggatcatgactacctct -gggtcagaaggaaatgtgatgggtaaaggaatcaactccatgtgga-----attttattt -tattttattttattttattttattttattttattttattttatt---------------- ---------------------------------------------------ttattttatt -ttattacgacaaggtctggctctgtcgcctaggctggagtgcattgtggtaatcttggct -tactgcaacctctgcctcccagactcaaccagtcctcccacctcagcctcccaagtagct -gggactacaagtacgtgccatcacgcctggccaatttttgtattttcagtagagaagggt -ttcaccatgttgcccaggctggtctcgaactcctgggttcaagcaatccaccctt ->p:HG002_1_chr20:17081016-17081610 -aaaacaacgttgattcagaaatgaagattgggaagaaatatacagagtatgatgctgtgt -aaaattttaaaacaaagaaaatgagactgtgtactttcaatgaatattcttttatgtagt -aaaagtataaaactatggctggtaaaaatgcatgccacattgtggatcatgactacctct -gggtcagaaggaaatgtgatgggtaaaggaatcaactccatgtgga-----attttattt -tattttattttattttattttattttattttattttattttatt---------------- ---------------------------------------------------ttattttatt -ttattacgacaaggtctggctctgtcgcctaggctggagtgcattgtggtaatcttggct -tactgcaacctctgcctcccagactcaaccagtcctcccacctcagcctcccaagtagct -gggactacaagtacgtgccatcaagcctggccaatttttgtattttcagtagagaagggt -ttcaccatgttgcccaggctggtctcgaactcctgggttcaagcaatccaccctt ->p:HG002_2_chr20:17081016-17081610 -aaaacaacgttgattcagaaatgaagattgggaagaaatatacagagtatgatgctgtgt -aaaattttaaaacaaagaaaatgagactgtgtactttcaatgaatattcttttatgtagt -aaaagtataaaactatggctggtaaaaatgcatgccacattgtggatcatgactacctct -gggtcagaaggaaatgtgatgggtaaaggaatcaactccatgtggaattttattttattt -tattttattttattttattttattttattttattttattttatt---------------- ---------------------------------------------------ttattttatt -ttattacgacaaggtctggctctgtcgcctaggctggagtgcattgtggtaatcttggct -tactgcaacctctgcctcccagactcaaccagtcctcccacctcagcctcccaagtagct -gggactacaagtacgtgccatcacgcctggccaatttttgtattttcagtagagaagggt -ttcaccatgttgcccaggctggtctcgaactcctgggttcaagcaatccaccctt ->ref_chr20:17081016-17081610 -aaaacaacgttgattcagaaatgaagattgggaagaaatatacagagtatgatgctgtgt -aaaattttaaaacaaagaaaatgagactgtgtactttcaatgaatattcttttatgtagt -aaaagtataaaactatggctggtaaaaatgcatgccacattgtggatcatgactacctct -gggtcagaaggaaatgtgatgggtaaaggaatcaactccatgtggaattttattttattt -tattttattttattttattttattttattttattttattttattattttattttatttta -ttttattttattttattttattttattttattttattttattttattttattattttatt -ttattacgacaaggtctggctctgtcgcctaggctggagtgcattgtggtaatcttggct -tactgcaacctctgcctcccagactcaaccagtcctcccacctcagcctcccaagtagct -gggactacaagtacgtgccatcacgcctggccaatttttgtattttcagtagagaagggt -ttcaccatgttgcccaggctggtctcgaactcctgggttcaagcaatccaccctt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_2307a87b554b16a5508fc630009a1a18.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2307a87b554b16a5508fc630009a1a18.msa deleted file mode 100644 index a03f6cff..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_2307a87b554b16a5508fc630009a1a18.msa +++ /dev/null @@ -1,110 +0,0 @@ ->syndip_1_chr20:63028876-63029402 -tatttcccatgatgactccaaacgcacccgagtcccccgggcctccgcgcctccgtgtgc -aggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcctctccgtgt -gcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgt -gtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctcc -gtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgtct -gtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc -ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc -gtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctcc -gcgtctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct -ccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggc -ctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgg -gcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtccccc -gggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtccc -ccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtc -ccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcagg -tcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgca -ggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtg -caggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtg -tgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccg -tgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctctgcgtctc -tgtgtgcaggctcaagtttgccaacgtccatgcacgtctc ->syndip_2_chr20:63028876-63029402 -tatttcccatgatgactccaaa-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------cgcacccgagtcccccgggcctccgcgcctccgtgtgcagg -tcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgca -ggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtg -caggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctccgtg -tgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccg -tgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcccccgggcccctgcgtctc -tgtgtgcaggctcaagtttgccaacgtccatgcacgtctc ->p:HG002_1_chr20:63028876-63029402 -tatttcccatgatgactccaaa-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------cgcacccgagtcccccgggcctccgcgcctccgtgtgcagg -tcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgca -ggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtg -caggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctccgtg -tgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccg -tgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcccccgggcccctgcgtctc -tgtgtgcaggctcaagtttgccaacgtccatgcacgtctc ->p:HG002_2_chr20:63028876-63029402 -tatttcccatgatgactccaaacgcacccgagtcccccgggcctccgcgcctccgtgtgc -aggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcctctccgtgt -gcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgt -gtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctcc -gtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgtct -gcgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc -ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc -gtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctcc -gcgtctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct -ccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggc -ctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgg -gcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtccccc -gggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtccc -ccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtc -ccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcagg -tcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgca -ggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtg -caggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtg -tgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccg -tgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctctgcgtctc -tgtgtgcaggctcaagtttgccaacgtccatgcacgtctc ->ref_chr20:63028876-63029402 -tatttcccatgatgactccaaa-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------cgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtccc -ccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtc -ccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcagg -tcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgca -ggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtg -caggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtg -tgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccg -tgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcccccgggcctctgcgtctc -tgtgtgcaggctcaagtttgccaacgtccatgcacgtctc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_2366b808d997972e49e20b3ea2af9a22.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2366b808d997972e49e20b3ea2af9a22.msa deleted file mode 100644 index aa6f8423..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_2366b808d997972e49e20b3ea2af9a22.msa +++ /dev/null @@ -1,130 +0,0 @@ ->syndip_1_chr20:63048833-63049612 -ggagccctctctcttgcacttaggtctctggagtgacagggatggccctgccccactgac -ccaggcgttcaccccagagaagcgtgcaggcaggtgagaagcttgtttggacctgaagac -cagcctgagcgaggagagtcttgtgcagacggtttatccaggaggagcccggggagaggg -gggtgggaaaagccacagttttggaggtcagcaaggtcatgtgggggcagactcctcctc -ctcctcctcttcctcctcc---------------------------tcctcctcttcctc -ttcctcctcctcctcctcttcctcttcctcctcctcctcctcttcctcctcctcctcttc -ctcctccccctcctcttcctcctcctcctcttccttctcctcctccttctcctcctcctc -ttcctcctcttcctcttcctcctcctcttcctcctcctcttcctcctcctctttctcctc -ctcttcctcttcctcctcttcctcctcctcttcctcctcctcctcttcctcctcctcctc -ttcctcctcctcctcttcctccttctcttcctcttcctcctcctcttcctcttcctcctc -ctcttcctctttctcctcctcctcctcttcctcttcctcctcc----------------- -----------------------tcttcctctttctcctcctcctcctcttcctcctcttc -ctcctcctcttcctcctcctcctcctcttcctcctcctcctcgtcttcctccttctcctc -ttcctcctcttcctcttcctcctcctcttcctcttcctcttcctcttcctcttcctcctc -ctcctcctctttctcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttc -ctcctcctcctcttcctcctcttcctcctcctcctcttcctcctcttcttcctcctcttc -ctcctcctcctcttcctcctcttcctcctcctcttcctcctcctcctcttcctcctcctc -ctcttcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcctc -ttcctcctcctcctcctcttcctcccctcctcctcctcttcctcctcctcctcttcctcc -cctcctcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctcttcctc -ctcgtcctcttcctccttctgccaggacccttcttccaggacccctgagaagcgcataga -atagcgtccaggactgtctgccccaggcacgctgaccactggctccactcccctgggcaa -gggtcgcccctgggctgctgcctcccagcgacacaggcaggacccagaagcctggtagaa -agtgaccatgtgtggcaggtacaagaggccgagtgcggtcaacttgaagggacaggaagc -ctgcaggcagtgaccactctctaggctgtgctcagaggagaggccaaggggacacaggc ->syndip_2_chr20:63048833-63049612 -ggagccctctctcttgcacttaggtctctggagtgacagggatggccctgccccactgac -ccaggcgttcaccccagagaagcgtgcaggcaggtgagaagcttgtttggacctgaagac -cagcctgagcgaggagagtcttgtgcagacggtttatccaggaggagcccggggagaggg -gggtgggaaaagccacagttttggaggtcagcaaggtcatgtgggggcagactcctcctc -ctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcttcctcctcctcctc -ctcttcctcttcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttc -ctcctccccctcctcttcctcctcctcctcttcctcctcctcctccttctcctcctcctc -ttcctcctcttcctcttcctcctcctcttcctcctcctctttctcctcctcttcctcttc -ctcctcttcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcctc -ctcttcctcctcctcttcctccttctcttcctcttcctcctcctcttcctcttcctcctc -ctcttcctctttctcctcctcctcctcttcctcctcttcctcctcctcttcctcctcctc -ctcctcttcctcctcctcctcgtcttcctccttctcctcttcctcctcttcctcttcctc -ctcctcttcctcttcctcttcctcttcctcctcctcctcctcttcctcctcctcctcctc -ttcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcctcctc -ttcctcctcttcctcctcctcctcttcctcctcttcttcctcctcttcctcctcctcctc -ttcctcctcttcctcctcctcttcctcctcctcctcttcctcctcctcttcctcctcttc -ttcctcctcttcctcctcctcctcttcctcctcttcctcctcctcttcctcctcctcctc -ctcttcctcc-cctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcctc -ttcctcctcctcctcctcttcctcccctcctcctcctcttcctcctcctcctcttcctcc -cctcctcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctcttcctc -ctcgtcctcttcctccttctgccaggacccttcttccaggacccctgagaagcgcataga -atagcgtccaggactgtctgccccaggcacgctgaccactggctccactcccctgggcaa -gggtcgcccctgggctgctgcctcccagcgacacaggcaggacccagaagcctggtagaa -agtgaccatgtgtggcaggtacaagaggccgagtgcggtcaacttgaagggacaggaagc -ctgcaggcagtgaccactctctaggctgtgctcagaggagaggccaaggggacacaggc ->p:HG002_1_chr20:63048833-63049612 -ggagccctctctcttgcacttaggtctctggagtgacagggatggccctgccccactgac -ccaggcgttcaccccagagaagcgtgcaggcaggtgagaagcttgtttggacctgaagac -cagcctgagcgaggagagtcttgtgcagacggtttatccaggaggagcccggggagaggg -gggtgggaaaagccacagttttggaggtcagcaaggtcatgtgggggcagactcctcctc -ctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcttcctcctcctcctc -ctcttcctcttcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttc -ctcctccccctcctcttcctcctcctcctcttcctcctcctcctccttctcctcctcctc -ttcctcctcttcctcttcctcctcctcttcctcctcctctttctcctcctcttcctcttc -ctcctcttcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcctc -ctcttcctcctcctcttcctccttctcttcctcttcctcctcctcttcctcttcctcctc -ctcttcctctttctcctcctcctcctcttcctcctcttcctcctcctcttcctcctcctc -ctcctcttcctcctcctcctcgtcttcctccttctcctcttcctcctcttcctcttcctc -ctcctcttcctcttcctcttcctcttcctcctcctcctcctcttcctcctcctcctcctc -ttcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcctcctc -ttcctcctcttcctcctcctcctcttcctcctcttcttcctcctcttcctcctcctcctc -ttcctcctcttcctcctcctcttcctcctcctcctcttcctcctcctcttcctcctcttc -ttcctcctcttcctcctcctcctcttcctcctcttcctcctcctcttcctcctcctcctc -ctcttcctcc-cctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcctc -ttcctcctcctcctcctcttcctcccctcctcctcctcttcctcctcctcctcttcctcc -cctcctcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctcttcctc -ctcgtcctcttcctccttctgccaggacccttcttccaggacccctgagaagcgcataga -atagcgtccaggactgtctgccccaggcacgctgaccactggctccactcccctgggcaa -gggtcgcccctgggctgctgcctcccagcgacacaggcaggacccagaagcctggtagaa -agtgaccatgtgtggcaggtacaagaggccgagtgcggtcaacttgaagggacaggaagc -ctgcaggcagtgaccactctctaggctgtgctcagaggagaggccaaggggacacaggc ->p:HG002_2_chr20:63048833-63049612 -ggagccctctctcttgcacttaggtctctggagtgacagggatggccctgccccactgac -ccaggcgttcaccccagagaagcgtgcaggcaggtgagaagcttgtttggacctgaagac -cagcctgagcgaggagagtcttgtgcagacggtttatccaggaggagcccggggagaggg -gggtgggaaaagccacagttttggaggtcagcaaggtcatgtgggggcagactcctcctc -ctcctcctcttcctcctcc---------------------------tcctcctcttcctc -ttcctcctcctcctcctcttcctcttcctcctcctcctcctcttcctcctcctcctcttc -ctcctccccctcctcttcctcctcctcctcttccttctcctcctccttctcctcctcctc -ttcctcctcttcctcttcctcctcctcttcctcctcctcttcctcctcctctttctcctc -ctcttcctcttcctcctcttcctcctcctcttcctcctcctcctcttcctcctcctcctc -ttcctcctcctcctcttcctccttctcttcctcttcctcctcctcttcctcttcctcctc -ctcttcctctttctcctcctcctcctcttcctcttcctcctcc----------------- -----------------------tcttcctctttctcctcctcctcctcttcctcctcttc -ctcctcctcttcctcctcctcctcctcttcctcctcctcctcgtcttcctccttctcctc -ttcctcctcttcctcttcctcctcctcttcctcttcctcttcctcttcctcttcctcctc -ctcctcctctttctcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttc -ctcctcctcctcttcctcctcttcctcctcctcctcttcctcctcttcttcctcctcttc -ctcctcctcctcttcctcctcttcctcctcctcttcctcctcctcctcttcctcctcctc -ctcttcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcctc -ttcctcctcctcctcctcttcctcccctcctcctcctcttcctcctcctcctcttcctcc -cctcctcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctcttcctc -ctcgtcctcttcctccttctgccaggacccttcttccaggacccctgagaagcgcataga -atagcgtccaggactgtctgccccaggcacgctgaccactggctccactcccctgggcaa -gggtcgcccctgggctgctgcctcccagcgacacaggcaggacccagaagcctggtagaa -agtgaccatgtgtggcaggtacaagaggccgagtgcggtcaacttgaagggacaggaagc -ctgcaggcagtgaccactctctaggctgtgctcagaggagaggccaaggggacacaggc ->ref_chr20:63048833-63049612 -ggagccctctctcttgcacttaggtctctggagtgacagggatggccctgccccactgac -ccaggcgttcaccccagagaagcgtgcaggcaggtgagaagcttgtttggacctgaagac -cagcctgagcgaggagagtcttgtgcagacggtttatccaggaggagcccggggagaggg -gggtgggaaaagccacagttttggaggtcagcaaggtcatgtgggggcagactcctcctc -ctcctcctcttcctcctcc---------------------------tcctcttcctcctc -ctcctcttcctcttcctcctcctcctcctcttcctcctcctcctcctcttcctc------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------cctcctcttcctcctcctcctcttcctcctcctc -ttcctcctcctcctcctcttcctcccctcctcctcctcttcctcctcctcctcttcctct -cctcctcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctcttcctc -ctcgtcctcttcctccttctgccaggacccttcttccaggacccctgagaagcgcataga -atagcgtccaggactgtctgccccaggcacgctgaccactggctccactcccctgggcaa -gggtcgcccctgggctgctgcctcccagcgacacaggcaggacccagaagcctggtagaa -agtgaccatgtgtggcaggtacaagaggccgagtgcggtcaacttgaagggacaggaagc -ctgcaggcagtgaccactctctaggctgtgctcagaggagaggccaaggggacacaggc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_2404771658108744496a59df4a81aa48.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2404771658108744496a59df4a81aa48.msa deleted file mode 100644 index 10546aa5..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_2404771658108744496a59df4a81aa48.msa +++ /dev/null @@ -1,175 +0,0 @@ ->syndip_1_chr20:20337185-20337724 -tggaaataaggaaacagggtttaggaaggcctcactagacctgttaggatggatgcatgg -atggatggatggatggacagaatgggtgggtggatggatggatggatggatggatggatg -gatagatgggtgggtggatggatggatggatagatgggtggatggatagatgggtggatg -gataaatggatggatggatggatggatagatgggtgggtagatggatggatggatggatg -gatggatggatggatggatggatggatagatgggtgggtgggtggatggatggatggatg -gatggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatg -ggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatggata -gatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatg -gatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggata -gatgggtggatggataaatggatggatggatggatggatagatgggtgggtggatggatg -gatggatggatggatggatggatggatagatagatggatagatgggtgggtggatggatg -gatggatggatggatggatggatggatggatagatgggtggatggatggatagatgggtg -ggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatg -gatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggata -gatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatg -gatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatg -gatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatg -gatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatg -gatggatggatggatggatggatagatgggtgggtggatggatggatggatagatgggtg -ggtggatggatggatggatggatggatggatggatggatggatagatggatagatgggtg -ggtggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatg -ggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggata -gatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatg -ggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggtg -ggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatg -ggtgggtggatggatggatggatggatggatagatggatagatgggtgggtggatggatg -gatggatagatgggtgggtggatggatggatggatggatggatggatggatggatggata -gatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatg -gatagatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtg -gatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatg -gatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtg -gatggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtg -ggtggatggatggatggatagatgggtgggtgggtggatggatggatggatggatagaat -aaaaaagaaagctaggacatggttctagtgttcttagcagac ->syndip_2_chr20:20337185-20337724 -tggaaataaggaaacagggtttaggaaggcctcactagacctgttaggatggatgcatgg -atggatggatggatggacagaatgggtgggtggatggatggatggatggatggatggatg -gatggatagatgggtgggtggatggatggatggatagatgggtggatggataaatggatg -gatggatggatggatagatgggtgggtaga----tggatggatggatggatggatggatg -gatggatggatggatggatagatgggtgggtgggtggatggatggatggatggatggatg -gatggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatg -ggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatggata -gatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatg -gatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggata -gatgggtggatggataaatggatggatggatggatggatagatgggtgggtggatggatg -gatggatggatggatggatggatggataga----------------tgggtgggtggatg -gatggatggatggatggatggatggatggatagatgggtggatggatggatagatgggtg -ggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatg -gatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggata -gatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatg -gatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatg -gatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatg -gatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatg -gatggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtg -gg----tggatggatggatggatggatggatggatggatggatagatggatagatgggtg -ggtggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatg -ggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggata -gatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggata---- -----------------gatggatagatgggtgggtggatggatggatggatagatgggtg -ggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatg -ggtgggtggatggatg----------------gatggatagatgggtgggtgggtggatg -gatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatg -gatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatg -gatggatagatgggtgggtgggtggatggatggatggatggataga-------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------------at -aaaaaagaaagctaggacatggttctagtgttcttagcagac ->p:HG002_1_chr20:20337185-20337724 -tggaaataaggaaacagggtttaggaaggcctcactagacctgttaggatggatgcatgg -atggatggatggatggacagaatgggtgggtggatggatggatggatagatggatggatg -gatggatggatggatggatggatggatggatggatagatgggtgggtgggtggatggatg -gatggatggatggatggatggatggatgga----tggatagatgggtgggtggatggatg -gatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatg -gatggatggatagatgggtggatggataaatggatggatggatggatggatagatgggtg -ggtggatggatggatggatggatggatggatggatggatagatggatggatagatggata -gatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatg -gatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggata -gatgggtggatggataaatggatggatggatggatggatagatgggtgggtggatggatg -gatggatggatggatggatagatggataga----------------tgggtgggtggatg -gatggatggatggatggatggatggatggatagatgggtggatggatggatagatgggtg -ggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatg -gatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggata -gatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatg -gatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatg -gatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatg -gatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatg -gatggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtg -gg----tggatggatggatggatggatggatggatggatggatagatggatagatgggtg -ggtggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatg -ggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggata -gatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggata---- -----------------gatggatagatgggtgggtggatggatggatggatagatgggtg -ggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatg -ggtgggtggatggatg----------------gatggatagatgggtgggtgggtggatg -gatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatg -gatagatggatgggtggatggatggatggatagatgggtgggtgggtggatggatggatg -gatggatagatgggtgggtgggtggatggatggatggatggataga-------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------------at -aaaaaagaaagctaggacatggttctagtgttcttagcagac ->p:HG002_2_chr20:20337185-20337724 -tggaaataaggaaacagggtttaggaaggcctcactagacctgttaggatggatgcatgg -atggatggatggatggacagaatgggtgggtggatggatggatggatggatggatggatg -gatagatgggtgggtggatggatggatggatagatgggtggatggatagatgggtggatg -gataaatggatggatggatggatggatagatgggtgggtggatggatggatggatggatg -gatggatggatggatggatagatggatagatgggtgggtggatggatggatggatggatg -gatggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatg -ggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatggata -gatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatg -gatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggata -gatgggtggatggataaatggatggatggatggatggatagatgtgtgggtggatggatg -gatggatggatggatggatggatggatggatagatggatagatgggtgggtggatggatg -gatggatggatggatggatggatggatggatagatgggtggatggatggatagatgggtg -ggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatg -gatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggata -gatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatg -gatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatg -gatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatg -gatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatg -gatggatggatggatggatggatagatgggtgggtggatggatggatggatagatgggtg -ggtggatggatggatggatggatggatggatggatggatggatagatggatagatgggtg -ggtggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatg -ggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggata -gatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatg -ggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggtg -ggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatg -ggtgggtggatggatggatggatggatggatagatggatagatgggtgggtggatggatg -gatggatagatgggtgggtggatagatggatggatggatggatggatggatggatggatg -gatggatggatagatgggtgggtgggtggatggatggatggatggatggatggatggatg -gatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtg -gatggatggatggatagatgggtgggtggatggatggatggatagatgggtggatggata -aatggatggatggatggatggatagatgggtgggtggatggatggatggatggatggatg -gatggatggatagatagatgggtgggtggatggatggatggatagatgggtgggtgggtg -gatggatggatggatggatagatgggtgggtgggtggatggatggatggatggatagaat -aaaaaagaaagctaggacatggttctagtgttcttagcagac ->ref_chr20:20337185-20337724 -tggaaataaggaaacagggtttaggaaggcctcactagacctgttaggatggatgcatgg -atggatggatggatggacagaatgggtgggtggatggatggatggatagatggatggatg -gatggatggatggatggatggatggatggatggatagatgggtgggtgggtggatggatg -gatggatggatggatggatggatggatgga----tggatagatgggtgggtggatggatg -gatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatg -gatggatggatagatgggtggatggataaatggatggatggatggatggatagatgggtg -ggtggatggatggatggatggatggatggatggatggatagat----------------- ------gtgggtggatggatggatggatagatgggtgggtgggtggatggatggatggatg -gatagatgggtgggtgggtggatggatggatggatggataga------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------------at -aaaaaagaaagctaggacatggttctagtgttcttagcagac diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_240f283b24b9659724b35b5aedc0d5c1.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_240f283b24b9659724b35b5aedc0d5c1.msa deleted file mode 100644 index db212aa6..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_240f283b24b9659724b35b5aedc0d5c1.msa +++ /dev/null @@ -1,275 +0,0 @@ ->syndip_1_chr20:63491389-63493264 -ggctactgggtctccaccctcacctcccagggctgtgagggaggcctgttgtagcctcca -gccaacttcactgaggccagtggctgtgctctgtgctggggtgagcatgatgcccccaca -gtgcacacagagatgcctgcaacatctttggctgcagcccactggctgggggtctcctat -cagtgcccttctctagggtctcagatttgtttatggtttctcttcttggtgggatggatg -gatggatggacggatggatggggaggtgggtggatggatggatggatgtatgaatggggt -ggtagatggatggggaggtggatggacagaaggatgggtggggagatggatgagtaggga -gatggatggatggattggtggatggatggatggatggatggatgaggaggtagatgagtg -gatggacagaaggatggatgggtaggaaggtgggtggatgaatggatggatggggaggtg -gatggatagatggatggatggatggatggatggatggatggatggatggggggatagatg -gatggatggatggatggatggacggacg----gatggggaggtggatggatggatggatg -gatggatggatggatggatgaggagatgaatggatggatgagatggatggatggatgatg -gagggaaggatggctgggtggggagatggatggatagagaggtggatgggtggatgggga -gatggatggatggatggatggatggggaagtggatggatggggaggtggatggatggata -ggtggatgggtggatggacagaaggatgaatgggtagggagatggatggatggatggatg -gggagggatggatggatggatggatggatgggtggatggatagaaggatggatgggtggg -gaggtgggtgggtgg----gtggatggatggagagatggatagatggata----gatgga -tggatggatggatggatggagagaaggatggatgggtggggaggtgggtgggtgggtgga -tgggtggatggatggatgggtggggaggtgggcgggtggatggatggatggatgcagagg -tgggtggatggatggatggagagaaggatggatgggtggggaggtgggtgggtggatgga -tggatgagtggggaggtgggtgggtgggtggatggatggatggatggatgcatggatgga -tgga-------------------------------------------------------- ------------------------------------------------------------t -ggagaggtgggtggacggatggatggattgggaggtgggtagatgggtggatggacagaa -ggatggatgggtggggaggtgggtgggtgggtggatggatggatggggaggtggatggat -ggatggttagatggggaggtgggtggatgggtggatggacagaaggatggatgggtaggg -aggtaggtgagtggatggatggatggggagatggatggatggatagagagaaggatggat -gggtgggacaatggatggatggatggatagaaggatggacgggtggggagatggatggat -ggatggatggatggatggatggatggacagaaggatgtatgggtggggaggtgggtggat -agatggatggatggatggatggggaaatggatggatggaaggatggatggatagggaggt -gggtggatggatggatggatggatgtacagaaggatggatgggtggggaggtgggtgagt -ggatgaatggatggatggatagatagaaggatggatgggtgggacaatagatggatggat -agagagaaggatggatgggtggggagatggatggatggatggatggatggatggatggat -ggatggatagagagaaggatggatggttgagaca----atggatggatggatggatggag -agatggatggatggacggatggacagaaggatggatgggtggggaggtggatggatggat -tgaaggatggatgggtgggga----catggatggatggatggatggatggatggatggat -ggacagaaggatgtatgggtggggaggtgggtggata--------gatggatggatgggg -aaatggatggatggaaggatggatggatagggaggtgggtggatggatggatggatggat -gtacagaaggatggatgggtggggaggtgggtgagtggatgaatggatggatggatagat -agaaggatggatgggtgggacaatagatggatggatagagagaaggatggatgggtgggg -agatggatggatggatggatggatggatggatagagagaaggatggatggttgagacaat -ggatggatggatggatggatggagagatggatggatggatggatggacagaaggatggat -gggtggggaggtggatggatggatggaaggatggatggatggatagagagaaggatggat -gggtgggacaatggatggatggatgcatggatggatggatggagggatagagagaaggat -ggatgggtgggacaatcaatggatggatggatggatggatggatagagagaaggatggat -gggtggggagatggatggatggatggagaggtggatggatggatggatggatggattgat -ggacagaaggatggatgggtggggaggtggatagatggagagatggagggatggttcgat -agagagaaggatggatggatgggacaatggatggatggatggatggagtgaaggatggat -gggtggggagatggatggatcgatggatggatggatggatagatagatggatggagaggt -ggatagatggatgggtggatggatggacagaggatggatgggtggggaggtgggtggatg -gatggatggatgtgggatggactgtcccacagaaagtgtgtggtaaggggagagattgga -gacagcccagtcttgagatgccttgtaggggcccctggtctagggcaggcagagctggcc -aggcaggagctccagcacagcgcccttgctcaccgccaatcttgtacacgtcctgcagcg -gcaggcgcaggggcttgtccgtggggcgcgtggggggcaggatggtgtccagggcctcca -gcagggacacgccgcttgcgttgccctccttacgctccacc ->syndip_2_chr20:63491389-63493264 -ggctactgggtctccaccctcacctcccagggctgtgagggaggcctgttgtagcctcca -gccaacttcactgaggccagtggctgtgctctgtgctggggtgagcatgatgcccccaca -gtgcacacagagatgcctgcaacatctttggctgcagcccactggctgggggtctcctat -cagtgcccttctctagggtctcagatttgtttatggtttctcttcttggtgggatggatg -gatggatggacggatggatggggaggtgggtggatggatggatggatgtatgaatggggt -ggtagatggatggggaggtggatggacagaaggatgggtggggagatggatgagtaggga -gatggatggatggattggtggatggatggatggatggatggatgaggaggtagatgagtg -gatggacagaaggatggatgggtaggaaggtgggtggatgaatggatggatggggaggtg -gatggatagatggatggatggatggatggatggatggatggatggatggggggatagatg -gatggatggatggatggacggacggatggggaggtggatggatggatggatggatggatg -gatggatggatggatggatgaggagatgaatggatggatgagatggatggatggatgatg -gagggaaggatggctgggtggggagatggatggatagagaggtggatgggtggatgggga -gatggatggatggatggatggatggggaagtggatggatggggaggtggatggatggata -ggtggatgggtggatggacagaaggatgaatgggtagggagatggatggatggatggatg -cggagggatggatggatggatggatggatgggtggatggatagaaggatggatgggtggg -gaggtgggtgggtgggtgcgtggatggatggagagatggatagatggatagatggatgga -tggatggatggatggatggagagaaggatggatgggtggggaggtgggtgggtgggtgga -tgggtggatggatggatgggtggggaggtgggcgggtggatggatggatggatgcagagg -tgggtggatggatggatggagagaaggatggatgggtggggaggtgggtgggtggatgga -tggatgagtggggaggtgggtgggtggatggatggatggatggatgcatggatggatgga -tggagaggtgggtggatgggtggatggacagaaggatggatgggtggggaggtgggtgag -tgggtggatggatgaatggggaggtggatggatggatggatggatgaaggatggatgggt -ggggaggtgggtggacggatggatggattgggaggtgggtagatgggtggatggacagaa -ggatggatgggtggggaggtgggtgggtgggtggatggatggatggggaggtggatggat -ggatggttagatggggaggtgggtggatgggtggatggacagaaggatggatgggtaggg -aggtaggtgagtggatggatggatggggagatggatggatggatagagagaaggatggat -gggtgggacaatggatggatggatggatagaaggatggacgggtgggga----gatggat -ggatggatggatggatggatggatggacagaaggatgtatgggtggggaggtgggtggat -agatggatggatggatggatggggaaatggatggatggaaggatggatggatagggaggt -gggtggatggatggatggatggatgtacagaaggatggatgggtggggaggtgggtgagt -ggatgaatggatggatggatagatagaaggatggatgggtgggacaatagatggatggat -agagagaaggatggatgggtgggga--------gatggatggatggatggatggatggat -ggatggatagagagaaggatggatggttgagacaatggatggatggatggatggatggag -agatggatggatggatggatggacagaaggatggatgggtggggaggtggatggatggat -tgaaggatggacgggtggggagatggatggatggatggatggatggatggatggatggat -ggacagaaggatgtatgggtggggaggtgggtggatagatggatggatggatggatgggg -aaatggatggatggaaggatggatggatagggaggtgggtggatggatggatggatggat -gtacagaaggatggatgggtggggaggtgggtgagtggatgaatggatggatggatagat -agaaggatggatgggtgggacaaca----gatggatagagagaaggatggatgggtgggg -a----gatggatggatggatggatggatggatagagagaaggatggatggttgagacaat -ggatggatggatggatggatggagagatggatggatggatggatggacagaaggatggat -gggtggggaggtggatggatggatggaaggatggatggatggatagagagaaggatggat -gggtgggacaatggatggatggatgcatggatggatggatggagggatagagagaaggat -ggatgggtgggacaatcaatggatggatggatggatggatggatagagagaaggatggat -gggtggggagatggatggatggatggagaggtggatggatggatggatggatggattgat -ggacagaaggatggatgggtggggaggtggatagatggagagatggagggatggttcgat -agagagaaggatggatggatgggacaatggatggatggatggatggagtgaaggatggat -gggtggggagatggatggatcgatggatggatggatggatagatagatggatggagaggt -ggatagatggatgggtggatggatggacagaggatggatgggtggggaggtgggtggatg -gatggatggatgtgggatggactgtcccacagaaagtgtgtggtaaggggagagattgga -gacagcccagtcttgagatgccttgtaggggcccctggtctagggcaggcagagctggcc -aggcaggagctccagcacagcgcccttgctcaccgccaatcttgtacacgtcctgcagcg -gcaggcgcaggggcttgtccgtggggcgcgtggggggcaggatggtgtccagggcctcca -gcagggacacgccgcttgcgttgccctccttacgctccacc ->p:HG002_1_chr20:63491389-63493264 -ggctactgggtctccaccctcacctcccagggctgtgagggaggcctgttgtagcctcca -gccaacttcactgaggccagtggctgtgctctgtgctggggtgagcatgatgcccccaca -gtgcacacagagatgcctgcaacatctttggctgcagcccactggctgggggtctcctat -cagtgcccttctctggggtctcagatttgtttatggtttctcttcttggtgggatggatg -gatggatggacggatggatggggaggtgggtggatggatggatggatgtatgaatggggt -ggtagatggatggggaggtggatggacagaaggatgggtggggagatggatgagtaggga -gatggatggatggattggtggatggatggatggatggatggatgaggaggtagatgagtg -gatggacagaaggatggatgggtaggaaggtgggtggatgaatggatggatggggaggtg -gatggatagatggatggatggatggatggatggatggatggatggatggggggatagatg -gatggatggatggatggacggacggatggggaggtggatggatggatggatggatggatg -gatggatggatggatggatgaggagatgaatggatggatgagatggatggatggatgatg -gagggaaggatggctgggtggggagatggatggatagagaggtggatgggtggatgggga -gatggatggatggatggatggatggggaagtggatggatggggaggtggatggatggata -ggtggatgggtggatggacagaaggatgaatgggtagggagatggatggatggatggatg -cggagggatggatggatggatggatggatgggtggatggatagaaggatggatgggtggg -gaggtgggtgggtgggtgcgtggatggatggagagatggatagatggatagatggatgga -tggatggatggatggatggagagaaggatggatgggtggggaggtgggtgggtgggtgga -tgggtggatggatggatgggtggggaggtgggcgggtggatggatggatggatgcagagg -tgggtggatggatggatggagagaaggatggatgggtggggaggtgggtgggtggatgga -tggatgagtggggaggtgggtgggtggatggatggatggatggatgcatggatggatgga -tggagaggtgggtggatgggtggatggacagaaggatggatgggtggggaggtgggtgag -tgggtggatggatgaatggggaggtggatggatggatggatggatgaaggatggatgggt -ggggaggtgggtggacggatggatggattgggaggtgggtagatgggtggatggacagaa -ggatggatgggtggggaggtgggtgggtgggtggatggatggatggggaggtggatggat -ggatggttagatggggaggtgggtggatgggtggatggacagaaggatggatgggtaggg -aggtaggtgagtggatggatggatggggagatggatggatggatagagagaaggatggat -gggtgggacaatggatggatggatggatagaaggatggacgggtgggga----gatggat -ggatggatggatggatggatggatggacagaaggatgtatgggtggggaggtgggtggat -agatggatggatggatggatggggaaatggatggatggaaggatggatggatagggaggt -gggtggatggatggatggatggatgtacagaaggatggatgggtggggaggtgggtgagt -ggatgaatggatggatggatagatagaaggatggatgggtgggacaatagatggatggat -agagagaaggatggatgggtgggga--------gatggatggatggatggatggatggat -ggatggatagagagaaggatggatggttgagacaatggatggatggatggatggatggag -agatggatggatggatggatggacagaaggatggatgggtggggaggtggatggatggat -tgaaggatggacgggtggggagatggatggatggatggatggatggatggatggatggat -ggacagaaggatgtatgggtggggaggtgggtggatagatggatggatggatggatgggg -aaatggatggatggaaggatggatggatagggaggtgggtggatggatggatggatggat -gtacagaaggatggatgggtggggaggtgggtgagtggatgaatggatggatggatagat -agaaggatggatgggtgggacaaca----gatggatagagagaaggatggatgggtgggg -a----gatggatggatggatggatggatggatagagagaaggatggatggttgagacaat -ggatggatggatggatggatggagagatggatggatggatggatggacagaaggatggat -gggtggggaggtggatggatggatggaaggatggatggatggatagagagaaggatggat -gggtgggacaatggatggatggatgcatggatggatggatggagggatagagagaaggat -ggatgggtgggacaatcaatggatggatggatggatggatggatagagagaaggatggat -gggtggggagatggatggatggatggagaggtggatggatggatggatggatggattgat -ggacagaaggatggatgggtggggaggtggatagatggagagatggagggatggttcgat -agagagaaggatggatggatgggacaatggatggatggatggatggagtgaaggatggat -gggtggggagatggatggatcgatggatggatggatggatagatagatggatggagaggt -ggatagatggatgggtggatggatggacagaggatggatgggtggggaggtgggtggatg -gatggatggatgtgggatggactgtcccacagaaagtgtgtggtaaggggagagattgga -gacagcccagtcttgagatgccttgtaggggcccctggtctagggcaggcagagctggcc -aggcaggagctccagcacagcgcccttgctcaccgccaatcttgtacacgtcctgcagcg -gcaggcgcaggggcttgtccgtggggcgcgtggggggcaggatggtgtccagggcctcca -gcagggacacgccgcttgcgttgccctccttacgctccacc ->p:HG002_2_chr20:63491389-63493264 -ggctactgggtctccaccctcacctcccagggctgtgagggaggcctgttgtagcctcca -gccaacttcactgaggccagtggctgtgctctgtgctggggtgagcatgatgcccccaca -gtgcacacagagatgcctgcaacatctttggctgcagcccactggctgggggtctcctat -cagtgcccttctctggggtctcagatttgtttatggtttctcttcttggtgggatggatg -gatggatggacggatggatggggaggtgggtggatggatggatggatgtatgaatggggt -ggtagatggatggggaggtggatggacagaaggatgggtggggagatggatgagtaggga -gatggatggatggattggtggatggatggatggatggatggatgaggaggtagatgagtg -gatggacagaaggatggatgggtaggaaggtgggtggatgaatggatggatggggaggtg -gatggatagatggatggatggatggatggatggatggatggatggatggggggatagatg -gatggatggatggatggatggacggacg----gatggggaggtggatggatggatggatg -gatggatggatggatggatgaggagatgaatggatggatgagatggatggatggatgatg -gagggaaggatggctgggtggggagatggatggatagagaggtggatgggtggatgggga -gatggatggatggatggatggatggggaagtggatggatggggaggtggatggatggata -ggtggatgggtggatggacagaaggatgaatgggtagggagatggatggatggatggatg -gggagggatggatggatggatggatggatgggtggatggatagaaggatggatgggtggg -gaggtgggtgggtgg----gtggatggatggagagatggatagatggata----gatgga -tggatggatggatggatggagagaaggatggatgggtggggaggtgggtgggtgggtgga -tgggtggatggatggatgggtggggaggtgggcgggtggatggatggatggatgcagagg -tgggtggatggatggatggagagaaggatggatgggtggggaggtgggtgggtggatgga -tggatgagtggggaggtgggtgggtgggtggatggatggatggatggatgcatggatgga -tgga-------------------------------------------------------- ------------------------------------------------------------t -ggagaggtgggtggacggatggatggattgggaggtgggtagatgggtggatggacagaa -ggatggatgggtggggaggtgggtgggtgggtggatggatggatggggaggtggatggat -ggatggttagatggggaggtgggtggatgggtggatggacagaaggatggatgggtaggg -aggtaggtgagtggatggatggatggggagatggatggatggatagagagaaggatggat -gggtgggacaatggatggatggatggatagaaggatggacgggtggggagatggatggat -ggatggatggatggatggatggatggacagaaggatgtatgggtggggaggtgggtggat -agatggatggatggatggatggggaaatggatggatggaaggatggatggatagggaggt -gggtggatggatggatggatggatgtacagaaggatggatgggtggggaggtgggtgagt -ggatgaatggatggatggatagatagaaggatggatgggtgggacaatagatggatggat -agagagaaggatggatgggtggggagatggatggatggatggatggatggatggatggat -ggatggatagagagaaggatggatggttgagaca----atggatggatggatggatggag -agatggatggatggacggatggacagaaggatggatgggtggggaggtggatggatggat -tgaaggatggatgggtgggga----catggatggatggatggatggatggatggatggat -ggacagaaggatgtatgggtggggaggtgggtggata--------gatggatggatgggg -aaatggatggatggaaggatggatggatagggaggtgggtggatggatggatggatggat -gtacagaaggatggatgggtggggaggtgggtgagtggatgaatggatggatggatagat -agaaggatggatgggtgggacaatagatggatggatagagagaaggatggatgggtgggg -agatggatggatggatggatggatggatggatagagagaaggatggatggttgagacaat -ggatggatggatggatggatggagagatggatggatggatggatggacagaaggatggat -gggtggggaggtggatggatggatggaaggatggatggatggatagagagaaggatggat -gggtgggacaatggatggatggatgcatggatggatggatggagggatagagagaaggat -ggatgggtgggacaatcaatggatggatggatggatggatggatagagagaaggatggat -gggtggggagatggatggatggatggagaggtggatggatggatggatggatggattgat -ggacagaaggatggatgggtggggaggtggatagatggagagatggagggatggttcgat -agagagaaggatggatggatgggacaatggatggatggatggatggagtgaaggatggat -gggtggggagatggatggatcgatggatggatggatggatagatagatggatggagaggt -ggatagatggatgggtggatggatggacagaggatggatgggtggggaggtgggtggatg -gatggatggatgtgggatggactgtcccacagaaagtgtgtggtaaggggagagattgga -gacagcccagtcttgagatgccttgtaggggcccctggtctagggcaggcagagctggcc -aggcaggagctccagcacagcgcccttgctcaccgccaatcttgtacacgtcctgcagcg -gcaggcgcaggggcttgtccgtggggcgcgtggggggcaggatggtgtccagggcctcca -gcagggacacgccgcttgcgttgccctccttacgctccacc ->ref_chr20:63491389-63493264 -ggctactgggtctccaccctcacctcccagggctgtgagggaggcctgttgtagcctcca -gccaacttcactgaggccagtggctgtgctctgtgctggggtgagcatgatgcccccaca -gtgcacacagagatgcctgcaacatctttggctgcagcccactggctgggggtctcctat -cagtgcccttctctagggtctcagatttgtttatggtttctcttcttggtgggatggatg -gatggatggacggatggatggggaggtgggtggatggatggatggatgtatgaatggggt -ggtagatggatggggaggtggatggacagaaggatgggtggggagatggatgagtaggga -gatggatggatggattggtggatggatggatggatggatggatgaggaggtagatgagtg -gatggacagaaggatggatgggtaggaaggtgggtggatgaatggatggatggggaggtg -gatggata----gatggatggatggatggatggatggatggatggatggggggatagatg -gatggatggatggatggacggacggatggggaggtggatggatggatggatggatggatg -gatggatggatggatggatgaggagatgaacggatggatgagatggatggatggatgatg -gagggaaggatggctgggtggggagatggatggatagagaggtggatgggtggatgggga -gatggatggatggatggatggatggggaagtggatggatggggaggtggatggat----- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------ggatgtatgggtgggtaggtgggtggat -agatggatg--------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------gatggatggatggat -aaatggatggatggaaggatggatggataggtaggtgggtggatggatggatggatggat -gtacagaaggatggatgggtgggtaggtgggtgagtggatgaatggatggatggatagat -agaaggatggatgggtgggtcaatagatggatggatagagagaaggatggatgggtgggt -a----gatggatggatggatggatggatggatagagagaaggatggatggttgagacaat -ggatggatggatggatggatggagagatggatggatggatggatggacagaaggatggat -gggtggggaggtggatggatggatggaaggatggatggatggatagagagaaggatggat -gggtgggacaatggatggatggatgcatggatggatggatggagggatagagagaaggat -ggatgggtgggacaatcaatggatggatggatggatggatggatagagagaaggatggat -gggtggggagatggatggatggatggagaggtggatggatggatggatggatggattgat -ggacagaaggatggatgggtggggaggtggatagatggagagatggagggatggttcgat -agagagaa----ggatggatgggacaatggatggatggatggatggagtgaaggatggat -gggtggggagatggatggatcgatggatggatggatggatagatagatggatggagaggt -ggatagatggatgggtggatggatggacagaggatggatgggtggggaggtgggtggatg -gatggatggatgtgggatggactgtcccacagaaagtgtgtggtaaggggagagattgga -gacagcccagtcttgagatgccttgtaggggcccctggtctagggcaggcagagctggcc -aggcaggagctccagcacagcgcccttgctcaccgccaatcttgtacacgtcctgcagcg -gcaggcgcaggggcttgtccgtggggcgcgtggggggcaggatggtgtccagggcctcca -gcagggacacgccgcttgcgttgccctccttacgctccacc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_241ebaea2bd4d12cce6bff185f492856.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_241ebaea2bd4d12cce6bff185f492856.msa deleted file mode 100644 index 683e67f5..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_241ebaea2bd4d12cce6bff185f492856.msa +++ /dev/null @@ -1,195 +0,0 @@ ->syndip_1_chr20:22082166-22084005 -tatgtatatataatatatgtatatactatacatgtatatattatattatacatgtatata -ttataagtatatactatacatgcatgtattatatgtatatactatacatgcatgtattat -atgtatatattatacatgcatgtattatatgtatatattatacatgcatgtattatatgt -atatattatacatgtatgtattatatgtatagattatacatgtatatattatatatgtat -atattacacatgtacatatatgtatatattaaacacgtttatattatttattatacatga -ctatattatataggtatatatgatatatgcatatatgtcatataggtatatatgacatat -atgcatatatcatgtaggtatatatgacatatgcatatatcatataggtatatatgacat -atgcatatatcatataggtatatatgatatatgcgcatatatcatataggtatatatgat -atatgcgcatatatcatataggtatatatgatatatgcgcatat---------atcatat -aggtatatatgatatatgcgcatatatcatataggtatatatgatatatgcgcatatatc -atataggtatatatgatatatgcgcatatatcatataggtatatatgatatatgcgcata -tatcatacaggtatatgcgcatatatcatataggtataggtataggtagatatatgatat -atgcacacatatcatataggtatatatgatatatg------------ataggtatatatg -atatatgataggtatatatgatatatgataggtatatatgatatatatcatatcggtata -tatgatatatatcatatcggtatatataggtatatatcataggtatatataggtatatat -cacataggtatatataggtatatatcatataggtatatataatatatgcatttatattat -ataggtatatatattacataggtatatgtaatatgtgcatatatattatataggtatata -tattatacaggcatatataatacgtatatatattatatgggcatatatatgtgtatatat -tatataggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtac -atattatgtgggtatatataatatatgtgtacatattatgtgggtatatataatatatgt -gtacatattatgtgggtatatataatatatgtgtatatattatgtgggtatatataatat -atgtgtatatattatgtgggtatatataatatatgtgtacatattatgtgggtatatata -atatatgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtata -tataatatatgtgtatatattatgtaggtatatataatatatgtgtatatattatgtagg -tatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatatattatg -taggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatatat -tatgtaggtatatataatatatgtgtatatattatatatgtaataggaagcaggaatgaa -tgcacagaagaccttagagtttaaggcattatttgtgtaatgagaaatattatatatacg ----------------------------------tatattaatatagacgtatatataata -tatacatatatacatatatagtatatactatgtatacatatatactatacatacgtatat -tatatacatgtgtattatatacatgtgtattatatatatgtgtatacatatatactatat -atacatacattatatacatacattatatatgtgtattatatatgtatatattatgtatgt -atatattatatatacgtatatattaatatacatatatatgtgtctcattataccaataat -gccttaaactctaaggtcttctgtgcattcattcctgcttcctattacatatatattata -tagatacatatataatatatacatatatactacataatatatgcatatataatatataca -tatgttgtatatgtatatataatatatacatatgttgtatatgtatatataatatataca -tatgttgtatatgtatatataatatatacatatgttgtatatgtatatataatatataca -tatgttgtatatgtatatataatatatacatatgttgtatatgtatatataata ->syndip_2_chr20:22082166-22084005 -tatgtatatataatatatgtatatactatacatgtatatattatattatacatgtatata -ttataagtatatactatacatgcatgtattatatgtatatac------------------ -----------tatacatgcatgtattatatgtatatattatacatgcatgtattatatgt -atatattatacatgcatgtattatatgtatatattatacatgtatgtattatatgtatag -at---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------tatacatgtatatattatatatgtatatattac -acatgtacatatat-------gtatatattaaacacgtttatattatttattatacatgt -aggtatatatgacatat--gcatatatcatataggtatatatgacatat--gcatatatc -atataggtatatatgatatatgcgcatatatcatataggtatatatgatatatgcgcata -tatcatacaggtatatgcgcatatatcatataggtataggtataggtagatatatgatat -atgcacacatatcatataggtatatatgatatatgcgcatatatcatataggtatatatg -atatatgataggtatatatgatatatgataggtatatatgatatatatcatatcggtata -tatgatatatatcatatcggtatatataggtatatatcataggtatatataggtatatat -cacataggtatatataggtatatatcatataggtatatataatatatgcatttatattat -ataggtatatatattacataggtatatgtaatatgtgcatatatattatataggtatata -tattatacaggcatatataatacgtatatatattatatgggcatatatatgtgtatatat -tatataggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtat -atattatgtgggtatatataatatatgtgtacatattatgtgggtatatataatatatgt -gtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatat -atgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatata -atatatgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtata -tataatatatgtgtatatattatgtaggtatatataatatatgtgtatatattatgtagg -tatatataatatatgtgtatatattatatatgta-------------------------- ------------------------------------------------------------- -------------------------------------------ataggaagcaggaatgaa -tgcacagaagaccttagagtttaaggcattatttgtgtaatgagaaatattatatatacg -tatattaatatagacgtatatataatatatacatatattaatatagacgtatatataata -tatacatatatacatatatagtatatactatgtatacatatatactatacatacgtatat -tatatacatgtgtattatatacatgtgtattatatatatgtgtatacatatatactatat -atacatacattatatacatacattatatatgtgtattatatatgtatatattatgtatgt -atatattatatatacgtatatattaatatacatatatatgtgtctcattataccaataat -gccttaaactctaaggtcttctgtgcattcattcctgcttcctattacatatatattata -tagatacatatataatatatacatatatactacataatatatgcatatataatatataca -tatgttgtatatgtatatataatatatacatatgttgtatatgtatatataatatataca -tatgttgtatatgtatatataata------------------------------------ ------------------------------------------------------- ->p:HG002_1_chr20:22082166-22084005 -tatgtatatataatatatgtatatactatacatgtatatattatattatacatgtatata -ttataagtatatactatacatgcatgtattatatgtatatac------------------ -----------tatacatgcatgtattatatgtatatattatacatgcatgtattatatgt -atatattatacatgcatgtattatatgtatatattatacatgtatgtattatatgtatag -at---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------tatacatgtatatattatatatgtatatattac -acatgtacatatat-------gtatatattaaacacgtttatattatttattatacatgt -aggtatatatgacatat--gcatatatcatataggtatatatgacatat--gcatatatc -atataggtatatatgatatatgcgcatatatcatataggtatatatgatatatgcgcata -tatcatacaggtatatgcgcatatatcatataggtataggtataggtagatatatgatat -atgcacacatatcatataggtatatatgatatatgcgcatatatcatataggtatatatg -atatatgataggtatatatgatatatgataggtatatatgatatatatcatatcggtata -tatgatatatatcatatcggtatatataggtatatatcataggtatatataggtatatat -cacataggtatatataggtatatatcatataggtatatataatatatgcatttatattat -ataggtatatatattacataggtatatgtaatatgtgcatatatattatataggtatata -tattatacaggcatatataatacgtatatatattatatgggcatatatatgtgtatatat -tatataggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtat -atattatgtgggtatatataatatatgtgtacatattatgtgggtatatataatatatgt -gtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatat -atgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatata -atatatgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtata -tataatatatgtgtatatattatgtaggtatatataatatatgtgtatatattatgtagg -tatatataatatatgtgtatatattatatatgta-------------------------- ------------------------------------------------------------- -------------------------------------------ataggaagcaggaatgaa -tgcacagaagaccttagagtttaaggcattatttgtgtaatgagaaatattatatatacg -tatattaatatagacgtatatataatatatacatatattaatatagacgtatatataata -tatacatatatacatatatagtatatactatgtatacatatatactatacatacgtatat -tatatacatgtgtattatatacatgtgtattatatatatgtgtatacatatatactatat -atacatacattatatacatacattatatatgtgtattatatatgtatatattatgtatgt -atatattatatatacgtatatattaatatacatatatatgtgtctcattataccaataat -gccttaaactctaaggtcttctgtgcattcattcctgcttcctattacatatatattata -tagatacatatataatatatacatatatactacataatatatgcatatataatatataca -tatgttgtatatgtatatataatatatacatatgttgtatatgtatatataatatataca -tatgttgtatatgtatatataata------------------------------------ ------------------------------------------------------- ->p:HG002_2_chr20:22082166-22084005 -tatgtatatataatatatgtatatactatacatgtatatattatattatacatgtatata -ttataagtatatactatacatgcatgtattatatgtatatactatacatgcatgtattat -atgtatatattatacatgcatgtattatatgtatatattatacatgcatgtattatatgt -atatattatacatgcatgtattatatgtatatattatacatgtatgtattatatgtatag -atattacacatgtacatatatgtatatattaaacacgtttatattatttattatacatga -ctatattatataggtatatatgatatatgcatatatgtcatataggtatatatgacatat -atgcatatatcatgtaggtatatatgacatatgcatatatcatataggtatatatgacat -atgcatatatcatataggtatatatgatatacatgtatatattatatatgtatatattac -acatgtacatatat-------gtatatattaaacacgtttatattatttattatacatgt -aggtatatatgacatat--gcatatatcatataggtatatatgacatat--gcatatatc -atataggtatatatgatatatgcgcatatatcatataggtatatatgatatatgcgcata -tatcatacaggtatatgcgcatatatcatataggtataggtataggtagatatatgatat -atgcacacatatcatataggtatatatgatatatgcgcatatatcatataggtatatatg -atatatgataggtatatatgat-----ataggtatatatgatatatatcatatcggtata -tatgatatatatcatatcggtatatataggtatatatcataggtatatataggtatatat -cacataggtatatataggtatatatcatataggtatatataatatatgcatttatattat -ataggtatatatattacataggtatatgtaatatgtgcatatatattatataggtatata -tattatacaggcatatataatacgtatatatattatatgggcatatatatgtgtatatat -tatataggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtat -atattatgtgggtatatataatatatgtgtacatattatgtgggtatatataatatatgt -gtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatat -atgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatata -atatatgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtata -tataatatatgtgtatatattatgtaggtatatataatatatgtgtatatattatgtagg -tatatataatatatgtgtatatattatatatgtatatataatatatgtgtatatattatg -taggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatatat -tatgtaggt---------------------------------ataggaagcaggaatgaa -tgcacagaagaccttagagtttaaggcattatttgtgtaatgagaaatattatatatacg -tatattaatatagacgtatatataatatatacatatattaatatagacgtatatataata -tatacatatatacatatatagtatatactatgtatacatatatactatacatacgtatat -tatatacatgtgtattatatacatgtgtattatatatatgtgtatacatatatactatat -atacatacattatatacatacattatatatgtgtattatatatgtatatattatgtatgt -atatattatatatacgtatatattaatatacatatatatgtgtctcattataccaataat -gccttaaactctaaggtcttctgtgcattcattcctgcttcctattacatatatattata -tagatacatatataatatatacatatatactacataatatatgcatatataatatataca -tatgttgtatatgtatatataatatatacatatgttgtatatgtatatataatatataca -tatgttgtatatgtatatataatatatacatatgttgtatatgtatatataatatataca -tatgttgtatatgtatatataatatatacatatgttgtatatgtatatataata ->ref_chr20:22082166-22084005 -tatgtatatataatatatgtatatactatacatgtatatattatattatacatgtatata -ttataagtatatactatacatgcatgtattatatgtatatactatacatgcatgtattat -atgtatatattatacatgcatgtattatatgtatatattatacatgcatgtattatatgt -atatattatacatgcatgtattatatgtatatattatacatgtatgtattatatgtatag -at---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------tatacatgtatatattatatatgtatatattac -acatgtacatatat-------gtatatattaaacacgtttatattatttattatacatgt -aggtatatatgacatat--gcatatatcatataggtatatatgacatat--gcatatatc -atataggtatatatgatatatgcgcatatatcatataggtatatatgatatatgcgcata -tatcatacaggtatatgcgcatatatcatataggtataggtataggtagatatatgatat -atgcacacatatcatataggtatatatgatatatgcgcatatatcatataggtatatatg -atatatgataggtatatatgatatatgataggtatatatgatatatatcatatcggtata -tatgatatatatcatatcggtatatataggtatatatcataggtatatataggtatatat -cacataggtatatataggtatatatcatataggtatatataatatatgcatttatattat -ataggtatatatattacataggtatatgtaatatgtgcatatatattatataggtatata -tattatacaggcatatataatacgtatatatattatatgggcatatatatgtgtatatat -tatataggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtat -atattatgtgggtatatataatatatgtgtacatattatgtgggtatatataatatatgt -gtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatat -atgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatata -atatatgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtata -tataatatatgtgtatatattatgtaggtatatataatatatgtgtatatattatgtagg -tatatataatatatgtgtatatattatatatgta-------------------------- ------------------------------------------------------------- -------------------------------------------ataggaagcaggaatgaa -tgcacagaagaccttagagtttaaggcattatttgtgtaatgagaaatattatatatacg -tatattaatatagacgtatatataatatatacatatattaatatagacgtatatataata -tatacatatatacatatatagtatatactatgtatacatatatactatacatacgtatat -tatatacatgtgtattatatacatgtgtattatatatatgtgtatacatatatactatat -atacatacattatatacatacattatatatgtgtattatatatgtatatattatgtatgt -atatattatatatacgtatatattaatatacatatatatgtgtctcattataccaataat -gccttaaactctaaggtcttctgtgcattcattcctgcttcctattacatatatattata -tagatacatatataatatatacatatatactacataatatatgcatatataatatataca -tatgttgtatatgtatatataatatatacatatgttgtatatgtatatataatatataca -tatgttgtatatgtatatataata------------------------------------ ------------------------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_24b6d6c9badcffee09ccc44d0cd7371b.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_24b6d6c9badcffee09ccc44d0cd7371b.msa deleted file mode 100644 index 64aeb271..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_24b6d6c9badcffee09ccc44d0cd7371b.msa +++ /dev/null @@ -1,75 +0,0 @@ ->syndip_1_chr20:35580476-35580966 -ctctactaaaaatacaaaaaaattagctgggtgtggtaacgggtggctgtaatcccagct -acttgggaagctgaggcagaagaatagcttgaacctgggaggcacaggttgcagtgagcc -gagatcgcgccactgcagcctaggcagcagagtgagactctgtcttaaaatatatattat -ggtttattttattttatggttaaaggccatatatatatatatat-atatatatataatat -atatatatataaaatatatatatataaaatatatatatatataaaatatatatatataaa -atatatatatatatataaaatatatatatataaaatatatatatataaaatatatatata -tataaaatatatatatatataaaatatatatatataaaatatatatatatataaaatata -tatatataaaatatatatatataaaatatatatatatataaaatatatatatataaaata -tatatatataaaatatatatatatataatatatatatataaaatatatatatat--aaaa -tatatataaaatatatatatataaaatatatatataatatatatatataaaatatatata -tataatatatatatataaaatatatatatataaaatatatatatatataaaatatatata -tatataaaatatatatatggaattccatatctatcaatggatcctaagggaaacaatttt -actactgtattggtgggtttattttatgtatttgtagatatatacatatatacacatata -tatgacaa ->syndip_2_chr20:35580476-35580966 -ctctactaaaaatacaaaaaaattagctgggtgtggtaacgggtggctgtaatcccagct -acttgggaagctgaggcagaagaatagcttgaacctgggaggcacaggttgcagtgagcc -gagatcgcgccactgcagcctaggcagcagagtgagactctgtcttaaaatatatattat -ggtttattttattttatggttaaaggccatatatatat---------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------a -tatatatatataaaatatatataaaatatatatatataatatatatataaaatatatata -tataatatatatatataaaatatatatatataaaatatatatatatataaaatatatata -tatataaaatatatatatggaattccatatctatcaatggatcctaagggaaacaatttt -actactgtattggtgggtttattttatgtatttgtagatatatacatatatacacatata -tatgacaa ->p:HG002_1_chr20:35580476-35580966 -ctctactaaaaatacaaaaaaattagctgggtgtggtaacgggtggctgtaatcccagct -acttgggaagctgaggcagaagaatagcttgaacctgggaggcacaggttgcagtgagcc -gagatcgcgccactgcagcctaggcagcagagtgagactctgtcttaaaatatatattat -ggtttattttattttatggttaaaggccatatatat------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------a -tatatataaaatatatatatataaaatatatatataatatatatatataaaatatatata -tataatatatatatataaaatatatatatataaaatatatatatatataaaatatatata -tatataaaatatatatatggaattccatatctatcaatggatcctaagggaaacaatttt -actactgtattggtgggtttattttatgtatttgtagatatatacatatatacacatata -tatgacaa ->p:HG002_2_chr20:35580476-35580966 -ctctactaaaaatacaaaaaaattagctgggtgtggtaacgggtggctgtaatcccagct -acttgggaagctgaggcagaagaatagcttgaacctgggaggcacaggttgcagtgagcc -gagatcgcgccactgcagcctaggcagcagagtgagactctgtcttaaaatatatattat -ggtttattttattttatggttaaaggccatatatatatatatataaaatatatatatata -atatatatataaaatatatatatataaaatatatatatatataaaatatatatatataaa -atatatatatatatataaaatatatatatataaaatatatatatataaaatatatatata -tataaaatatatatatatataaaatatatatatataaaatatatatatatataaaatata -tatatataaaatatatatatataaaatatatatatatataaaatatatatatataaaata -tatatatataaaatatatatatatataatatatatatataaaatatatatatataaaaaa -tatatataaaatatatatatataaaatatatatataatatatatatataaaatatatata -tataatatatatatataaaatatatatatataaaatatatatatatataaaatatatata -tatataaaatatatatatggaattccatatctatcaatggatcctaagggaaacaatttt -actactgtattggtgggtttattttatgtatttgtagatatatacatatatacacatata -tatgacaa ->ref_chr20:35580476-35580966 -ctctactaaaaatacaaaaaaattagctgggtgtggtaacgggtggctgtaatcccagct -acttgggaagctgaggcagaagaatagcttgaacctgggaggcacaggttgcagtgagcc -gagatcgcgccactgcagcctaggcagcagagtgagactctgtcttaaaatatatattat -ggtttattttattttatggttaaaggccatatatatatatatat---------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------aaaatatatatatat--aaaa -tatatataaaatatatatatataaaatatatatataatatatatatataaaatatatata -tataatatatatatataaaatatatatatataaaatatatatatatataaaatatatata -tatataaaatatatatatggaattccatatctatcaatggatcctaagggaaacaatttt -actactgtattggtgggtttattttatgtatttgtagatatatacatatatacacatata -tatgacaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_252c1c64f7c209ff60c00d0861d18483.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_252c1c64f7c209ff60c00d0861d18483.msa deleted file mode 100644 index 0c540701..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_252c1c64f7c209ff60c00d0861d18483.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:57189946-57190540 -tgacagtggggcacagtgtacagggcagagtgagccatgggaggttttggggaggaaatg -ttcctggcagagggaatggcacatgccaggttcatgagaaatacacggtgtgtgtcagca -cagtgaagaggccagtgaggctggagaagtgagccaggaaccagagaggttgagactgga -gatagtgagcgaggaaccggagggggtgaagctggagagagtgagccaggaatcagagga -ggtgaggccagagagagtgagcgaggaaccagagggggtgaggctggagagagtgaccga -ggaaccagaggaggtgaggcc----agagtgagtgaggagcttgaaggggtgaggctgga -gacagtgagcgaggaaccagagggggtgaggctggagagagtgagccaggaaccagagga -ggtgaggccaga----gtgagtgaggagcttgaaggggtgaggctggagacagtgagcga -ggaaccagagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggctgga -gagagtgagtgaggagcccaagggggtgaagccgaggtgggtatggggctgggtcacct ->syndip_2_chr20:57189946-57190540 -tgacagtggggcacagtgtacagggcagagtgagccatgggaggttttggggaggaaatg -ttcctggcagagggaatggcacatgccaggttcatgagaaatacacggtgtgtgtcagca -cagtgaagaggccagtgaggctggagaagtgagccaggaaccagaggggttgaggctgga -gatagtgagcgaggaaccggagggggtgaagctggagagagtgagccaggaatcagagga -ggtgaggccagagagagtgagcgaggaaccagagggggtgaggctggagagagtgaccga -ggaaccagaggaggtgaggctggagagagtgagccaggaaccagaggaggtgaggccag- ----agtgagtgaggagcttgaaggggtgaggctggagacagtgagcgaggaacca----- --------------------------------gagggggtgaggctggagagcgtgagtga -ggagcccgagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggctgga -gagagtgagtgaggagcccaagggggtgaagccgaggtgggtatggggctgggtcacct ->p:HG002_1_chr20:57189946-57190540 -tgacagtggggcacagtgtacagggcagagtgagccatgggaggctttggggaggaaatg -ttcctggcagagggaatggcacatgccaggttcatgagaaatacacggtgtgtgtcagca -cagtgaagaggccagtgaggctggagaagtgagccaggaaccagaggggttgaggctgga -gatagtgagcgaggaaccggagggggtgaagctggagagagtgagccaggaatcagagga -ggtgaggccagagagagtgagcgaggaaccagagggggtgaggctggagagagtgaccga -ggaaccagaggaggtgaggctggagagagtgagccaggaaccagaggaggtgaggccag- ----agtgagtgaggagcttgaaggggtgaggctggagacagtgagcgaggaacca----- --------------------------------gagggggtgaggctggagagcgtgagtga -ggagcccgagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggctgga -gagagtgagtgaggagcccaagggggtgaagccgaggtgggtatggggctgggtcacct ->p:HG002_2_chr20:57189946-57190540 -tgacagtggggcacagtgtacagggcagagtgagccatgggaggctttggggaggaaatg -ttcctggcagagggaatggcacatgccaggttcatgagaaatacacggtgtgtgtcagca -cagtgaagaggccagtgaggctggagaagtgagccaggaaccagagaggttgagactgga -gatagtgagcgaggaaccggagggggtgaagctggagagagtgagccaggaatcagagga -ggtgaggccagagagagtgagcgaggaaccagagggggtgaggctggagagagtgaccga -ggaaccagaggaggtgaggcc----agagtgagtgaggagcttgaaggggtgaggctgga -gacagtgagcgaggaaccagagggggtgaggctggagagagtgagccaggaaccagagga -ggtgaggccaga----gtgagtgaggagcttgaaggggtgaggctggagacagtgagcga -ggaaccagagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggctgga -gagagtgagtgaggagcccaagggggtgaagccgaggtgggtatggggctgggtcacct ->ref_chr20:57189946-57190540 -tgacagtggggcacagtgtacagggcagagtgagccatgggaggttttggggaggaaatg -ttcctggcagagggaatggcacatgccaggttcatgagaaatacacggtgtgtgtcagca -cagtgaagaggccagtgaggctggagaagtgagccaggaaccagagaggttgagactgga -gatagtgagcgaggaaccggagggggtgaagctggagagagtgagccaggaatcagagga -ggtgaggccagagagagtgagcgaggaaccagagggggtgaggctggagagagtgaccga -ggaaccagaggaggtgaggctggagagagtgagccaggaaccagaggaggtgaggccag- ----agtgagtgaggagcttgaaggggtgaggctggagacagtgagcgaggaaccagaggg -ggtgaggctggagagcgtgagtgaggagcccgagggggtgaggctggagagcgtgagtga -ggagcccgagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggctgga -gagagtgagtgaggagcccaagggggtgaagccgaggtgggtatggggctgggtcacct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_25ee7b1fd5e90a4d785bc948dc3ec3cc.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_25ee7b1fd5e90a4d785bc948dc3ec3cc.msa deleted file mode 100644 index 680759c2..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_25ee7b1fd5e90a4d785bc948dc3ec3cc.msa +++ /dev/null @@ -1,80 +0,0 @@ ->syndip_1_chr20:2240750-2241500 -gtgagaataaattataaagtcaaatctaatttctgaggggaagacactgactgacataga -taaaaacatgtttatgtgacccttaggtaaatcgttccaactctctgagcctcagtgttg -ttatctacaaatgggagaatcaaggcaccctcctacaagcggcggctcatcagctcactt -ggaaaatgtagtcatcttctcaaagttttctttttctttctttctttttcctttctttct -ttctttttctttctttctctctctctccttccttccttctttccttccctccctcccttc -cttttttcttctttctttcattttctttctttctctctttcttctttctcttcctttc-- ------------------------------------------------------ttctttc -ttttcctcctt-------cctcccttcttt--------------ccttcccttccttctt -ccctccctccctctttgtttctttctttctctccctc----------------------- ------------------------------------------------------------- -------------cttccctccctccctttctttctcctt-----------ttcttccttc -cctccctgcctgtctccctctttctttctcttttttcttttccttccttccgtctttttc -ctcccttctttcctccctcctccctccctccctcctccctctttttctttctttctttct -tttttctttctctcttctttttttttttttttttttaagagatagggtctgttgcccagg -ctggagtgcagtggcatgatcatggttcactgcagcctt ->syndip_2_chr20:2240750-2241500 -gtgagaataaattataaagtcaaatctaatttctgaggggaagacactgactgacataga -taaaaacatgtttatgtgacccttaggtaaatcgttccaactctctgagcctcagtgttg -ttatctacaaatgggagaatcaaggcaccctcctacaagcggcggctcatcagctcactt -ggaaaatgtagtcatcttctcaaagttttctt-------------------tttctttct -ttctttttctttctttctctctctctccttccttccttctttccttccctccctcccttc -cttttttcttcttcctttcattttctttctttctctctttcttctttctcttcctttc-- ------------------------------------------------------ttctttc -ttttcctcctt-------cctcccttcttt--------------ccttcccttccttctt -ccctccctccctctttgtttctttctttctctccctccttccctccctccctttcttcct -tctttccttatccctcccttctttccttccttccctttgtttctctttctttctttcttt -ctctctctcttccttccttccctccctccctccctccttcctcccttctttccttccctc -cctgcctctctgtctccctctttctttctcttttttcttttccttccttccgtctttttc -ctcccttctttcctccctcctccctccctccctcctccctctttttctttctttctttct -tttttctttctctcttctttttttttttttttttttaagagatagggtctgttgcccagg -ctggagtgcagtggcatgatcatggttcactgcagcctt ->p:HG002_1_chr20:2240750-2241500 -gtgagaataaattataaagtcaaatctaatttctgaggggaagacactgactgacataga -taaaaacatgtttatgtgacccttaggtaaatcgttccaactctctgagcctcagtgttg -ttatctacaaatgggagaatcaaggcaccctcctacaagcggcggctcatcagctcactt -ggaaaatgtagtcatcttctcaaagttttctttttctttctttctttttcctttctttct -ttctttttctttctttctctctctctccttccttccttctttccttccctccctcccttc -cttttttcttctttctttcattttctttctttctctctttcttctttctcttcctttctt -tccttccgtccctcccttccttccttttttcttcttcctttcattttctttctttctctc -tttcttctttcctccctttcttccttctttccttatccctcccttcttcctttcttcttt -cttttcctccttcctcccttctttccttcccttcctt----------------------- ------------------------------------------------------------- -------------cttccctccctccctctttgtttctttctttctctccctccttccctc -cctccctttctgtctccctctttctttctcttttttcttttccttccttccgtctttttc -ctcccttctttcctccctcctccctccctccctcctccctctttttctttctttctttct -tttttctttctctcttctttttttttttttttttttaagagatagggtctgttgcccagg -ctggagtgcagtggcatgatcatggttcactgcagcctt ->p:HG002_2_chr20:2240750-2241500 -gtgagaataaattataaagtcaaatctaatttctgaggggaagacactgactgacataga -taaaaacatgtttatgtgacccttaggtaaatcgttccaactctctgagcctcagtgttg -ttatctacaaatgggagaatcaaggcaccctcctacaagcggcggctcatcagctcactt -ggaaaatgtagtcatcttctcaaagttttctttttctttctttctttttcctttctttct -ttctttttctttctttctctctctctccttccttccttctttccttccctccctcccttc -cttttttcttctttctttcattttctttctttctctctttcttctttctcttcctttc-- ------------------------------------------------------ttctctc -tttcttctttc---------------------------------tcttcctttcttcttt -cttttcctccttcctcccttctttccttcccttcctt----------------------- ------------------------------------------------------------- -------------cttccctccctccctctttgtttctttctttctctccctccttccctc -cctccctttctgtctccctctttctttctcttttttcttttccttccttccgtctttttc -ctcccttctttcctccctcctccctccctccctcctccctctttttctttctttctttct -tttttctttctctcttctttttttttttttttttttaagagatagggtctgttgcccagg -ctggagtgcagtggcatgatcatggttcactgcagcctt ->ref_chr20:2240750-2241500 -gtgagaataaattataaagtcaaatctaatttctgaggggaagacactgactgacataga -taaaaacatgtttatgtgacccttaggtaaatcgttccaactctctgagcctcagtgttg -ttatctacaaatgggagaatcaaggcaccctcctacaagcggcggctcatcagctcactt -ggaaaatgtagtcatcttctcaaagttttctttttctttctttctttttcctttctttct -ttctttttctttctttctctctctctccttccttccttctttccttccctccctcccttc -cttttttcttctttctttcattttctttctttctctctttcttctttctcttcctttctt -tccttccgtccctcccttccttccttttttcttcttcctttcattttctttctttctctc -tttcttctttc---------------------------------tcttcctttcttcttt -cttttcctccttcctcccttctttccttcccttcctt----------------------- ------------------------------------------------------------- -------------cttccctccctccctctttgtttctttctttctctccctccttccctc -cctccctttctgtctccctctttctttctcttttttcttttccttccttccgtctttttc -ctcccttctttcctccctcctccctccctccctcctccctctttttctttctttctttct -tttttctttctctcttctttttttttttttttttttaagagatagggtctgttgcccagg -ctggagtgcagtggcatgatcatggttcactgcagcctt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_26ab402df211fd6a9c97a9666a6eaf40.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_26ab402df211fd6a9c97a9666a6eaf40.msa deleted file mode 100644 index 19de6693..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_26ab402df211fd6a9c97a9666a6eaf40.msa +++ /dev/null @@ -1,210 +0,0 @@ ->syndip_1_chr20:16257741-16259345 -atctgaaatcagatatcatacccacaccccaaaacacacacactccttccccatcccaaa -gagacacaccccttccccatcccaaagagacacaccccttccccatcccaaagagacaca -ccccttccccatcccaaacacacacaccccttccccatcccaaacacacacaccccttcc -ccatcccaaacacacacacccctttcccatcccaaacacacacacccattgcccatccta -aacacacacacaccttcccttcgcaaacacacacaccccttccccatcacaaacacacac -accctttccctatcccatgcacacacaccttccacttcccaaacacacacaccccttccc -catcccaaacacacacaacccttccccaattctaaacacacacacctcttccccatccca -aacacaaacaccccttccccatcccaaacacacccaccctttcctgcatcccaaacaccc -acaccccttccccatcccaaacacacaccccatccccaattccaaacacacacacccctt -ccccatcccaaacacacacaccccttccacatcagaaacacacacaccccttctcatccc -aaacacaaacacacccattccccatcacaaacacacg----------------------- ----caccccttccccatcccaaacacacacaccccttccccaattctaaacacacacacc -ccttccccatcccaaacacacaccccccttccccatcccaaacacacaccccccttcccc -atcccaaacacacccaccccttcccacatcccaaacacacacaccccttccctatcccaa -acacacactccatccccaattccaaacacacacaccccttccccatcccaaacacacaca -ccccttcccccatcccaaacgcacacaccccttccctatcccaaacacacaccccttccc -tttccaaaacacacccatcccttccccatcccaaacacacacaacccttcccatcccaga -cacacccaccccttcccatctcaaatacacgcaacccttccccatcccaaacacacacac -ctattccccatccgaaacacacacaccccttcctcatcccacacacacccattccccatc -ccagacacacccatcccttccccatactaaacacaaccaccccttccccatcccacacac -acacaccccttccccaattccaaacacacacaccccttccccattcaaaacacacgcacc -ccttcccatctgaaacacacccactccttcccatctgaaacacacccactccttcccatc -ccaaacacacccactccttcccatcccaaacacacacaccccttccccatcccaaaaaca -cacaccctttcgcaatcccaaatacacaagccccttcccaaattccacacacacacacct -cttccccatcccaaacaaacccaccctttccccattcgaaacacacacaccccttctcca -attccaaacacacacaccccttcccatctcaaacacacggacaccttccacatcccaaat -acacacaccccttcccatcccaaacacacacatcccttccccaattccaaaaacacacac -cccttccccatcccaaacacccccaccccttcccatccccaaaacacacacccctttccc -atcccaaatacacaaaccccttccctaattccacacacacacaccccttccccatcccaa -acacacataccccttcccatcccaaagacacacactcattctgcatcccaaacacacaca -ccccttcccatcccaaacacacacactacctccgcatcccaaacacatataccccttccc -catcccaaacacatacaccccttccccatcgccaacacacacaccccttccccatcccaa -acacacacacccctttccatcccaaacacacacccattccccatcccagacacacccacc -cgttccccatcccagacacacacaacccttccccaattccaaacacacaccccttcccat -cccaaacacacacacccatttcccatcccagacacatccaccccttccacaactctgaac -acccaccccttccccatcccaaacacacacaccccttccccatcccaaacacacacaccc -attccccatcccaaacacacacacccattccccatcccaaacacaaccaccccttcccca -tcccaaacacacacaccccttccccatcccaaacacacacaca----------------- ---------ccttccccatcccaaacacacccacccttactccatctcaaacatgtacacc -ccttcccctatcccaaaatacacacatccatccctacacaccctcacccatttccccatc -ccagaacctatgcaccaactcagtttat ->syndip_2_chr20:16257741-16259345 -atctgaaatcagatatcatacccacaccccaaaacacacacactccttccccatcccaaa -gagacacaccccttccccatcccaaagagacacaccccttccccatcccaaagag----- ----------------------acacaccccttccccatcccaaacacacacaccccttcc -ccatcccaaacacacacacccctttcccatcccaaacacacacacccattgcccatccta -aacacacacacaccttcccttcgcaaacacacacaccccttccccatcacaaacacacac -accctttccctatcccatgcacacacaccttccacttcccaaacacacacaccccttccc -catcccaaacacacacaacccttccccaattctaaacacacacacctcttccccatccca -aacacaaacaccccttccccatcccaaacacacccaccctttcctgcatcccaaacacac -acaccccttccccatcccaaacacacaccccatccccaattccaaacacacacacccctt -ccccatcccaaacacacacaccccttccacatcagaaacacacacaccccttctcatccc -aaacacaaacacacccattccccatcacaaacacacgcaccccttccccatcccaaacat -acacaccccttccccatcccaaacacacacaccccttccccaattctaaacacacacacc -ccttccccatcccaaacacacaccccccttccccatcccaaacacacaccccccttcccc -atcccaaacacacccaccccttcccacatcccaaacacacacaccccttccctatcccaa -acacacactccatccccaattccaaacacacacaccccttccccatcccaaacacacaca -ccccttcccccatcccaaacgcacacaccccttccctatcccaaacacacaccccttccc -tttccaaaacacacccatcccttccccatcccaaacacacacaacccttcccatcccaga -cacacccaccccttcccatctcaaatacacgcaacccttc-------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------cccatcccaaacacacacaccccttccccatcccaaaaaca -cacaccctttcgcaatcccaaatacacaagccccttcccaaattccacacacacacacct -cttccccatcccaaacaaacccaccctttccccattcgaaacacacacaccccttctcca -attccaaacacacacaccccttcccatctcaaacacacggacaccttccacatcccaaat -acacacaccccttcccatcccaaacacacacatcccttccccaattccaaaaacacacac -cccttccccatcccaaacacccccaccccttcccatccccaaaacacacacccctttccc -atcccaaatacacaaaccccttccctaattccacacacacacaccccttccccatcccaa -acacacataccccttcccatcccaaagacacacactcattctgcatcccaaacacacaca -ccccttcccatcccaaacacacacactacctccgcatcccaaacacatataccccttccc -catcccaaacacatacaccccttccccatcgccaacacacacaccccttccccatcccaa -acacacacacccctttccatcccaaacacacacccattccccatcccagacacacccacc -cgttccccatcccagacacacacaacccttccccaattccaaacacacaccccttcccat -cccaaacacacacacccatttcccatcccagacacatccaccccttccacaactccgaac -acccaccccttccccatcccaaacacacacaccccttccccatcccaaacacacacaccc -attccccatcccaaacacacacacccattccccatcccaaacacaaccaccccttcccca -tcccaaacacacacaccccttccccatcccaaacacacacacaccttcccatcccaaaca -cacacaccccttccccatcccaaacacacccacccttactccatctcaaacatgtacacc -ccttcccctatcccaaaatacacacatccatccctacacaccctcacccatttccccatc -ccagaacctatgcaccaactcagtttat ->p:HG002_1_chr20:16257741-16259345 -atctgaaatcagatatcatacccacaccccaaaacacacacactccttccccatcccaaa -gagacacaccccttccccatcccaaagagacacaccccttccccatcccaaagag----- ----------------------acacaccccttccccatcccaaacacacacaccccttcc -ccatcccaaacacacacacccctttcccatcccaaacacacacacccattgcccatccta -aacacacacacaccttcccttcgcaaacacacacaccccttccccatcacaaacacacac -accctttccctatcccatgcacacacaccttccacttcccaaacacacacaccccttccc -catcccaaacacacacaacccttccccaattctaaacacacacacctcttccccatccca -aacacaaacaccccttccccatcccaaacacacccaccctttcctgcatcccaaacacac -acaccccttccccatcccaaacacacaccccatccccaattccaaacacacacacccctt -ccccatcccaaacacacacaccccttccacatcagaaacacacacaccccttctcatccc -aaacacaaacacacccattccccatcacaaacacacgcaccccttccccatcccaaacat -acacaccccttccccatcccaaacacacacaccccttccccaattctaaacacacacacc -ccttccccatcccaaacacacaccccccttccccatcccaaacacacaccccccttcccc -atcccaaacacacccaccccttcccacatcccaaacacacacaccccttccctatcccaa -acacacactccatccccaattccaaacacacacaccccttccccatcccaaacacacaca -ccccttcccccatcccaaacgcacacaccccttccctatcccaaacacacaccccttccc -tttccaaaacacacccatcccttccccatcccaaacacacacaacccttcccatcccaga -cacacccaccccttcccatctcaaatacacgcaacccttc-------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------cccatcccaaacacacacaccccttccccatcccaaaaaca -cacaccctttcgcaatcccaaatacacaagccccttcccaaattccacacacacacacct -cttccccatcccaaacaaacccaccctttccccattcgaaacacacacaccccttctcca -attccaaacacacacaccccttcccatctcaaacacacggacaccttccacatcccaaat -acacacaccccttcccatcccaaacacacacatcccttccccaattccaaaaacacacac -cccttccccatcccaaacacccccaccccttcccatccccaaaacacacacccctttccc -atcccaaatacacaaaccccttccctaattccacacacacacaccccttccccatcccaa -acacacataccccttcccatcccaaagacacacactcattctgcatcccaaacacacaca -ccccttcccatcccaaacacacacactacctccgcatcccaaacacatataccccttccc -catcccaaacacatacaccccttccccatcg----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------- ->p:HG002_2_chr20:16257741-16259345 -atctgaaatcagatatcatacccacaccccaaaacacacacactccttccccatcccaaa -gagacacaccccttccccatcccaaagagacacaccccttccccatcccaaagagacaca -ccccttccccatcccaaacacacacaccccttccccatcccaaacacacacaccccttcc -ccatcccaaacacacacacccctttcccatcccaaacacacacacccattgcccatccta -aacacacacacaccttcccttcgcaaacacacacaccccttccccatcacaaacacacac -accctttccctatcccatgcacacacaccttccacttcccaaacacacacaccccttccc -catcccaaacacacacaacccttccccaattctaaacacacacacctcttccccatccca -aacacaaacaccccttccccatcccaaacacacccaccctttcctgcatcccaaacaccc -acaccccttccccatcccaaacacacaccccatccccaattccaaacacacacacccctt -ccccatcccaaacacacacaccccttccacatcagaaacacacacaccccttctcatccc -aaacacaaacacacccattccccatcacaaacacacg----------------------- ----caccccttccccatcccaaacacacacaccccttccccaattctaaacacacacacc -ccttccccatcccaaacacacaccccccttccccatcccaaacacacaccccccttcccc -atcccaaacacacccaccccttcccacatcccaaacacacacaccccttccctatcccaa -acacacactccatccccaattccaaacacacacaccccttccccatcccaaacacacaca -ccccttcccccatcccaaacgcacacaccccttccctatcccaaacacacaccccttccc -tttccaaaacacacccatcccttccccatcccaaacacacacaacccttcccatcccaga -cacacccaccccttcccatctcaaatacacgcaacccttccccatcccaaacacacacac -ctattccccatccgaaacacacacaccccttcctcatcccacacacacccattccccatc -ccagacacacccatcccttccccatactaaacacaaccaccccttccccatcccacacac -acacaccccttccccaattccaaacacacacaccccttccccattcaaaacacacgcacc -ccttcccatctgaaacacacccactccttcccatctgaaacacacccactccttcccatc -ccaaacacacccactccttcccatcccaaacacacacaccccttccccatcccaaaaaca -cacaccctttcgcaatcccaaatacacaagccccttcccaaattccacacacacacacct -cttccccatcccaaacaaacccaccctttccccattcgaaacacacacaccccttctcca -attccaaacacacacaccccttcccatctcaaacacacggacaccttccacatcccaaat -acacacaccccttcccatcccaaacacacacatcccttccccaattccaaaaacacacac -cccttccccatcccaaacacccccaccccttcccatccccaaaacacacacccctttccc -atcccaaatacacaaaccccttccctaattccacacacacacaccccttccccatcccaa -acacacataccccttcccatcccaaagacacacactcattctgcatcccaaacacacaca -ccccttcccatcccaaacacacacactacctccgcatcccaaacacatataccccttccc -catcccaaacacatacaccccttccccatcgccaacacacacaccccttccccatcccaa -acacacacacccctttccatcccaaacacacacccattccccatcccagacacacccacc -cgttccccatcccagacacacacaacccttccccaattccaaacacacaccccttcccat -cccaaacacacacacccatttcccatcccagacacatccaccccttccacaactctgaac -acccaccccttccccatcccaaacacacacaccccttccccatcccaaacacacacaccc -attccccatcccaaacacacacacccattccccatcccaaacacaaccaccccttcccca -tcccaaacacacacaccccttccccatcccaaacacacacaca----------------- ---------ccttccccatcccaaacacacccacccttactccatctcaaacatgtacacc -ccttcccctatcccaaaatacacacatccatccctacacaccctcacccatttccccatc -ccagaacctatgcaccaactcagtttat ->ref_chr20:16257741-16259345 -atctgaaatcagatatcatacccacaccccaaaacacacacactccttccccatcccaaa -gagacacaccccttccccatcccaaagagacacaccccttccccatcccaaagagacaca -ccccttccccatcccaaacacacacaccccttccccatcccaaacacacacaccccttcc -ccatcccaaacacacacacccctttcccatcccaaacacacacacccattgcccatccta -aacacacacacaccttgccttcgcaaacacacacaccccttccccatcacaaacacacac -accctttccctatcccatgcacacacaccttccacttcccaaacacacacaccccttccc -catgccaaacacacacaacccttccccaattctaaacacacacacctcttccccatccca -aacacaaacaccccttccccatcccaaacacacccaccctttcctgcatgccaaacaccc -acaccccttccccatcccaaacacacaccccatccccaattccaaacacacacacccctt -ccccatcccaaacacacacaccccttccacatgagaaacacacacaccccttctcatccc -aaacacaaacacacccattccccatcacaaacacacg----------------------- ----caccccttccccatcccaaacacacacaccccttccccaattgt------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------aaacacacacaccccttctcca -attccaaacacacacaccccttcccatcacaaacacacacacaccttccacatcccaaat -acacacaccccttcccatctcaaacacacacatcccttccccaattccaaaaacacacac -cccttccccatcccaaacacccccaccccttcccatcccc-aaacacacacccctttccc -atcccaaatacacaaaccccttccctaattccacacacacacaccccttccccatcccaa -acacacataccccttcccatcccaaagacacacactcattctgcatcccaaacacacaca -ccccttcccatcccaaacacacacactacctccgcatcccaaacacatataccccttccc -catcccaaacacatacaccccttccccatcgccaacacacacaccccttccccatcccaa -acacacacacccctttccatcccaaacacacacccattccccatcccagacacacccacc -cgttccccatcccagacacacacaacccttccccaattccaaacacacaccccttcccat -cccaaacacacacacccatttcccatcccagacacatccaccccttccacaactctgaac -acccaccccttccccatcccaaacacacacaccccttccccatcccaaacacacacaccc -attccccatcccaaacacacacacccattccccatcccaaacacaaccaccccttcccca -tcccaaacacacacaccccttccccatcccaaacacacacaca----------------- ---------ccttccccatcccaaacacacccacccttactccatctcaaacatgtacacc -ccttcccctatcccaaaatacacacatccatccctacacaccctcacccatttccccatc -ccagaacctatgcaccaactcagtttat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_285d8d282ead2b572c27341ddee09aee.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_285d8d282ead2b572c27341ddee09aee.msa deleted file mode 100644 index 3d69d85c..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_285d8d282ead2b572c27341ddee09aee.msa +++ /dev/null @@ -1,70 +0,0 @@ ->syndip_1_chr20:21120012-21120739 -tgtcccagctacttgggagactgaggcaggaggatcacttgagcccaggaattcaaggct -gcagtgagccatgatcatgccactgcactccagcctggtgacagactgagactttgtctt -aaaatcaaattaatttaatttaaaaaacaaatgcctttgagcaaagtgctgttagtaacc -tcatgtcttcctgtattcatcagggttcttcagagaaacagaaccagtaggacacacaca -cacgcacacacacacacgtgtgtgtatatatatgtgtgtatgtatatatatatata---- ------------------------------------------------------------- ------------------------------------------------------------- -tatatttatatatatatatatatt----tatatatatatatatttatatatatatatata -tatatggagagagagagatttatttttaggaagtggttcatgagattgtgagggacttca -ttcttttctcctaaggccttcaactgactggatgaggcccatccacattttggagagcag -tctactttcctcaaagcctactgcttcaaatattaacaacatctaaaaaaaaagtcttca -cagtcatgtctagactggtgtttgataaagcaactgaccaccatggcctagccaagttga -cacataaa ->syndip_2_chr20:21120012-21120739 -tgtcccagctacttgggagactgaggcaggaggatcacttgagcccaggaattcaaggct -gcagtgagccatgatcatgccactgcactccagcctggtgacagactgagactttgtctt -aaaatcaaattaatttaatttaaaaaacaaatgcctttgagcaaagtgctgttagtaacc -tcatgtcttcctgtattcatcagggttcttcagagaaacagaaccagtaggacacacaca -cacgcacacacacacacgtgtgtgtatatatatgtgtgtatgtatatatatatata---- ------------------------------------------------------------- ------------------------------------------------------------- -tatatttatatatatatatatatttatatatatatatatatatttatatatatatatata -tatatggagagagagagatttatttttaggaagtggttcatgagattgtgagggacttca -ttcttttctcctaaggccttcaactgactggatgaggcccatccacattttggagagcag -tctactttcctcaaagcctactgcttcaaatattaacaacatctaaaaaaaaagtcttca -cagtcatgtctagactggtgtttgataaagcaactgaccaccatggcctagccaagttga -cacataaa ->p:HG002_1_chr20:21120012-21120739 -tgtcccagctacttgggagactgaggcaggaggatcacttgagcccaggaattcaaggct -gcagtgagccatgatcatgccactgcactccagcctggtgacagactgagactttgtctt -aaaatcaaattaatttaatttaaaaaacaaatgcctttgagcaaagtgctgttagtaacc -tcatgtcttcctgtattcatcagggttcttcagagaaacagaaccagtaggacacacaca -cacgcacacacacacacgtgtgtgtatatatatgtgtgtatgtatatatatatata---- ------------------------------------------------------------- ------------------------------------------------------------- -tatatttatatatatatatatatttatatatatatatatatatttatatatatatatata -tatatggagagagagagatttatttttaggaagtggttcatgagattgtgagggacttca -ttcttttctcctaaggccttcaactgactggatgaggcccatccacattttggagagcag -tctactttcctcaaagcctactgcttcaaatattaacaacatctaaaaaaaaagtcttca -cagtcatgtctagactggtgtttgataaagcaactgaccaccatggcctagccaagttga -cacataaa ->p:HG002_2_chr20:21120012-21120739 -tgtcccagctacttgggagactgaggcaggaggatcacttgagcccaggaattcaaggct -gcagtgagccatgatcatgccactgcactccagcctggtgacagactgagactttgtctt -aaaatcaaattaatttaatttaaaaaacaaatgcctttgagcaaagtgctgttagtaacc -tcatgtcttcctgtattcatcagggttcttcagagaaacagaaccagtaggacacacaca -cacgcacacacacacacgtgtgtgtatatatatgtgtgtatgtatatatatatata---- ------------------------------------------------------------- ------------------------------------------------------------- -tatatttatatatatatatatatt----tatatatatatatatttatatatatatatata -tatatggagagagagagatttatttttaggaagtggttcatgagattgtgagggacttca -ttcttttctcctaaggccttcaactgactggatgaggcccatccacattttggagagcag -tctactttcctcaaagcctactgcttcaaatattaacaacatctaaaaaaaaagtcttca -cagtcatgtctagactggtgtttgataaagcaactgaccaccatggcctagccaagttga -cacataaa ->ref_chr20:21120012-21120739 -tgtcccagctacttgggagactgaggcaggaggatcacttgagcccaggaattcaaggct -gcagtgagccatgatcatgccactgcactccagcctggtgacagactgagactttgtctt -aaaatcaaattaatttaatttaaaaaacaaatgcctttgagcaaagtgctgttagtaacc -tcatgtcttcctgtattcatcagggttcttcagagaaacagaaccagtaggacacacaca -cacgcacacacacacacgtgtgtgtatatatatgtgtgtatgtatatatatatatatatt -tatatatatatatatttatatatatatatttatatatatatatttatatatatatatatt -tatatatatatatttatatatatatatttatatatatatatatttatatatatatatatt -tatatatatatatttatatatatatatatttatatatatatatttatatatatatatatt -tatatggagagagagagatttatttttaggaagtggttcatgagattgtgagggacttca -ttcttttctcctaaggccttcaactgactggatgaggcccatccacattttggagagcag -tctactttcctcaaagcctactgcttcaaatattaacaacatctaaaaaaaaagtcttca -cagtcatgtctagactggtgtttgataaagcaactgaccaccatggcctagccaagttga -cacataaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_2acb877c85cd2b044d5bd5f0537d9b2e.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2acb877c85cd2b044d5bd5f0537d9b2e.msa deleted file mode 100644 index a58724da..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_2acb877c85cd2b044d5bd5f0537d9b2e.msa +++ /dev/null @@ -1,110 +0,0 @@ ->syndip_1_chr20:38123699-38124103 -taataataatatataatatttataataataatatatataatatgtatatataatatacat -atacctattatatataatatacctattatatataatatacatatacctattatatataat -atacctattatatataagatacctattatatataatatacatatacctattatatatata -atatacct----------------attatatat-------atataatatacctattatat -atataatatacctat--tatatatataatatacctattatatatataatatacctattat -atatataatatacctat--tatatataatatacctattatatataa-------aatatac -ctattatatataatatacctattatatacattatatataatatacctattatatgcatta -tatataatatacctattatatgcattatatataatatacctattatatgcattatatata -atatacctattatatgcattatatataatatacctattatatgcattatataatatatta -tatataatatgcatattatatgtattatatattatatattatatatataatatacatatt -atatgtattatatattatatattatatatataatatacatattatatgtattatatatta -tatataatatacatattatatattatatattatatacatattatatattatatattatat -acatattatatattatatacatattatatattatatattatatacatattatacattata -tatatctaaaatatataatacacattatatattatataatacacattatatataatatat -aatacacattatatattatatataatacacattatatattatatataatacacattatat -at-----------------------tatataatacacattatatattatatataatacac -attatatattatatataatacacattatatattatatataatacacattatatattatat -aatacacattatatattatatataatacacattatatatataatacacattatatattat -atataatacataatacacattatatattatatataatacacattatatataatatataac -acacattatatataatatataacacacattatatattatatataatacacattatatatt -atat ->syndip_2_chr20:38123699-38124103 -taataataatatataatatttataataataatatatataatatgtatatataatatacat -atacctattatatataatatacctattatatataatatacatatacctattatatataat -atacctattatatataagatacctattatatataatatacatatacctattatatatata -atatacct----------------attatatat-------atataatatacctattatat -atataatatacctat--tatatatataatatacctattatatatataatatacctattat -atatataatatacctat--tatatataatatacctattatatataa-------aatatac -ctattatatataatatacctattatata---------------------------catta -tatataatatacctattatatgcattatatataatatacctattatatgcattatatata -atatacctattatatgcattatatataatatacctattatatgcattatataatatatta -tatataatatgcatattatatgtattatatattatatattatatatataatatacatatt -atatgtattatatattatatattatatatataatatacatattatatgtattatatatta -tatataatatacatattatatattatatattatatacatattatatattatatattatat -acatattatatattatatacatattatatattatatattatatacatattatacattata -tatatctaaaatatataatacacattatatattatataatacacattatatataatatat -aatacacattatatattatatataatacacattatatattatatataatacacattatat -attatataatacacattatatattatatataatacacattatatattatatataatacac -attatatattatatataatacacattatatattatatataatacacattatatattatat -aatacacattatatattatatataatacacattatatatataatacacattatatattat -atataatacataatacacattatatattatatataatacacattatatataatatataac -acacattatatataatatataacacacattatatattatatataatacacattatatatt -atat ->p:HG002_1_chr20:38123699-38124103 -taataataatatataatatttataataataatatatataatatgtatatataatatacat -atacctattatatataatatacctattatatataatatacataaacctattatatataat -atacctattatatataagatacctattatatataatatacctatacctattatatatata -agatacct----------------attatatataatatacatacctattacctattatat -atataatatacctattatatatatataatatacctattatatatataatatacctat--- ---------tatacctat--tatatataatatacctattatatatat-------aatatac -ctattatatataatatacctattatata---------------------------catta -tatataatatacctattatatgcattatatataatatacctattatatgcattatatata -atatacctattatatgcattatatataatatacctattatatgcattatataatatatta -tatataatatgcatattatatgtattatatattatatattatatatataatatacatatt -atatgtattatatattatatattatatatataatatacatattatatgtattatatatta -tatataatatacatattatatattatatattatatacatattatatattatatattatat -acatattatatattatatacatattatatattatatattatatacatattatacattata -tatatctaaaatatataatacacattatatattatataatacacattatatataatatat -aatacacattatatattatatataatacacattatatattatatataatacacattatat -attatataatacacattatatattatatataatacacattatatattatatataatacac -attatatattatatataatacacattatatattatatataatacacattatatattatat -aatacacattatatattatatataatacacattatatatataatacacattatatattat -atataatacataatacacattatatattatatataatacacattatatataatatataac -acacattatatataatatataacacacattatatattatatataatacacattatatatt -atat ->p:HG002_2_chr20:38123699-38124103 -taataataatatataatatttataataataatatatataatatgtatatataatatacat -atacctattatatataatatacctattatatataatatacataaacctattatatataat -atacctattatatataagatacctattatatataatatacctatacctattatatatata -atataccttatatataagatacctattatatataatatacata-----tacctattatat -atataatatacctattatatatatataatatacctattatatatataatatacctattat -atatataatatacctat--tatatatataatacctattatatataatatacctattatat -acattatatataatatacctattatatg---------------------------catta -tatataatatacctattatatgcattatatataatatacctattatatgcattatatata -atatacctattatatgcattatatataatatacctattatatgcattatataatatatta -tatataatatgcatattatatgtattatatattatatattatatatataatatacatatt -atatgtattatatattatatattatatatataatatacatattatatgtattatatatta -tatataatatacatattatatattatatattatatacatattatatattatatattatat -acatattatatattatatacatattatatattatatattatatacatattatacattata -tatatctaaaatatataatacacattatatattatataatacacattatatataatatat -aatacacattatatattatatataatacacattatatattatatataatacacattatat -at-----------------------tatataatacacattatatattatatataatacac -attatatattatatataatacacattatatattatatataatacacattatatattatat -aatacacattatatattatatataatacacattatatatataatacacattatatattat -atataatacataatacacattacctattatatataatacacattatatataatatataac -acacattatatataatatataacacacattatatattatatataatacacattatatatt -atat ->ref_chr20:38123699-38124103 -taataataatatataatatttataataataatatatataatatgtatatataatatacat -atacctattatatataatatacctattatatataatatacataaacctattatatataat -atacctattatatataagatacctattatatataatatacctat--------tatatata -agatacct----------------attatatataatatacata-----tacctattatat -atataatatacctattatatatatataatatacctattatatatataatatacctattat -atatataatatacctattatatatataatatacctattatatataa-----------tac -acattatatataata----tataacaca---------------------------catta -tatataata----tataacacacattatatattata----tataatacacattatatatt -atat-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_2cc8c537fa6f6cf120276dd31256362a.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2cc8c537fa6f6cf120276dd31256362a.msa deleted file mode 100644 index a6b21aa2..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_2cc8c537fa6f6cf120276dd31256362a.msa +++ /dev/null @@ -1,200 +0,0 @@ ->syndip_1_chr20:18208897-18210927 -attatgagtgaaagagacagggatggaggaaggaatgggggaaggaggagaggagtaggt -aaggaaggaatgcacgtcaatctgagtaaagggtatataggtattctttgtactgttttt -atttttgcaacttttctgtgtttacagttatttccaaataaaaaataagcagaaaggaaa -agctaatcatctccccctattccagtcccccaggcatgtatccttccgtagcttctccac -acctacacgaacctagacgattccttccacaccttccccacacccacacgaacctagacg -attccttccacaccttccccacacccacacgaacctagatgaattccttccacaccttct -ccacacccacacgaacctagacgattccttccacaccttccccacacccattctccacac -ccacacgaacctagacgattccttccacacctccacacccacacgaacctagatgaattc -cttccacaccttccccacacccacacaaacctagacgattccttccacaccttctccaca -cccacacgaacctagacgaattccttccagaccttctccacacccacacagacctagacg -attccttccacacctccacacccacacgaacctagacgaattccttccacaccttctcca -cacccacacgaacctagacgaattccttccacaccttctccacacccacacgaacctaga -cgaattccttccacaccttctccacacccacacgaacctagacgattccttccacacttt -ccccacacccacacgaacctagacg-attccttccacac---ctccacacccacacgaac -ctagatgaattccttccacaccttccccacacccacacaaacctagacgattccttccac -accttctccacacccacacaaacctagacaattccttccacacacacatgaacctagatg -aattccttccacaccttctccacacccacatgaacctagacgattccttccacaccttct -ccacacccacacacacctagatgaattccttccacaccttccccacacccacacagacct -agacgaattccttccacaccttctccacacccacacgaacctagacgattccttccacac -cttctccatacccacacgaacctagacaattccttccacaccttctcacacccacacaaa -cctagatgaattccttccacaccttctccacacccacacgaacctaaacgattccttcca -caccttctccacacccacacacacctagatgaattccttccacaccttccccacacccac -acagacctagacgaattccttccacaccttctccacacccacacgaacctagacgattcc -ttccacaccttctccatacccacacgaacctagacaattccttccacaccttctcacacc -cacacaaacctagatgaattccttccacaccttccccacacccacacagacctagacgaa -ttccttccacaccttctccacacccacacgaacctagacaattccttccacaccttctca -cacccacacaaacctagacgaattccttccacaccttctccacacccacacaaacctaga -tgaattccttccacaccttcctcacacccacacgaacctagacgattccttccacacctt -ccccacacccacacagacctagacgaattccttccacaccttctccacacccacacgaac -ctagacgattccttccacaccttccccacacccacacgaacctagacaattccttccaca -ccttctcacacccacacaaacctagatgaattccttccacaccttctccacacccacaca -aacctagacgaattccttccacaccttcctcacacccacacgaacctagacgattccttc -cacaccttccccacacccacacagacctagacgaattccttccacaccttcctaacaccc -acacgaacctagagaattccttccacaccttcacacccacacaaacctagacgaattcct -tccacaccttctccacacccacacaaacctagacaaattcttatacacttaaaatgggat -tttgttgttttattaaaatgcagtcattctctatgcattaattattgtgcagcttgattt -ttctcctttttttttgttaaatcttcctccgtcatccaggctggagtgcagtggcgtgat -ctcagctcactgcaacctccacctcctaggttcaagtgattctcctgcctcagcctcctg -agtagctaggatcacagagttgtacgataa ->syndip_2_chr20:18208897-18210927 -attatgagtgaaagagacagggatggaggaaggaatgggggaaggaggagaggagtaggt -aaggaaggaatgcacgtcaatctgagtaaagggtatataggtattctttgtactgttttt -atttttgcaacttttctgtgtttacagttatttccaaataaaaaataagcagaaaggaaa -agctaatcatctccccctattccagtcccccaggcatgtatccttccgtagcttctccac -acctacacgaacctagacgattccttccacaccttccccacacccacacgaacctagacg -attccttccacaccttccccacacccacacgaacctagatgaattccttccacaccttct -ccacacccacacgaacctagacgattccttccacaccttccccacacccattctccacac -ccacacgaacctagacgattccttccacacctccacacccacacgaacctagatgaattc -cttccacaccttccccacacccacacaaacctagacgattccttccacaccttctccaca -cccacacgaacctagacgaattccttccagaccttctccacacccacacagacctagacg -attccttccacacctccacacccacacgaacctagacgaattccttccacaccttctcca -cacccacacgaacctagacgaattccttccacaccttctccacacccacacgaacctaga -cgaattccttccacaccttctccacacccacacgaacctagacgattccttccacacttt -ccccacacccacaagaacctagacg-attccttccacac---ctccacacccacacgaac -ctagatgaattccttccacaccttccccacacccacacaaacctagacgattccttccac -accttctccacacccacacaaacctagacaattccttccacacacacatgaacctagatg -aattccttccacaccttctccacacccacatgaacctagacgattccttccacaccttct -ccacacccacacacacctagatgaattccttccacaccttccccacacccacacagacct -agacgaattccttccacacattctccacacccacacgaacctagacgattccttccacac -cttctccatacccacacgaacctagacaattccttccacaccttctcacacccacacaaa -cctagatgaattccttccacaccttctccacacccacacgaacctaaacgattccttcca -caccttctccacacccacacacacctagatgaattccttccacaccttccccacacccac -acagacctagacgaattccttccacaccttctccacacccacacgaacctagacgattcc -ttccaca------------ccacacgaacctagacaattccttccacaccttctcacacc -cacacaaacctagatgaattccttccacaccttccccacacccacacagacctagacgaa -ttccttccacaccttctccacacccacacgaacctagacaattccttccacaccttctca -cacccacacaaacctagacgaattccttccacaccttctccacacccacacaaacctaga -cgaattccttccacaccttcctcacacccacacgaacctagacgattccttccacacctt -ccccacacccacacagacctagacgaattccttccacaccttctccacacccacacgaac -ctagacgattccttccacaccttccccacacccacacgaacctagacaattccttccaca -ccttctcacacccacacaaacctagatgaattccttccacaccttctccacacccacaca -aacctagacgaattccttccacaccttcctcacacccacacgaacctagacgattccttc -cacaccttccccacacccacacagacctagacgaattccttccacaccttcctaacaccc -acacgaacctagagaattccttccacaccttcacacccacacaaacctagacgaattcct -tccacaccttctccacacccacacaaacctagacaaattcttatacacttaaaatgggat -tttgttgttttattaaaatgcagtcattctctatgcattaattattgtgcagcttgattt -ttctcctttttttttgttaaatcttcctccgtcatccaggctggagtgcagtggcgtgat -ctcagctcactgcaacctccacctcctaggttcaagtgattctcctgcctcagcctcctg -agtagctaggatcacagagttgtacgataa ->p:HG002_1_chr20:18208897-18210927 -attatgagtgaaagagacagggatggaggaaggaatgggggaaggaggagaggagtaggt -aaggaaggaatgcacgtcaatctgagtaaagggtatataggtattctttgtactgttttt -atttttgcaacttttctgtgtttacagttatttccaaataaaaaataagcagaaaggaaa -agctaatcatctccccctattccagtcccccaggcatgtatccttccgtagcttctccac -acctacacgaacctagacgattccttccacaccttccccacacccacacgaacctagacg -attccttccacaccttccccacacccacacgaacctagatgaattccttccacaccttct -ccacacccacacgaacctagacgattccttccacaccttccccacacccattctccacac -ccacacgaacctagacgattccttccacacctccacacccacacgaacctagatgaattc -cttccacaccttccccacacccacacaaacctagacgattccttccacaccttctccaca -cccacacgaacctagacgaattccttccagaccttctccacacccacacagacctagacg -attccttccacacctccacacccacacgaacctagacgaattccttccacaccttctcca -cacccacacgaacctagacgaattccttccacaccttctccacacccacacgaacctaga -cgaattccttccacaccttctccacacccacacgaacctagacgattccttccacacttt -ccccacacccacaagaacctagacg-attccttccacac---ctccacacccacacgaac -ctagatgaattccttccacaccttccccacacccacacaaacctagacgattccttccac -accttctccacacccacacaaacctagacaattccttccacacacacatgaacctagatg -aattccttccacaccttctccacacccacatgaacctagacgattccttccacaccttct -ccacacccacacacacctagatgaattccttccacaccttccccacacccacacagacct -agacgaattccttccacacattctccacacccacacgaacctagacgattccttccacac -cttctccatacccacacgaacctagacaattccttccacaccttctcacacccacacaaa -cctagatgaattccttccacaccttctccacacccacacgaacctaaacgattccttcca -caccttctccacacccacacacacctagatgaattccttccacaccttccccacacccac -acagacctagacgaattccttccacaccttctccacacccacacgaacctagacgattcc -ttccaca------------ccacacgaacctagacaattccttccacaccttctcacacc -cacacaaacctagatgaattccttccacaccttccccacacccacacagacctagacgaa -ttccttccacaccttctccacacccacacgaacctagacaattccttccacaccttctca -cacccacacaaacctagacgaattccttccacaccttctccacacccacacaaacctaga -cgaattccttccacaccttcctcacacccacacgaacctagacgattccttccacacctt -ccccacacccacacagacctagacgaattccttccacaccttctccacacccacacgaac -ctagacgattccttccacaccttccccacacccacacgaacctagacaattccttccaca -ccttctcacacccacacaaacctagatgaattccttccacaccttctccacacccacaca -aacctagacgaattccttccacaccttcctcacacccacacgaacctagacgattccttc -cacaccttccccacacccacacagacctagacgaattccttccacaccttcctaacaccc -acacgaacctagagaattccttccacaccttcacacccacacaaacctagacgaattcct -tccacaccttctccacacccacacaaacctagacaaattcttatacacttaaaatgggat -tttgttgttttattaaaatgcagtcattctctatgcattaattattgtgcagcttgattt -ttctcctttttttttgttaaatcttcctccgtcatccaggctggagttcagtggcgtgat -ctcagctcactgcaacctccacctcctaggttcaagtgattctcctgcctcagcctcctg -agtagctaggatcacagagttgtacgataa ->p:HG002_2_chr20:18208897-18210927 -attatgagtgaaagagacagggatggaggaaggaatgggggaaggaggagaggagtaggt -aaggaaggaatgcacgtcaatctgagtaaagggtatataggtattctttgtactgttttt -atttttgcaacttttctgtgtttacagttatttccaaataaaaaataagcagaaaggaaa -agctaatcatctccccctattccagtcccccaggcatgtatccttccgtagcttctccac -acctacacgaacctagacgattccttccacaccttccccacacccacacgaacctagacg -attccttccacaccttccccacacccacacgaacctagatgaattccttccacaccttct -ccacacccacacgaacctagacgattccttccacaccttccccacacccattctccacac -ccacacgaacctagacgattccttccacacctccacacccacacgaacctagatgaattc -cttccacaccttccccacacccacacaaacctagacgattccttccacaccttctccaca -cccacacgaacctagacgaattccttccagaccttctccacacccacacagacctagacg -attccttccacacctccacacccacacgaacctagacgaattccttccacaccttctcca -cacccacacgaacctagacgaattccttccacaccttctccacacccacacgaacctaga -cgaattccttccacaccttctccacacccacacgaacctagacgattccttccacacttt -ccccacacccacacgaacctagacg-attccttccacac---ctccacacccacacgaac -ctagatgaattccttccacaccttccccacacccacacaaacctagacgattccttccac -accttctccacacccacacaaacctagacaattccttccacacacacatgaacctagatg -aattccttccacaccttctccacacccacatgaacctagacgattccttccacaccttct -ccacacccacacacacctagatgaattccttccacaccttccccacacccacacagacct -agacgaattccttccacaccttctccacacccacacgaacctagacgattccttccacac -cttctccatacccacacgaacctagacaattccttccacaccttctcacacccacacaaa -cctagatgaattccttccacaccttctccacacccacacgaacctaaacgattccttcca -caccttctccacacccacacacacctagatgaattccttccacaccttccccacacccac -acagacctagacgaattccttccacaccttctccacacccacacgaacctagacgattcc -ttccacaccttctccatacccacacgaacctagacaattccttccacaccttctcacacc -cacacaaacctagatgaattccttccacaccttccccacacccacacagacctagacgaa -ttccttccacaccttctccacacccacacgaacctagacaattccttccacaccttctca -cacccacacaaacctagacgaattccttccacaccttctccacacccacacaaacctaga -tgaattccttccacaccttcctcacacccacacgaacctagacgattccttccacacctt -ccccacacccacacagacctagacgaattccttccacaccttctccacacccacacgaac -ctagacgattccttccacaccttccccacacccacacgaacctagacaattccttccaca -ccttctcacacccacacaaacctagatgaattccttccacaccttctccacacccacaca -aacctagacgaattccttccacaccttcctcacacccacacgaacctagacgattccttc -cacaccttccccacacccacacagacctagacgaattccttccacaccttcctaacaccc -acacgaacctagagaattccttccacaccttcacacccacacaaacctagacgaattcct -tccacaccttctccacacccacacaaacctagacaaattcttatacacttaaaatgggat -tttgttgttttattaaaatgcagtcattctctatgcattaattattgtgcagcttgattt -ttctcctttttttttgttaaatcttcctccgtcatccaggctggagtgcagtggcgtgat -ctcagctcactgcaacctccacctcctaggttcaagtgattctcctgcctcagcctcctg -agtagctaggatcacagagttgtacgataa ->ref_chr20:18208897-18210927 -attatgagtgaaagagacagggatggaggaaggaatgggggaaggaggagaggagtaggt -aaggaaggaatgcacgtcaatctgagtaaagggtatataggtattctttgtactgttttt -atttttgcaacttttctgtgtttacagttatttccaaataaaaaataagcagaaaggaaa -agctaatcatctccccctattccagtcccccaggcatgtatccttccgtagcttctccac -acct-----------------------------------------acacgaacctagacg -attccttccacaccttccccacacccacacgaacctagatgaattccttccacaccttct -ccacacccacacgaacctagacgattccttccacaccttccccacacccattctccacac -ccacacgaacctagacgattccttccacacctccacacccacacgaacctagatgaattc -cttccacaccttccccacacccacacaaacctagacgattccttccacaccttctccaca -cccacacgaacctagacgaattccttccagaccttctccacacccacacagacctagacg -attccttccacacctccacacccacacgaacctagacgaattccttccacaccttgtgca -cacccacacgaacctagacgaattccttccacaccttctccacacccacacgaacctaga -cgaattccttccacaccttctccacacccacacgaacctagacgattccttccacacctt -ccccacacccacacagacctagacgaattccttgcacaccttctccacacccacacgaac -ctagacgaattccttccacaccttctccatacccacacgaacctagacaattccttccac -accttct-------------------------------cacacccacacaaacctagatg -aattccttccacaccttctccacacccacacgaacctaaacgattccttccacaccttct -ccacacccacacacacctagatgaattccttccacaccttccccacacccacacagacct -agacgaattccttccacaccttctccacacccacacgaacctagacgattccttccacac -cttctccatacccacacgaacctagacaattccttccacaccttctcacacccacacaa- ------------------------------------------------------------- -----------------------acctagatgaattccttccacaccttccccacacccac -acagacctagacgaattccttccacaccttctccacacccacacgaacctagacg----- ------------------------------------------------------------- ------------------------------------------------------------a -ttccttccacaccttccccacacccacacgaacctagacaattccttgcacaccttctca -cacccacacaaacctagacgaattccttccacaccttctccacacccacacaaacctaga -cgaattccttccacaccttcctcacacccacacgaacctagacgattccttccacacctt -ccccacacccacacagacctagacgaattccttccacaccttctccacacccacacgaac -ctagacgattccttccacaccttccccacacccacacgaacctagacaattccttccaca -ccttctcacacccacacaaacctagatgaattccttccacaccttctccacacccacaca -aacctagacgaattccttccacaccttcctcacacccacacgaacctagatgattccttc -cacaccttccccacacccacacagacctagacgaattccttccacaccttcctaacaccc -acacgaacctagagaattccttccacaccttcacacccacacaaacctagacgaattcct -tccacaccttctccacacccacacaaacctagacaaattcttatacacttaaaatgggat -tttgttgttttattaaaatgcagtcattctctatgcattaattattgtgcagcttgattt -ttctcctttttttttgttaaatcttcctccgtcatccaggctggagtgcagtggcgtgat -ctcagctcactgcaacctccacctcctaggttcaagtgattctcctgcctcagcctcctg -agtagctaggatcacagagttgtacgataa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_2f38352f5d313e362f1612ebf90ffbf9.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2f38352f5d313e362f1612ebf90ffbf9.msa deleted file mode 100644 index 22e0052d..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_2f38352f5d313e362f1612ebf90ffbf9.msa +++ /dev/null @@ -1,15 +0,0 @@ ->syndip_1_chr20:7720911-7721003 -agttaaatctaaatctaacaaatgacattttctttttcttttcttttctttctttttttt -tttttttttgggatggagttccactcttgttgc ->syndip_2_chr20:7720911-7721003 -agttaaatctaaatctaacaaatgacgttttctttttcttttc---------------tt -tttttttttgggatggagttccactcttgttgc ->p:HG002_1_chr20:7720911-7721003 -agttaaatctaaatctaacaaatgacgttttctttttcttttc---------------tt -tttttttttgggatggagttccactcttgttgc ->p:HG002_2_chr20:7720911-7721003 -agttaaatctaaatctaacaaatgacattttctttttcttttcttttctttctttttttt -tttttttttgggatggagttccactcttgttgc ->ref_chr20:7720911-7721003 -agttaaatctaaatctaacaaatgacattttctttttcttttcttttctttctttttttt -tttttttttgggatggagttccactcttgttgc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_2fe0750ba4d442fbe27fdc6937471d27.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2fe0750ba4d442fbe27fdc6937471d27.msa deleted file mode 100644 index 598cc812..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_2fe0750ba4d442fbe27fdc6937471d27.msa +++ /dev/null @@ -1,220 +0,0 @@ ->syndip_1_chr20:63948314-63948958 -ctctttgtagcttcctgcagcggcacagtctgtccaccgcgctccggagttccacaggaa -atggaacgctccacagatgccagttacgcccgaaaacgacacagaacacaggtgcggaca -gggaacggcatcctcagagcatggtcaggggagaaaagcaagctggaaggagagatgatt -ccatctgtataaaatccaggaaacgaaggacgctcaccgccatgcgcctcggtgtgagga -gggaggcgtgtgtgagagggaggggcgtgtgtgagaggga-ggggcgtgtgtgagaggga -ggggcgtgtgtgagggaggggtgtgtgtgagagggaggggcgtgtgtgagagggaggggg -cgtgtgtgagaggcagggg-gcgtgtgtgtgaggggcgtgtgtgagagggaggggcgtgt -gtgagagggagggg-gcgtgtgtgagggggggcgtgtgtgagaggtaggggcgtgtgtga -gagggaggggcgtgtgtgagggagggggcgtgtgtgagaggg-----------------a -ggggcgtgtgtgtgagggaggggcgtgtgagag-ggagggggcgtgtgtgagaggcaggg -gcgtgtgtgtgagggaggggcgtgagagggaggggcgtgtgtgagagggagggggcgtgt -gtgagggggggcgtgtgtgagaggtaggggcgtgtgt----gggagggggcgtgtgtgag -agggagggggcgtgtgtgagagggaggggcgtgtgtgagacggaggggcgtgtgtgagag -ggagggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggag -ggg---gcgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggag -aggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagagggaggggc -gtgtgagaggg-aggggcgtgtgtgagagg----------gagggggcgtgtgtgagagg -gagggggcgtgtgtgagagggaggggcgtgtgtgaagggaggggcgtgtgtgagagggag -ggggcgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcg -tgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgt -gtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagag--------ggagggggc -gtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagaggga-ggggcgtg -tgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagagggagggggcgtgtgtg -agagggagggggcgtgt-------------gtgagagggagaggcgtgtgtgagagggag -gggcgtgtgtgagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggg -cgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtg -tgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtg -tgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtga -gagggag--------------ggggcgtgtgtgagagggaggggcgtgtgtgagagggag -gggcgtgtgtgagagggagggggcgtgtgtgagaggga-ggggcgtgtgtgagagggagg -ggcgtgtgtgaagggaggggcgtgtgtgagagtgggggcgtgtgtgagttaggggcgtga -gaggtaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtg-----ag -agggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagg -gagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggca -ggggcgtgtgtgagggaggggcgtgtgtgagagggagggg-gcgtgtgagagggaggggc -gtgtgtgagagggaggggc--gtgtgagagggaggggcgtgtgtgagaggga-ggggcgt -gtgtgagagggagggg-cgtgtgtgagagggaggggcgtgagagggagggggc--gtgtg -tgagggaggggcgtgtgtgagaggg-aggggggcgtgtgtgagagggagggggcgtgtgt -gagagggagggggtgtgtgtgagaccgagggggcgtgtaagggagggggtgtgtgtgaga -gggaagcgtgtgcacacaccagccctaaccatgatcactctctggccaccaagatttgga -acagcaacttctgtcacatttgaatgtttttaaagcaggtgccactttgttgccataaac -caaaccgtagtctgtctttgaaggtggcatctccagcgtgggaacactgattcccacctg -ggcactcctccccgtgcacccgtgacacccacagccaggaggacagtgtccgtg ->syndip_2_chr20:63948314-63948958 -ctctttgtagcttcctgcagcggcacagtctgtccaccgcgctccggagttccacaggaa -atggaacgctccacagatgccagttacgcccgaaaacgacacagaacacaggtgcggaca -gggaacggcatcctcagagcatggtcaggggagaaaagcaagctggaaggagagatgatt -ccatctgtataaaatccaggaaacgaaggacgctcaccgccatgcgcctcggtgtgagga -gggaggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagaggga -ggggcgtgtgtgagggaggggtgtgtgtgagagggaggggcgtgtgtgagagggaggggg -cgtgtgtgaaagggaggggcgtgtgtgagggaggggcgtgtgtgagagggaggggcgtgt -gtgagaggcaggggcgtgtgtgagggagggggcgtgtgtgagagggaggggcgtgtgtga -gaggcaggggcgtgtgtgagagtgggggcgtgtgtgagggggggcgtgtgtgagagggag -ggggcgtgtgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggg -gcgtgtgtgagaggcaggggcgtgtgtggggggggcgtgtgtgag-gggggggcgtgtgt -gagagggagggggcgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgtg -aggga-ggggcgtgtgtgagagggaggggcgtgtgtga---agggaggggtgtgtgtgag -agtgggggcgtgtgtgagaggg--------gcgtgagaggtaggggcgtgtgtgagaggg -aggggtgtgtgtgagagggaggggcgtgtgtgagaggga-ggggcgtgtgtgag-ggagg -gggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagagggaggggc -gtgtgtgagagtgggggcgtgtgtgggggggcgtgtgtgagggggggcgtgtgtgagagg -ta-ggggcgtgtgtgagagggaggggcgtgtgtg-agggaggggcgtgtgtgagaggcag -gggcgtgtgtgggggggggcgtgtgt--gaggggggggcgtgtgtgagagggagggggcg -tgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgt -gtgagaggcaggggcgtgtgtggggggggcgtgtgtgaggggggcgtgtgagagggaggg -gcgtgtgtggggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtg -tgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgaagggaggggtgtgtgtg -agagtgggggcgtgtgtgagagttaggggcgtgagaggtaggggcgtgtgtgagagggag -gggcgtgtgtgaggga-ggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggg -cgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtg -tgcgagagggaggggcgtgtgtgagagggagggggcgtgtgtgag-ggagggggcgtgtg -tgagagggaggggcgtgtgagag-ggagggggcgtgtgtgagaggcaggggcgtgtgtgt -gagggaggggcgtgagagggaggggcgtgtgtga---gggggggcgtgtgtgagaggtag -gggcgtgtgtgagagggagggggcgtgtgtgagagggagggggcgtgtgtgagagggagg -ggcgtgtgtgagggagggggcgtgt-------------------------------gtga -gagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgaga -gggagggggcgtgtgtgagagggaggggcgtgtgtga-agggaggggcgtgtgtgagagt -gggggcgtgtgtgagaggg----------gcgtgagaggtaggggcgtgtgtgagaggga -gggg-gcgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggc -gtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagagggagggggcgt -gtgtgagagggagggg-cgtgt---------------gtgagagggaaggggc--gtgtg -agagggaggggcgtgtgtgagaggg-aggggcgtgtgtgaga---gggaggggcgtgtgt -gagagggagggggtgtgtgtgagaccgagggggcgtgtaagggagggggtgtgtgtgaga -gggaagcgtgtgcacacaccagccctaaccatgatcactctctggccaccaagatttgga -acagcaacttctgtcacatttgaatgtttttaaagcaggtgccactttgttgccataaac -caaaccgtagtctgtctttgaaggtggcatctccagcgtgggaacactgattcccacctg -ggcactcctccccgtgcacccgtgacacccacagccaggaggacagtgtccgtg ->p:HG002_1_chr20:63948314-63948958 -ctctttgtagcttcctgcagcggcacagtctgtccaccgcgctccggagttccacaggaa -atggaacgctccacagatgccagttacgcccgaaaacgacacagaacacaggtgcggaca -gggaacggcatcctcagagcatggtcaggggagaaaagcaagctggaaggagagatgatt -ccatctgtataaaatccaggaaacgaaggacgctcaccgccatgcgcctcggtgtgagga -gggaggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagaggga -ggggcgtgtgtgagggaggggtgtgtgtgagagggaggggcgtgtgtgagagggaggggg -cgtgtgtgaaagggaggggcgtgtgtgagggaggggcgtgtgtgagagggaggggcgtgt -gtgagaggcaggggcgtgtgtgagggagggggcgtgtgtgagagggaggggcgtgtgtga -gaggcaggggcgtgtgtgagagtgggggcgtgtgtgagggggggcgtgtgtgagagggag -ggggcgtgtgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggg -gcgtgtgtgagaggcaggggcgtgtgtggggggggcgtgtgtgag-gggggggcgtgtgt -gagagggagggggcgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgtg -aggga-ggggcgtgtgtgagagggaggggcgtgtgtga---agggaggggtgtgtgtgag -agtgggggcgtgtgtgagaggg--------gcgtgagaggtaggggcgtgtgtgagaggg -aggggtgtgtgtgagagggaggggcgtgtgtgagaggga-ggggcgtgtgtgag-ggagg -gggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagagggaggggc -gtgtgtgagagtgggggcgtgtgtgggggggcgtgtgtgagggggggcgtgtgtgagagg -ta-ggggcgtgtgtgagagggaggggcgtgtgtg-agggaggggcgtgtgtgagaggcag -gggcgtgtgtgggggggggcgtgtgt--gaggggggggcgtgtgtgagagggagggggcg -tgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgt -gtgagaggcaggggcgtgtgtggggggggcgtgtgtgaggggggcgtgtgagagggaggg -gcgtgtgtggggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtg -tgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgaagggaggggtgtgtgtg -agagtgggggcgtgtgtgagagttaggggcgtgagaggtaggggcgtgtgtgagagggag -gggcgtgtgtgaggga-ggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggg -cgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtg -tgcgagagggaggggcgtgtgtgagagggagggggcgtgtgtgag-ggagggggcgtgtg -tgagagggaggggcgtgtgagag-ggagggggcgtgtgtgagaggcaggggcgtgtgtgt -gagggaggggcgtgagagggaggggcgtgtgtga---gggggggcgtgtgtgagaggtag -gggcgtgtgtgagagggagggggcgtgtgtgagagggagggggcgtgtgtgagagggagg -ggcgtgtgtgagggagggggcgtgt-------------------------------gtga -gagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgaga -gggagggggcgtgtgtgagagggaggggcgtgtgtga-agggaggggcgtgtgtgagagt -gggggcgtgtgtgagaggg----------gcgtgagaggtaggggcgtgtgtgagaggga -gggg-gcgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggc -gtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagagggagggggcgt -gtgtgagagggagggg-cgtgt---------------gtgagagggaaggggc--gtgtg -agagggaggggcgtgtgtgagaggg-aggggcgtgtgtgaga---gggaggggcgtgtgt -gagagggagggggtgtgtgtgagaccgagggggcgtgtaagggagggggtgtgtgtgaga -gggaagcgtgtgcacacaccagccctaaccatgatcactctctggccaccaagatttgga -acagcaacttctgtcacatttgaatgtttttaaagcaggtgccactttgttgccataaac -caaaccgtagtctgtctttgaaggtggcatctccagcgtgggaacactgattcccacctg -ggcactcctccccgtgcacccgtgacacccacagccaggaggacagtgtccgtg ->p:HG002_2_chr20:63948314-63948958 -ctctttgtagcttcctgcagcggcacagtctgtccaccgcgctccggagttccacaggaa -atggaacgctccacagatgccagttacgcccgaaaacgacacagaacacaggtgcggaca -gggaacggcatcctcagagcatggtcaggggagaaaagcaagctggaaggagagatgatt -ccatctgtataaaatccaggaaacgaaggacgctcaccgccatgcgcctcggtgtgagga -gggaggcgtgtgtgagagggaggggcgtgtgtgagaggga-ggggcgtgtgtgagaggga -ggggcgtgtgtgagggaggggtgtgtgtgagagggaggggcgtgtgtgagagggaggggg -cgtgtgtgagaggcagggg-gcgtgtgtgtgaggggcgtgtgtgagagggaggggcgtgt -gtgagagggagggg-gcgtgtgtgagggggggcgtgtgtgagaggtaggggcgtgtgtga -gagggaggggcgtgtgtgagggagggggcgtgtgtgagaggg-----------------a -ggggcgtgtgtgtgagggaggggcgtgtgagag-ggagggggcgtgtgtgagaggcaggg -gcgtgtgtgtgagggaggggcgtgagagggaggggcgtgtgtgagagggagggggcgtgt -gtgagggggggcgtgtgtgagaggtaggggcgtgtgt----gggagggggcgtgtgtgag -agggagggggcgtgtgtgagagggaggggcgtgtgtgagacggaggggcgtgtgtgagag -ggagggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggag -ggg---gcgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggag -aggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagagggaggggc -gtgtgagaggg-aggggcgtgtgtgagagg----------gagggggcgtgtgtgagagg -gagggggcgtgtgtgagagggaggggcgtgtgtgaagggaggggcgtgtgtgagagggag -ggggcgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcg -tgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgt -gtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagag--------ggagggggc -gtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagaggga-ggggcgtg -tgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagagggagggggcgtgtgtg -agagggagggggcgtgt-------------gtgagagggagaggcgtgtgtgagagggag -gggcgtgtgtgagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggg -cgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtg -tgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtg -tgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtga -gagggag--------------ggggcgtgtgtgagagggaggggcgtgtgtgagagggag -gggcgtgtgtgagagggagggggcgtgtgtgagaggga-ggggcgtgtgtgagagggagg -ggcgtgtgtgaagggaggggcgtgtgtgagagtgggggcgtgtgtgagttaggggcgtga -gaggtaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtg-----ag -agggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagg -gagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggca -ggggcgtgtgtgagggaggggcgtgtgtgagagggagggg-gcgtgtgagagggaggggc -gtgtgtgagagggaggggc--gtgtgagagggaggggcgtgtgtgagaggga-ggggcgt -gtgtgagagggagggg-cgtgtgtgagagggaggggcgtgagagggagggggc--gtgtg -tgagggaggggcgtgtgtgagaggg-aggggggcgtgtgtgagagggagggggcgtgtgt -gagagggagggggtgtgtgtgagaccgagggggcgtgtaagggagggggtgtgtgtgaga -gggaagcgtgtgcacacaccagccctaaccatgatcactctctggccaccaagatttgga -acagcaacttctgtcacatttgaatgtttttaaagcaggtgccactttgttgccataaac -caaaccgtagtctgtctttgaaggtggcatctccagcgtgggaacactgattcccacctg -ggcactcctccccgtgcacccgtgacacccacagccaggaggacagtgtccgtg ->ref_chr20:63948314-63948958 -ctctttgtagcttcctgcagcggcacagtctgtccaccgcgctccggagttccacaggaa -atggaacgctccacagatgccagttacgcccgaaaacgacacagaacacaggtgcggaca -gggaacggcatcctcagagcatggtcaggggagaaaagcaagctggaaggagagatgatt -ccatctgtataaaatccaggaaacgaaggacgctcaccgccatgcgcctcg--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------gtgtgaggagggaggcgt -gtgtgagagggaggggatgtgt---------------gtgagagggagggggcgtgtgtg -agagggaggggcgtgtgtgagagggaaggggcgtgtgtgaga---gggaggggcgtgtgt -gagagggagggggtgtgtgtgagaccgagggggcgtgtaagggagggggtgtgtgtgaga -gggaagcgtgtgcacacaccagccctaaccatgatcactctctggccaccaagatttgga -acagcaacttctgtcacatttgaatgtttttaaagcaggtgccactttgttgccataaac -caaaccgtagtctgtctttgaaggtggcatctccagcgtgggaacactgattcccacctg -ggcactcctccccgtgcacccgtgacacccacagccaggaggacagtgtccgtg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_32f6f2dff38622b1e9f06443baeb622f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_32f6f2dff38622b1e9f06443baeb622f.msa deleted file mode 100644 index d5ef8898..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_32f6f2dff38622b1e9f06443baeb622f.msa +++ /dev/null @@ -1,60 +0,0 @@ ->syndip_1_chr20:62270313-62270927 -ctcctggcctctctgggtcctctccttgtccctcctggcctctctgggtcctctccttgt -ccctccctgacctctctgggtcctctccttgtccctctctggcctctctgggtcctctcc -ttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtc -cctc-ctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctct -ctggcctctctgggtcctctct---gacctctctgagtcctctccttgtccctctctgg- -----------------------------gtcctctccttgtccctctctgggtcctctcc -ttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtc -cctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctct -ctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtcc -ctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctc -tggcctctctgggtcc ->syndip_2_chr20:62270313-62270927 -ctcctggcctctctgggtcctctccttgtccctcctggcctctctgggtcctctccttgt -ccctccctgacctctctgggtcctctccttgtccctctctggcctctctgggtcctctcc -ttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtc -cctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctc- -ctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctga- -------------------------------------------cctctctgggtcctctcc -ttgtccctctctgggtcctctccttgtc-------------------------------- ----------cctctctgggtcctctccttgtccctctctgggtcctctccttgtccctct -ctggcctctctgggtcctctccttgtccctctctggcctctctgggtcc----------- ------------------------------------------------------------- ----------------- ->p:HG002_1_chr20:62270313-62270927 -ctcctggcctctctgggtcctctccttgtccctcctggcctctctgggtcctctccttgt -ccctccctgacctctctgggtcctctccttgtccctctctggcctctctgggtcctctcc -ttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtc -cctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctc- -ctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctgg- -------------------------------------------cctctctgggtcctctc- -----------------------------------------ctctgggtcctctccttgtc -cctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctct -ctggcctctctgggtcctctccttgtccctctctggcctctctgggtcc----------- ------------------------------------------------------------- ----------------- ->p:HG002_2_chr20:62270313-62270927 -ctcctggcctctctgggtcctctccttgtccctcctggcctctctgggtcctctccttgt -ccctccctgacctctctgggtcctctccttgtccctctctggcctctctgggtcctctcc -ttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtc -cctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctc- -ctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctgg- -----------------------------gtcctctccttgtccctctctgggtcctctcc -ttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtc -cctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctct -ctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtcc -ctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctc -tggcctctctgggtcc ->ref_chr20:62270313-62270927 -ctcctggcctctctgggtcctctccttgtccctcctggcctctctgggtcctctccttgt -ccctccctgacctctctgggtcctctccttgtccctctctggcctctctgggtcctctcc -ttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtc -cctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctc- -ctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggc -ctctctgggtcctctctgacctctctgggtcctctccttgtccctctctgggtcctctcc -ttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtc -cctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctct -ctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtcc -ctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctc -tggcctctctgggtcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_35335f6151c790b9a47a9350279b1936.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_35335f6151c790b9a47a9350279b1936.msa deleted file mode 100644 index 5194c214..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_35335f6151c790b9a47a9350279b1936.msa +++ /dev/null @@ -1,80 +0,0 @@ ->syndip_1_chr20:20295914-20296430 -cagaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacc -aacgcctgcatgcttccctccttccttccttccttccctcctttccttccttctttcttt -tcttcctccctcccttcct---tcccttccttcccttccttccctccttttcttccttct -ttccttccttccttccctccctccttcccttccttccttccttcccttccttccttctct -ccttccttccttccctccctccttcccttccttccttctctccttccttc--ccttcctt -ccttctctccttccttcccttccttccttctctccttccttcccttccttccttctctcc -ttccttcccttccttccttctctccttccttcccttgctt--cctttcttccttcctttg -cttccttgcttccttctttcctttcttcatccctccctccctccttccttcctttccttc -cttccctctatccttccttccttcctttctttctccctcccttccttcccttccttcctt -ccctcttttccttccatctttcctttcttcctccctccctccctccttccctccttcatt -ccttccttccctcctttccttccttcacctccttcccttctctcctcccttcatcccttc -cttcctttcttccttccctccctcttccttcctttcttcacccctcccccttccctcatc -ccttccctccttcccttccttccttccttccctccttccttcccttccttccttccttgc -ttccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttcct -tctttctttcttttctttcttcctcc ->syndip_2_chr20:20295914-20296430 -cagaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacc -aacgcctgcatgcttccctccttccttccttccttccctcc-ttccttccttccttcctt -ccttcctgcctgcctgcctgccttcctgccttcccttcctccctccc--tccctacctcc -ctccctccttccttcccttcctccctccctcccttctttacttccttcc-------tcct -tccctcctcctttcctccatccttccctcccttctttcctttcttcctcctgccctccct -ccttctttcccttcctccctcccttccttcccatcctccttccc-tccctccttccttcc -tgccttccttccttccctccatccttccttccttcctttcttcctccctcccttccttcc -tcccttccttcccttccttcct-----------tccctcttttccttccatctttccttt -cttcctccctccctccctccttccctccttcattccttccttccctcctttccttccttc -acctccttcccttctctcctcccttcatcccttccttcctttcttccttccctccctctt -ccttcctttcttcacccctcccccttccctcatcccttccctccttcccttccttccttc -cttccctccttccttccct---tccttccttccttccctccttccttcccttccttcctt -gcttccttccttccttcccttccttccttgcttccttccttccttcccttccttccttgc -ttccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttcct -tctttctttcttttctttcttcctcc ->p:HG002_1_chr20:20295914-20296430 -cagaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacc -aacgcctgcatgcttccctccttccttccttccttccctcc-ttccttccttccttcctt -ccttcctgcctgcctgcctgccttcctgccttcccttcctccctccc--tccctacctcc -ctccctccttccttcccttcctccctccctcccttctttacttccttcc-------tcct -tccctcctcctttcctccatccttccctcccttctttcctttcttcctcctgccctccct -ccttctttcccttcctccctcccttccttcccatcctccttccc-tccctccttccttcc -ttctttcttttcttcctccctcccttccttcccttccttc--ccttccttccctcctttt -cttccttctttccttccttcct-----------tccctccctccttcccttccttccttc -cttcctccctccctccctccttccctccttcattccttccttccctcctttccttccttc -acctccttcccttctctcctcccttcatcccttccttcctttcttccttccctccctctt -ccttcctttcttcacccctcccccttccctcatcccttccctccttcccttccttccttc -cttccctccttccttccct---tccttccttccttccctccttccttcccttccttcctt -gcttccttccttccttcccttccttccttgcttccttccttccttcccttccttccttgc -ttccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttcct -tctttctttcttttctttcttcctcc ->p:HG002_2_chr20:20295914-20296430 -cagaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacc -aacgcctgcatgcttccctccttccttccttccttccctcctttccttccttctttcttt -tcttcctccctcccttcct---tcccttccttcccttccttccctccttttcttccttct -ttccttccttccttccctccctccttcccttccttccttccttcccttccttccttctct -ccttccttccttccctccctccttcccttccttccttctctccttccttc--ccttcctt -ccttctctccttccttcccttccttccttctctccttccttcccttccttccttctctcc -ttccttcccttccttccttctctccttccttcccttgctt--cctttcttccttcctttg -cttccttgcttccttctttcctttcttcatccctccctccctccttccttcctttccttc -cttccctctatccttccttccttcctttctttctccctcccttccttcccttccttcctt -ccctcttttccttccatctttcctttcttcctccctccctccctccttccctccttcatt -ccttccttccctcctttccttccttcacctccttcccttctctcctcccttcatcccttc -cttcctttcttccttccctccctcttccttcctttcttcacccctcccccttccctcatc -ccttccctccttcccttccttccttccttccctccttccttcccttccttccttccttgc -ttccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttcct -tctttctttcttttctttcttcctcc ->ref_chr20:20295914-20296430 -cagaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacc -aacgcctgcatgcttccctccttccttccttccttccctcctttccttccttctttcttt -tcttcctccctcccttcct---tcccttccttc--------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------ccttccttccctcctttt -cttccttctttccttccttcct-----------tccctccctccttcccttccttccttc -cttcctccctccctccctccttccctccttcattccttccttccctcctttccttccttc -acctccttcccttctctcctcccttcatcccttccttcctttcttccttccctccctctt -ccttcctttcttcacccctcccccttccctcatcccttccctccttcccttccttccttc -cttccctccttccttccct----------------------------------------- ----------------------------------------------tccttccttccttgc -ttccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttcct -tctttctttcttttctttcttcctcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_39ba40884061f686140345a2ae738511.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_39ba40884061f686140345a2ae738511.msa deleted file mode 100644 index d87300a3..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_39ba40884061f686140345a2ae738511.msa +++ /dev/null @@ -1,100 +0,0 @@ ->syndip_1_chr20:63641579-63642335 -gaccaaggacgggtttcctgggagctggctgggccccgcttctagctcgtaccggagccg -agcttccttcagggcactttcaatataatgaatttagccatctattactgcggctagtta -ctgtcccgccaggaccagactctggacctgcctcgtgcgctgctggggacgcccagtaaa -cacgggaggagcccccgacccccaccccagctcagcgcctcggagtccccggccccgctc -tgcgcccctccgagctccgccctagccccgcccccgcccagtgccccgccccctgcctgc -tgctagccctgcccccgccccggcccctgcccgctccgagctccgccctggccccgcccc -ggcccctgcccgctccgagctccgccctggccccgccccccgcccagtgccccgccccct -gcctgctgctagccctgcccccgccccggcccctgcccgctccgagctccgccccgg--- ------------------------------------------------------------- ------------------------------------------------------------- -----------ccccgccccggcccctgcccgctccgagctccgccctggccccgcccccg -cccagtgccccgccccctgactgctgctagccctgcccccgccccggcccctgcccgctc -cgagctccgccccggccccgccccggcccctgcccgctccgagctccgccccggccccgc -cccggcccctgcccgctccgagcttcgccccggccccgccccggcccctgcccgctccga -gctccgccccggccccgcccccgcaccttctcgcgcagccgctcgcgcagtgcggccagg -tgtgcctcgcggatctccttgctgagctccatcttgtagttgagcttctcctccgcctgg -cggctgaagttgttattctcctccagcgccttgtgcagcacctcgcgctcgtgctcgcgc -cgctccgccagctgcttcagcacctgcgcctcctgcgtctgtgcggggccggcgggcgcg -cgtgagcggcaacc ->syndip_2_chr20:63641579-63642335 -gaccaaggacgggtttcctgggagctggctgggccccgcttctagctcgtaccggagccg -agcttccttcagggcactttcaatataatgaatttagccatctattactgcggctagtta -ctgtcccgccaggaccagactctggacctgcctcgtgcgctgctggggacgcccagtaaa -cacgggaggagcccccgacccccaccccagctcagcgcctcggagtccccggccccgctc -tgcgcccctccgagctccgccctagccccgcccccgcccagtgccccgccccctgcctgc -tgctagccctgcccccgccccggcccctgcccgctccgagctccgccctggccccgcccc -ggcccctgcccgctccgagctccgccctggccccg-cccccgcccagtgccccgccccct -gcctgctgctagccctgcccccgccccggcccctgcccgctccgagctccaccctggccc -cgcccccgcccagtgccccgccccctgcctgctgcttgccctgccccctccccggcccct -gcccgctccgagctccgccccggccccgccccggcccagtgccccgccccctgcctgctg -ctagccctgcccccgccccggcccctgcccgctccgagctccgccctggccccgcccccg -cccagtgccccgccccctgcctgctgcttgccctgccccctccccggcccctgcccgctc -cgagctccgccccggcctcgccccggcccctgcccgctccgagcttcgccccggccccgc -cccggcccctgcccgctccgagcttcgccccggccccgccccggcccctgcccgctccga -actccgccccggccccgcccccgcaccttctcgcgcagccgctcgcgcagtgcggccagg -tgtgcctcgcggatctccttgctgagctccatcttgtagttgagcttctcctccgcctgg -cggctgaagttgttattctcctccagcgccttgtgcagcacctcgcgctcgtgctcgcgc -cgctccgccagctgcttcagcacctgcgcctcctgcgtctgtgcggggccggcgggcgcg -cgtgagcggcaacc ->p:HG002_1_chr20:63641579-63642335 -gaccaaggacgggtttcctgggagctggctgggccccgcttctagctcgtaccggagccg -agcttccttcagggcactttcaatataatgaatttagccatctattactgcggctagtta -ctgtcccgccaggaccagactctggacctgcctcgtgcgctgctggggacgcccagtaaa -cacgggaggagcccccgatccccaccccagctcagcgcctcggagtccccggccccgctc -tgcgcccctccgagctccgccctagccccgcccccgcccagtgccccgccccctgcctgc -tgctagccctgcccccgccccggcccctgcccgctccgagctccgccctggccccgcccc -ggcccctgcccgctccgagctccgccctggccccg-cccccgcccagtgccccgccccct -gcctgctgctagccctgcccccgccccggcccctgcccgctccgagctccaccctggccc -cgcccccgcccagtgccccgccccctgcctgctgcttgccctgccccctccccggcccct -gcccgctccgagctccgccccggccccgccccggcccagtgccccgccccctgcctgctg -ctagccctgcccccgccccggcccctgcccgctccgagctccgccctggccccgcccccg -cccagtgccccgccccctgcctgctgcttgccctgccccctccccggcccctgcccgctc -cgagctccgccccggcctcgccccggcccctgcccgctccgagcttcgccccggccccgc -cccggcccctgcccgctccgagcttcgccccggccccgccccggcccctgcccgctccga -actccgccccggccccgcccccgcaccttctcgcgcagccgctcgcgcagtgcggccagg -tgtgcctcgcggatctccttgctgagctccatcttgtagttgagcttctcctccgcctgg -cggctgaagttgttattctcctccagcgccttgtgcagcacctcgcgctcgtgctcgcgc -cgctccgccagctgcttcagcacctgcgcctcctgcgtctgtgcggggccggcgggcgcg -cgtgagcggcaacc ->p:HG002_2_chr20:63641579-63642335 -gaccaaggacgggtttcctgggagctggctgggccccgcttctagctcgtaccggagccg -agcttccttcagggcactttcaatataatgaatttagccatctattactgcggctagtta -ctgtcccgccaggaccagactctggacctgcctcgtgcgctgctggggacgcccagtaaa -cacgggaggagcccccgacccccaccccagctcagcgcctcggagtccccggccccgctc -tgcgcccctccgagctccgccctagccccgcccccgcccagtgccccgccccctgcctgc -tgctagccctgcccccgccccggcccctgcccgctccgagctccgccctggccccgcccc -ggcccctgcccgctccgagctccgccctggccccgccccccgcccagtgccccgccccct -gcctgctgctagccctgcccccgccccggcccctgcccgctccgagctccgccccgg--- ------------------------------------------------------------- ------------------------------------------------------------- -----------ccccgccccggcccctgcccgctccgagctccgccctggccccgcccccg -cccagtgccccgccccctgactgctgctagccctgcccccgccccggcccctgcccgctc -cgagctccgccccggccccgccccggcccctgcccgctccgagctccgccccggccccgc -cccggcccctgcccgctccgagcttcgccccggccccgccccggcccctgcccgctccga -gctccgccccggccccgcccccgcaccttctcgcgcagccgctcgcgcagtgcggccagg -tgtgcctcgcggatctccttgctgagctccatcttgtagttgagcttctcctccgcctgg -cggctgaagttgttattctcctccagcgccttgtgcagcacctcgcgctcgtgctcgcgc -cgctccgccagctgcttcagcacctgcgcctcctgcgtctgtgcggggccggcgggcgcg -cgtgagcggcaacc ->ref_chr20:63641579-63642335 -gaccaaggacgggtttcctgggagctggctgggccccgcttctagctcgtaccggagccg -agcttccttcagggcactttcaatataatgaatttagccatctattactgcggctagtta -ctgtcccgccaggaccagactctggacctgcctcgtgcgctgctggggacgcccagtaaa -cacgggaggagcccccgacccccaccccagctcagcgcctcggagtccccggccccgctc -tgcgcccctccgagctccgccctagccccgcccccgcccagtgccccgccccctgcctgc -tgctagccctgcccccgccccggcccctgcccgctccgagctccgccccggccccgcccc -ggcccctgcccgctccgagctccgccctggccccg-cccccgcccagtgccccgccccct -gactgctgctagccctgc------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------ccccgc -cccggcccctgcccgctccgagcttcgccccggccccgccccggcccctgcccgctccga -gctccgccccggccccgcccccgcaccttctcgcgcagccgctcgcgcagtgcggccagg -tgtgcctcgcggatctccttgctgagctccatcttgtagttgagcttctcctccgcctgg -cggctgaagttgttattctcctccagcgccttgtgcagcacctcgcgctcgtgctcgcgc -cgctccgccagctgcttcagcacctgcgcctcctgcgtctgtgcggggccggcgggcgcg -cgtgagcggcaacc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_39ca1f8997116d6bd1f696595f583494.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_39ca1f8997116d6bd1f696595f583494.msa deleted file mode 100644 index 69ac96b5..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_39ca1f8997116d6bd1f696595f583494.msa +++ /dev/null @@ -1,145 +0,0 @@ ->syndip_1_chr20:48449505-48450661 -gatgggtaatacaagaagaataaagggcgctgccctggactcagggagctcactcctcct -ctctgggcaacagagaaaagtcacccactgcagcaaaagccatgagaatatgctcagtga -taaggcagtggcgttaaatctgcaggcagtgggctatctgtgggtccttaaatctattta -gtgcatcttgaacagtatttttaagctgggataagtggaataggaaggagtggagtggag -catgatggtatgggatgggatggatgggatgggatggatggatggatggggtgggatggg -atgggatg-----ggatggatggatgggatggatggatgggatgggataggatggatggg -gtgagatgggatggaatggatgggatgggatggatggatgggatgggatggatgggatgg -gatggatgggatgggatggatgggatggatgggatggaatgggatggatgggatgggatg -ggattggatggggtgggatgggatggatggatgggatggatggatgggatggaatggatg -gatgggatgggatggatgggatgggatggatggatgggatgggatggatgcaatggatgg -atgggatgggatgggatgggatggatggaatggatggatgggatgggatgggatggatgg -ggtgggatgagatggatgggatggatgggatgggatggatggat---------------- --------ggatgggatgggatggatggatgggatgggatgggatggggtggatgggatgg -atggatggatgggatgggatggatggatgggatggaatggatgaatgggatgtgatggat -gggatggaatgggatagatgggatgggattggatgggatggggtgggatggggtaagatg -gggtgggatgggatggtatgggatggatggatgagatgggatgggatgagatgggattgg -atggggtgggatgcaatgggatgagatgagatgagatgagatgggatggatggcatggga -tgggatgggattggatggggtgggatgggatggggtaggatgggatgggatgggatggga -tgggatgggatgggatgggatgggatggggtgggatgggttgggatgggatggggtgggt -tgggatggggtggggtgggatgggatgggatgggatggggtggggtggggtggggtggga -tggggtgggatggggtgggatgggatggggtgggatgggatgggatggggtgggatggga -tggggtggggtggggtggggtgggatgaggtggggtgggatgggatgggatggggtgggg -tggggtgggatgggatgggatggggtggggtgggatgggattggatggggtgggatgcga -tgg-----gatgagatgagatggatggcatgggatgggtgggaggggatgggatattatc -agatggcaaaagtaagaagtgttcatattttgtcttcaaaatataaatatgagtgcataa -tggcttgtgatgcaaaatacatttcttactaaagatcatggacaaagcacttaaaaccac -acagtgtaagggactacagtcccttaggagctgcttttgcaataatttacctgaaaactg -gtatgaaaatgagtcatgaattggacacttgatgtcagattttt ->syndip_2_chr20:48449505-48450661 -gatgggtaatacaagaagaataaagggcgctgccctggactcagggagctcactcctcct -ctctgggcaacagagaaaagtcacccactgcagcaaaagccatgagaatatgctcagtga -taaggcagtggcgttaaatctgcaggcagtgggctatctgtgggtccttaaatctattta -gtgcatcttgaacagtatttttaagctgggataagtggaataggaaggagtggagtggag -catgatggtatgggatgggatggatgggatgggatggatggatggatggggtgggatggg -atgggatg-------------ggatggggtggatggatgggatgggataggatggatggg -gtgagatgggatggaatggatggaatgggatggatggatgggatgggatggatgggatgg -gatggatgggatggatgggatgggatggatgggatggaatgggatggatgggatgggatg -ggattggatggggtgggatgggatggatggatgggatggatggatgggatggaatggatg -gatgggatgggatggatgggatgggatggatggatgggatgggatggatgcaatggatgg -atgggatgggatgggatgggatggatggaatggatggatgggatgggatgggatggatgg -ggtgggatgagatggatgggatggatgggatgggatggatggatggatgggatgggatgg -atggatgggatgggatgggatggatggatgggatgggatgggatggggtggatgggatgg -atggatggatgggatgggatggatggatgggatggaatggatgaatgggatgtgatggat -gggatggaatgggatagatgggatgggattggatgggatggggtgggatggggtaagatg -gggtgggatgggatggtatgggatggatggatgagatgggatgggatgagatgggattgg -atggggtgggatgcaatgggatgagatgagatgagatgagatgggatggatggcatggga -tggaatgggattggatggggtgggatgggatggggtaggatgggatgggatgggatggga -tgggatgggatggggtgggatgggttgggatgggatggggtgggttgggatgggg----- ------tggggtgggatgggatgggatggggtgggatggggtgggatggggtgggatgggg -tgggatgggatggggtgggatgggatgggatgggatggggtgggatggggtgggatggga -tggggtggggtggggtggggtgggatgaggtggggtgggatgggatgggatggggtgggg -tggggtgggatgggatgggatggggtggggtgggatgggattggatggggtgggatgcga -tgggatgagatgagatgagatgaatggcatgggatgggtgggaggggatgggatattatc -agatggcaaaagtaagaagtgttcatattttgtcttcaaaatataaatatgagtgcataa -tggcttgtgatgcaaaatacatttcttactaaagatcatggacaaagcacttaaaaccac -acagtgtaagggactacagtcccttaggagctgcttttgcaataatttacctgaaaactg -gtatgaaaatgagtcatgaattggacacttgatgtcagattttt ->p:HG002_1_chr20:48449505-48450661 -gatgggtaatacaagaagaataaagggcgctgccctggactcagggagctcactcctcct -ctctgggcaacagagaaaagtcacccactgcagcaaaagccatgagaatatgctcagtga -taaggcagtggcgttaaatctgcaggcagtgggctatctgtgggtccttaaatctattta -gtgcatcttgaacagtatttttaagctgggataagtggaataggaaggagtggagtggag -catgatggtatgggatgggatggatgggatgggatggatggatggatggggtgggatggg -atgggatg-------------ggatggggtggatggatgggatgggataggatggatggg -gtgagatgggatggaatggatggaatgggatggatggatgggatgggatggatgggatgg -gatggatgggatggatgggatgggatggatgggatggaatgggatggatgggatgggatg -ggattggatggggtgggatgggatggatggatgggatggatggatgggatggaatggatg -gatgggatgggatggatgggatgggatggatggatgggatgggatggatgcaatggatgg -atgggatgggatgggatgggatggatggaatggatggatgggatgggatgggatggatgg -ggtgggatgagatggatgggatggatgggatgggatggatggatggatgggatgggatgg -atggatgggatgggatgggatggatggatgggatgggatgggatggggtggatgggatgg -atggatggatgggatgggatggatggatgggatggaatggatgaatgggatgtgatggat -gggatggaatgggatagatgggatgggattggatgggatggggtgggatggggtaagatg -gggtgggatgggatggtatgggatggatggatgagatgggatgggatgagatgggattgg -atggggtgggatgcaatgggatgagatgagatgagatgagatgggatggatggcatggga -tggaatgggattggatggggtgggatgggatggggtaggatgggatgggatgggatggga -tgggatgggatggggtgggatgggttgggatgggatggggtgggttgggatgggg----- ------tggggtgggatgggatgggatggggtgggatggggtgggatggggtgggatgggg -tgggatgggatggggtgggatgggatgggatgggatggggtgggatggggtgggatggga -tggggtggggtggggtggggtgggatgaggtggggtgggatgggatgggatggggtgggg -tggggtgggatgggatgggatggggtggggtgggatgggattggatggggtgggatgcga -tgggatgagatgagatgagatgaatggcatgggatgggtgggaggggatgggatattatc -agatggcaaaagtaagaagtgttcatattttgtcttcaaaatataaatatgagtgcataa -tggcttgtgatgcaaaatacatttcttactaaagatcatggacaaagcacttaaaaccac -acagtgtaagggactacagtcccttaggagctgcttttgcaataatttacctgaaaactg -gtatgaaaatgagtcatgaattggacacttgatgtcagattttt ->p:HG002_2_chr20:48449505-48450661 -gatgggtaatacaagaagaataaagggcgctgccctggactcagggagctcactcctcct -ctctgggcaacagagaaaagtcacccactgcagcaaaagccatgagaatatgctcagtga -taaggcagtggcgttaaatctgcaggcagtgggctatctgtgggtccttaaatctattta -gtgcatcttgaacagtatttttaagctgggataagtggaataggaaggagtggagtggag -catgatggtatgggatgggatggatgggatgggatggatggatggatggggtgggatggg -atgggatg-----ggatggatggatgggatggatggatgggatgggataggatggatggg -gtgagatgggatggaatggatgggatgggatggatggatgggatgggatggatgggatgg -gatggatgggatgggatggatgggatggatgggatggaatgggatggatgggatgggatg -ggattggatggggtgggatgggatggatggatgggatggatggatgggatggaatggatg -gatgggatgggatggatgggatgggatggatggatgggatgggatggatgcaatggatgg -atgggatgggatgggatgggatggatggaatggatggatgggatgggatgggatggatgg -ggtgggatgagatggatgggatggatgggatgggatggatggat---------------- --------ggatgggatgggatggatggatgggatgggatgggatggggtggatgggatgg -atggatggatgggatgggatggatggatgggatggaatggatgaatgggatgtgatggat -gggatggaatgggatagatgggatgggattggatgggatggggtgggatggggtaagatg -gggtgggatgggatggtatgggatggatggatgagatgggatgggatgagatgggattgg -atggggtgggatgcaatgggatgagatgagatgagatgagatgggatggatggcatggga -tgggatgggattggatggggtgggatgggatggggtaggatgggatgggatgggatggga -tgggatgggatgggatgggatgggatggggtgggatgggttgggatgggatggggtgggt -tgggatggggtggggtgggatgggatgggatgggatggggtggggtggggtggggtggga -tggggtgggatggggtgggatgggatggggtgggatgggatgggatggggtgggatggga -tggggtggggtggggtggggtgggatgaggtggggtgggatgggatgggatggggtgggg -tggggtgggatgggatgggatggggtggggtgggatgggattggatggggtgggatgcga -tgg-----gatgagatgagatggatggcatgggatgggtgggaggggatgggatattatc -agatggcaaaagtaagaagtgttcatattttgtcttcaaaatataaatatgagtgcataa -tggcttgtgatgcaaaatacatttcttactaaagatcatggacaaagcacttaaaaccac -acagtgtaagggactacagtcccttaggagctgcttttgcaataatttacctgaaaactg -gtatgaaaatgagtcatgaattggacacttgatgtcagattttt ->ref_chr20:48449505-48450661 -gatgggtaatacaagaagaataaagggcgctgccctggactcagggagctcactcctcct -ctctgggcaacagagaaaagtcacccactgcagcaaaagccatgagaatatgctcagtga -taaggcagtggcgttaaatctgcaggcagtgggctatctgtgggtccttaaatctattta -gtgcatcttgaacagtatttttaagctgggataagtggaataggaaggagtggagtggag -catgatggtatgggatgggatggatgggatgggatggatggatggatggggtgggatggg -atgggatgggatgggatggatggatgggatggatggatgggatgggataggatggatggg -gtgagatgggatggaatggatgggatgggatggatggatgggatgggatggatgggatgg -gatggatgggatgggatggatgggatggatgggatggaatgggatggatgggatgggatg -ggattggatggggtgggatgggatggatggatgggatggatggatgggatggaatggatg -gatgggatgggatggatgggatgggatggatggatgggatgggatggatgcaatggatgg -atgggatgggatgggatgggatggatggaatggatggatgggatgggatgggatggatgg -ggtgggatgagatggatgggatggatgggatgggatggatggat---------------- --------ggatgggatgggatggatggatgggatgggatgggatggggtggatgggatgg -atggatggatgggatgggatggatggatgggatgggat---------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------ggatgggatgggatggggtgggg -tggggtgggatgggatgggatggggtggggtgggatgggattggatggggtgggatgcga -tgg-----gatgagatgagatggatggcatgggatgggtgggaggggatgggatattatc -agatggcaaaagtaagaagtgttcatattttgtcttcaaaatataaatatgagtgcataa -tggcttgtgatgcaaaatacatttcttactaaagatcatggacaaagcacttaaaaccac -acagtgtaagggactacagtcccttaggagctgcttttgcaataatttacctgaaaactg -gtatgaaaatgagtcatgaattggacacttgatgtcagattttt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_3b4dc3fdc0731baf1f3751384209e4c4.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_3b4dc3fdc0731baf1f3751384209e4c4.msa deleted file mode 100644 index 88cd2b19..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_3b4dc3fdc0731baf1f3751384209e4c4.msa +++ /dev/null @@ -1,400 +0,0 @@ ->syndip_1_chr20:63167187-63167827 -acagctcagtctttgactaagtcacatcctcattgctcctgtttccacagagcagacacc -gacgtccagacatccagactggctgccaccagctcactggaatggccagcccgtcccgcc -gaggccagtggacatgccaaatccctcccgcaacaagttgctatccatcccctcgactaa -tacttaccaaattaattccagatttggagtcactcacggttcccaccagcactcagcccc -atctcagcccccatctcagcccccaccgcagcctcacctcagtgcccacctcagccccct -cctcagcccccacctccgcccccacctcagcccct------------------------c -ctcagcccccacctcagccccctcctcagcccccacctcc-------------------- ----gcccccacctccgcccccacctctgcccct-------------cctcagcccccacc -tcagccccctcctcagcccccacctccgcccccacctccgcccccacctctgcccct--- -----------------------------------cctcagcccccacctcagccccctcc -tcagcccccacctccgcccccacctccgcccccacctctgcccctcctcagcccccacct -cagccccctcctcag-----------cccccacctccgccccctcctcagcccccacctc -tgcccct------------cctcagcccccacctcagccccctcctcagcccccacctcc -gcccccacctccgcccccacctccgcccctcctccgcccccacctcagcccccacctcc- -----------------------gccccctcctcagcccccacctctgcccctcctcagcc -cccacctcagcccccacctcagcccccacctc---------------------------- ------------------------------------------------------------- ---------ccccctcctcagcccccacctcagcccccacctcagccccctcctcagcccc -cacctcagcccccacctccgcccct------------cctcagcccccacctccgccccc -acctcagcccccacctcagcccccacctccgcccccacctcagcccccacctccgccccc -acctcagcccccacctccgcccccacctcagcccccacctctgcccctcctcagccccca -cctccgccccctcctcagcccccacctctg------------------------------ -------cccctcctcagcccccacctcagcccccacctcagcccccacctcc-cccctcc -tcagcccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacc -tcagcccccacctccgcccctcctcagcccccacctcagcccccacctccgcccctcctc -agcccccacctcag---------------------------------------------- -------------------------------------------------ccccctcctcag -cccccacctccgcccccacctccgcccccacctctgcccctcctcagcccccacctcagc -cccctcctcagcccccacctccgcccccacctccgcccccacctccgcccctcctccgcc -cccacctcagcccccacctccgccccct-------------------------------- ---cctcagcccccacctctgcccctcctcagcccccacctcagcccccacctcagccccc -acct-------------------------cccccctcctcagcccccacctcagccccca -cctccgcccctcctcagcccccacctccgccccca------------------------- -----------------------------------cctcagcccccacctcagcccccacc -tccgcccccacctcagcccccacctccgcccccacctcagcccccacctcc--------- ---gcccccacctcagcccccacctctgcccctcctcagcccccacctccgccccctcctc -agcccccacctctgcccctcctcagcccccacctcagcccccacctcagcccccacct-- ------------------------cccccctcctcagccccca------------------ ------------------cctcagcccccacctcagccccctcctcagcccccacctcagc -ccccacctcagcccccacctccgcccctcctcagccccca-------------------- ----cctcagcccccacctccgcccctcctccgcccccacctcagccccctcctcagcccc -cacctctgcccctcctcagcccccacctcagcccccacctccgcccccacctcagccccc -tcctcagcccccacctc-------------------------------------ccccct -cctccgcccccacctcagcccccacctcagcccccacctcagcccccacctc-------- ------------------------------------------------------------- ----------------------------------------ccccctcctccgcccccacct -cagccccca-----------cctcagcccccacctccgcccccacctcagcccccacctc -c----------------------------------------------------------- ------------------------------------------------cccctcctcagcc -cccacctcagcccccacctccgccccca-----------cctcagcccccacctcagccc -ccacctcagcccccacctccgcccctcctcagcccccacctccgcccccacctcagcccc -cacctcagcccccacctccgccccca---------------------------------- ------------------------------------cctcagcccccacctccgcccccac -ctcagcccccacctccgcccccacctcagcccccacctccgcccccacctccgcccccac -ctcc-----------gcccccacctcagcccccacctcagcccccacctccgccccca-- ---------------------------------------------cctcagcccccacctc -agcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccctcctcag -cccccacctcagcccccacctcagcccccacctcagcccct------------------- -------cctcagcccccacctcagccccctcctcagccccctcctcagcccccacctcag -cccccacctccgcccccacctccgcccccacctcagccccacctcagcccctcctcagcc -cccacctcagccc----------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------cctcagcccccacctcagcccccacctccgcc -cccacctccgcccccacctcc--------------------------------------- ---------------------------------------------gcccctcctcagcccc -cacctcagcccccacctcagcccctcctcagcccccacctcc------------------ ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------acccccacct -ccgtccccacctccgccccctcctcagccccctcctcagcccccacctcagcccccacct -ccgcccccacctcagcccctcctcagcccccacctctgcccccacctcagaccctcctca -gcccctcctcagcccctcctcatcccctcctcagcagctgctggaatgggctaccctcag -gagttggcaccccacaggctccttcccttcccacctccgccacaccctgacgagggaaaa -atggggagctgctgggagggaacttgcaccctgttgggcgccttgtatccccagcctcct -ctcacaccacaggctgctggggccccgtcagcggagcacggctgcagcgaatgttgaaac -caccagttcccattcctagcagggc ->syndip_2_chr20:63167187-63167827 -acagctcagtctttgactaagtcacatcctcattgctcctgtttccacagagcagacacc -gacgtccagacatccagactggctgccaccagctcactggaatggccagcccgtcccgcc -gaggccagtggacatgccaaatccctcccgcaacaagttgctatccatcccctcgactaa -tacttaccaaattaattccagatttggattcactcacggttcccaccagcactcagcccc -atctcagcccccatctcagcccccaccgcagcctcacctcagtgcccacctcagccccct -cctcagcccccacctccgcccccacctccgccccctcctcagcccctcctccgcccccac -ctcagcccccacctcagccccctcctcagcccccacctccgcccctcctcagcccccacc -tcagcccccacctcagcccccacctccgccccctcctcagcccccacctcagcccccacc -tcagccccctcctcagcccccacctcagcccccacctccgcccccacctcagcccccacc -tcagccccctcctcagcccccacctcagcccccacctcagcccccacctcagccccctcc -tcagcccccacctcagcccccacctccgccccctcctcagcccccacctcccccccacct -ccgccccctcctcagcccccacctcccccccacctccgccccctcctcagcccccacctc -tgcccctcctcaggccccacctcagcccccacctcagccccctcctcagcccccacctca -gcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctccg -cccctcctctgcccccacctcagccccctcctcagcccccacctctgcccctcctcagcc -cccacctcagcccccacctccgcccccacctcagcccccacctcagcccccacctccccc -cctcctcagcccccacctccacccccacctcagcccccacctcagcccccacctcccccc -ctcctcagcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccc -cacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctccgccccc -acctccgcccccacctcagcccccacctccgccccctcctcagcccccacctcagccccc -acctcagcccccacctccacccccacctcagcccccacctcagcccccacctccccccca -cctccgccccctcctcagcccccacctctgcccctcctcaggccccacctcagcccccac -ctcagccccctcctcagcccccacctcagcccccacctcagcccccacctccgcccctcc -tcagcccccacctcagcccccacctccacccccacctcagcccccacctccgcccccacc -tcagcccccacctccgcccctcctcagcccccacctcagcccccacctccgcccctcctc -tgcccccacctcagccccctcctcagcccccacctctgcccctcctcagcccccacctca -gcccccacctccgcccccacctcagcccccacctcagcccccacctccccccctcctcag -cccccacctccacccccacctcagcccccacctccgcccctcctcagcccccacctcagc -ccccacctccacccccacctcagcccccacctccgcccccacctccgcccctcctcagcc -cccacctccgcccccacctcagcccctcctcagcccccacctccgcccctcctcagcccc -cacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctccaccccc -acctcagcccccacctcagcccccacctcccccccacctccgccccctcctcagccccca -cctctgcccctcctcaggccccacctcagcccccacctcagccccctcctcagcccccac -ctcagcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccccacc -tccacccccacctcagcccccacctccgcccccacctcagcccccacctccgcccctcct -cagcccccacctcagcccccacctccgcccctcctctgcccccacctcagccccctcctc -agcccccacctctgcccctcctcagcccccacctcagcccccacctccgcccccacctca -gcccccacctcagcccccacctccccccctcctcagcccccacctccacccccacctcag -cccccacctccgcccctcctcagcccccacctcagcccccacctccacccccacctcagc -ccccacctcagcccccacctccgcccctcctcagcccccacctccgcccccacctcagcc -cctcctcagcccccacctccgcccctcctcagcccccacctccgcccccacctcagcccc -ctcctccgcccctcctcagcccccacctccacccccacctcagcccccacctcagccccc -tcctcagcccccacctccgcccctcctcagcccccacctcagcccccacctcagccccca -cctccgccccctcctcagcccccacctcagcccccacctcagccccctcctccacccctc -ctcagcccccacctccgcccccacctcagcccccacctccgcccctcctcagcccccacc -tccacccccacctcagcccccacctccgcccctcctcagcccccacctccgcccccacct -cagcccccacctccccccctcctcagcccccacctccgcccccacctcagcccccacctc -cgcccctcctcagcccccacctccacccccacctcagcccccacctccgcccctcctcag -cccccacctccgcccccacctcagcccctcctcagcccccacctccgcccctcctcagcc -cccacctccgcccccacctcagcccccacctccccccctcctcagcccccacctccgccc -ccacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctccacccc -cacctcagcccccacctcagcccccacctccgcccctcctcagcccccacctccgccccc -acctcagcccctcctcagcccccacctccgcccctcctcagcccccacctccgcccccac -ctcagcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccac -ctccgcccctcctcagcccccacctcagcccccacctcagaccccacctccgcccccacc -tccgcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacctc -cgcccccacctccgcccccacctccgcccctcctcagcccccacctcagcccctcctcag -cccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctccg -cccccacctcagccccctcctcagcccccacctcagccccctcctcagcccccacctcag -cccccacctccgcccccacctccgcccccacctcagccccacctcagcccctcctcagcc -cccacctcagcccctcctcagcccccacctcagcccctcctcagcccccacctcagcccc -ctcagcccccacctcagcccccacctccgcccccacctccgcccctcctcagcccccacc -tcagcccccacctcagcccctcctcagcccccacctccgcccccacctccgcccccacct -cagcccctcctcagcccccacctcagcccccacctcagccccctcctcagcccccacctc -cgcccccacctccgcccccacctcagccccacctcagcccctcctcagcccccacctcag -cccctcctcagcccccacctcagcccctcctcagcccccacctcagcccccacctccgcc -cccacctccgcccccacctccgcccccacctcagcccctcctcagcccccacctcagccc -ccacctcagccccctcctcagcccccacctccgcccccacctcagcccctcctcagcccc -cacctcagcccccacctcagcccctcctcagcccccacctccgcccccacctccgccccc -acctcagcccctcctcagcccccacctcagcccccacctcagccccctcctcagccccca -cctccgcccccacctccgcccccacctcagccccacctcagcccctcctcagcccccacc -tcagcccctcctcagccccctcctcagcccccacctcagcccccacctcagcccccacct -ccgcccccacctccgcccccacctcagccccctcctcagccccctcctcagcccccacct -cagcccccacctcagcccctcctcagcccccacctccgcccccacctcaga--------- ---ccctcctcagcccctcctcatcccctcctcagcagctgctggaatgggctaccctcag -gagttggcaccccacaggctccttcccttcccacctccgccacaccctgacgagggaaaa -atggggagctgctgggagggaacttgcaccctgttgggcgccttgtatccccagcctcct -ctcacaccacaggctgctggggccccgtcagcggagcacggctgcagcgaatgttgaaac -caccagttcccattcctagcagggc ->p:HG002_1_chr20:63167187-63167827 -acagctcagtctttgactaagtcacatcctcattgctcctgtttccacagagcagacacc -gacgtccagacatccagactggctgccaccagctcactggaatggccagcccgtcccgcc -gaggccagtggacatgccaaatccctcccgcaacaagttgctatccatcccctcgactaa -tacttaccaaattaattccagatttggattcactcacggttcccaccagcactcagcccc -atctcagcccccatctcagcccccaccgcagcctcacctcagtgcccacctcagccccct -cctcagcccccacctccgcccccacctccgccccctcctcagcccctcctccgcccccac -ctcagcccccacctcagccccctcctcagcccccacctccgcccctcctcagcccccacc -tcagcccccacctcagcccccacctccgccccctcctcagcccccacctcagcccccacc -tcagccccctcctcagcccccacctcagcccccacctccgcccccacctcagcccccacc -tcagccccctcctcagcccccacctcagcccccacctcagcccccacctcagccccctcc -tcagcccccacctcagcccccacctccgccccctcctcagcccccacctcccccccacct -ccgccccctcctcagcccccacctcccccccacctccgccccctcctcagcccccacctc -tgcccctcctcaggccccacctcagcccccacctcagccccctcctcagcccccacctca -gcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctccg -cccctcctctgcccccacctcagccccctcctcagcccccacctctgcccctcctcagcc -cccacctcagcccccacctccgcccccacctcagcccccacctcagcccccacctccccc -cctcctcagcccccacctccacccccacctcagcccccacctcagcccccacctcccccc -ctcctcagcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccc -cacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctccgccccc -acctccgcccccacctcagcccccacctccgccccctcctcagcccccacctcagccccc -acctcagcccccacctccacccccacctcagcccccacctcagcccccacctccccccca -cctccgccccctcctcagcccccacctctgcccctcctcaggccccacctcagcccccac -ctcagccccctcctcagcccccacctcagcccccacctcagcccccacctccgcccctcc -tcagcccccacctcagcccccacctccacccccacctcagcccccacctccgcccccacc -tcagcccccacctccgcccctcctcagcccccacctcagcccccacctccgcccctcctc -tgcccccacctcagccccctcctcagcccccacctctgcccctcctcagcccccacctca -gcccccacctccgcccccacctcagcccccacctcagcccccacctccccccctcctcag -cccccacctccacccccacctcagcccccacctccgcccctcctcagcccccacctcagc -ccccacctccacccccacctcagcccccacctccgcccccacctccgcccctcctcagcc -cccacctccgcccccacctcagcccctcctcagcccccacctccgcccctcctcagcccc -cacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctccaccccc -acctcagcccccacctcagcccccacctcccccccacctccgccccctcctcagccccca -cctctgcccctcctcaggccccacctcagcccccacctcagccccctcctcagcccccac -ctcagcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccccacc -tccacccccacctcagcccccacctccgcccccacctcagcccccacctccgcccctcct -cagcccccacctcagcccccacctccgcccctcctctgcccccacctcagccccctcctc -agcccccacctctgcccctcctcagcccccacctcagcccccacctccgcccccacctca -gcccccacctcagcccccacctccccccctcctcagcccccacctccacccccacctcag -cccccacctccgcccctcctcagcccccacctcagcccccacctccacccccacctcagc -ccccacctcagcccccacctccgcccctcctcagcccccacctccgcccccacctcagcc -cctcctcagcccccacctccgcccctcctcagcccccacctccgcccccacctcagcccc -ctcctccgcccctcctcagcccccacctccacccccacctcagcccccacctcagccccc -tcctcagcccccacctccgcccctcctcagcccccacctcagcccccacctcagccccca -cctccgccccctcctcagcccccacctcagcccccacctcagccccctcctccacccctc -ctcagcccccacctccgcccccacctcagcccccacctccgcccctcctcagcccccacc -tccacccccacctcagcccccacctccgcccctcctcagcccccacctccgcccccacct -cagcccccacctccccccctcctcagcccccacctccgcccccacctcagcccccacctc -cgcccctcctcagcccccacctccacccccacctcagcccccacctccgcccctcctcag -cccccacctccgcccccacctcagcccctcctcagcccccacctccgcccctcctcagcc -cccacctccgcccccacctcagcccccacctccccccctcctcagcccccacctccgccc -ccacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctccacccc -cacctcagcccccacctcagcccccacctccgcccctcctcagcccccacctccgccccc -acctcagcccctcctcagcccccacctccgcccctcctcagcccccacctccgcccccac -ctcagcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccac -ctccgcccctcctcagcccccacctcagcccccacctcagaccccacctccgcccccacc -tccgcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacctc -cgcccccacctccgcccccacctccgcccctcctcagcccccacctcagcccctcctcag -cccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctccg -cccccacctcagccccctcctcagcccccacctcagccccctcctcagcccccacctcag -cccccacctccgcccccacctccgcccccacctcagccccacctcagcccctcctcagcc -cccacctcagcccctcctcagcccccacctcagcccctcctcagcccccacctcagcccc -ctcagcccccacctcagcccccacctccgcccccacctccgcccctcctcagcccccacc -tcagcccccacctcagcccctcctcagcccccacctccgcccccacctccgcccccacct -cagcccctcctcagcccccacctcagcccccacctcagccccctcctcagcccccacctc -cgcccccacctccgcccccacctcagccccacctcagcccctcctcagcccccacctcag -cccctcctcagcccccacctcagcccctcctcagcccccacctcagcccccacctccgcc -cccacctccgcccccacctccgcccccacctcagcccctcctcagcccccacctcagccc -ccacctcagccccctcctcagcccccacctccgcccccacctcagcccctcctcagcccc -cacctcagcccccacctcagcccctcctcagcccccacctccgcccccacctccgccccc -acctcagcccctcctcagcccccacctcagcccccacctcagccccctcctcagccccca -cctccgcccccacctccgcccccacctcagccccacctcagcccctcctcagcccccacc -tcagcccctcctcagccccctcctcagcccccacctcagcccccacctcagcccccacct -ccgcccccacctccgcccccacctcagccccctcctcagccccctcctcagcccccacct -cagcccccacctcagcccctcctcagcccccacctccgcccccacctcaga--------- ---ccctcctcagcccctcctcatcccctcctcagcagctgctggaatgggctaccctcag -gagttggcaccccacaggctccttcccttcccacctccgccacaccctgacgagggaaaa -atggggagctgctgggagggaacttgcaccctgttgggcgccttgtatccccagcctcct -ctcacaccacaggctgctggggccccgtcagcggagcacggctgcagcgaatgttgaaac -caccagttcccattcctagcagggc ->p:HG002_2_chr20:63167187-63167827 -acagctcagtctttgactaagtcacatcctcattgctcctgtttccacagagcagacacc -gacgtccagacatccagactggctgccaccagctcactggaatggccagcccgtcccgcc -gaggccagtggacatgccaaatccctcccgcaacaagttgctatccatcccctcgactaa -tacttaccaaattaattccagatttggagtcactcacggttcccaccagcactcagcccc -atctcagcccccatctcagcccccaccgcagcctcacctcagtgcccacctcagccccct -cctcagcccccacctccgcccccacctcagcccct------------------------c -ctcagcccccacctcagccccctcctcagcccccacctcc-------------------- ----gcccccacctccgcccccacctctgcccct-------------cctcagcccccacc -tcagccccctcctcagcccccacctccgcccccacctccgcccccacctctgcccct--- -----------------------------------cctcagcccccacctcagccccctcc -tcagcccccacctccgcccccacctccgcccccacctctgcccctcctcagcccccacct -cagccccctcctcag-----------cccccacctccgccccctcctcagcccccacctc -tgcccct------------cctcagcccccacctcagccccctcctcagcccccacctcc -gcccccacctccgcccccacctccgcccctcctccgcccccacctcagcccccacctcc- -----------------------gccccctcctcagcccccacctctgcccctcctcagcc -cccacctcagcccccacctcagcccccacctc---------------------------- ------------------------------------------------------------- ---------ccccctcctcagcccccacctcagcccccacctcagccccctcctcagcccc -cacctcagcccccacctccgcccct------------cctcagcccccacctccgccccc -acctcagcccccacctcagcccccacctccgcccccacctcagcccccacctccgccccc -acctcagcccccacctccgcccccacctcagcccccacctctgcccctcctcagccccca -cctccgccccctcctcagcccccacctctg------------------------------ -------cccctcctcagcccccacctcagcccccacctcagcccccacctcc-cccctcc -tcagcccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacc -tcagcccccacctccgcccctcctcagcccccacctcagcccccacctccgcccctcctc -agcccccacctcag---------------------------------------------- -------------------------------------------------ccccctcctcag -cccccacctccgcccccacctccgcccccacctctgcccctcctcagcccccacctcagc -cccctcctcagcccccacctccgcccccacctccgcccccacctccgcccctcctccgcc -cccacctcagcccccacctccgccccct-------------------------------- ---cctcagcccccacctctgcccctcctcagcccccacctcagcccccacctcagccccc -acct-------------------------cccccctcctcagcccccacctcagccccca -cctccgcccctcctcagcccccacctccgccccca------------------------- -----------------------------------cctcagcccccacctcagcccccacc -tccgcccccacctcagcccccacctccgcccccacctcagcccccacctcc--------- ---gcccccacctcagcccccacctctgcccctcctcagcccccacctccgccccctcctc -agcccccacctctgcccctcctcagcccccacctcagcccccacctcagcccccacct-- ------------------------cccccctcctcagccccca------------------ ------------------cctcagcccccacctcagccccctcctcagcccccacctcagc -ccccacctcagcccccacctccgcccctcctcagccccca-------------------- ----cctcagcccccacctccgcccctcctccgcccccacctcagccccctcctcagcccc -cacctctgcccctcctcagcccccacctcagcccccacctccgcccccacctcagccccc -tcctcagcccccacctc-------------------------------------ccccct -cctccgcccccacctcagcccccacctcagcccccacctcagcccccacctc-------- ------------------------------------------------------------- ----------------------------------------ccccctcctccgcccccacct -cagccccca-----------cctcagcccccacctccgcccccacctcagcccccacctc -c----------------------------------------------------------- ------------------------------------------------cccctcctcagcc -cccacctcagcccccacctccgccccca-----------cctcagcccccacctcagccc -ccacctcagcccccacctccgcccctcctcagcccccacctccgcccccacctcagcccc -cacctcagcccccacctccgccccca---------------------------------- ------------------------------------cctcagcccccacctccgcccccac -ctcagcccccacctccgcccccacctcagcccccacctccgcccccacctccgcccccac -ctcc-----------gcccccacctcagcccccacctcagcccccacctccgccccca-- ---------------------------------------------cctcagcccccacctc -agcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccctcctcag -cccccacctcagcccccacctcagcccccacctcagcccct------------------- -------cctcagcccccacctcagccccctcctcagccccctcctcagcccccacctcag -cccccacctccgcccccacctccgcccccacctcagccccacctcagcccctcctcagcc -cccacctcagccc----------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------cctcagcccccacctcagcccccacctccgcc -cccacctccgcccccacctcc--------------------------------------- ---------------------------------------------gcccctcctcagcccc -cacctcagcccccacctcagcccctcctcagcccccacctcc------------------ ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------acccccacct -ccgtccccacctccgccccctcctcagccccctcctcagcccccacctcagcccccacct -ccgcccccacctcagcccctcctcagcccccacctctgcccccacctcagaccctcctca -gcccctcctcagcccctcctcatcccctcctcagcagctgctggaatgggctaccctcag -gagttggcaccccacagcctccttcccttcccacctccgccacaccctgacgagggaaaa -atggggagctgctgggagggaacttgcaccctgttgggcgccttgtatccccagcctcct -ctcacaccacaggctgctggggccccgtcagcggagcacggctgcagcgaatgttgaaac -caccagttcccattcctagcagggc ->ref_chr20:63167187-63167827 -acagctcagtctttgactaagtcacatcctcattgctcctgtttccacagagcagacacc -gacgtccagacatccagactggctgccaccagctcactggaatggccagcccgtcccgcc -gaggccagtggacatgccaaatccctcccgcaacaagttgctatccatcccctcgactaa -tacttaccaaattaattccagatttggagtcactcatggttcccaccagcactcagcccc -atctcagcccccatctcagcccccaccgcagcctcacctcagtgcccacctcagccccct -cctcagccccca------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------cctcagcccccacct -ccgcccccacctcagcccctcctcagcccccacctccgcccccacctcaga--------- ---ccctcctcagcccctcctcatcccctcctcagcagctgctggaatgggctaccctcag -gagttggcaccccacaggctccttcccttcccacctccgccacaccctgacgagggaaaa -atggggagctgctgggagggaacttgcaccctgttgggcgccttgtatccccagcctcct -ctcacaccacaggctgctggggccccgtcagcggagcacggctgcagcgaatgttgaaac -caccagttcccattcctagcagggc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_3bf3c09b9cdcb2860cb21a8cada13b32.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_3bf3c09b9cdcb2860cb21a8cada13b32.msa deleted file mode 100644 index b574dbec..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_3bf3c09b9cdcb2860cb21a8cada13b32.msa +++ /dev/null @@ -1,50 +0,0 @@ ->syndip_1_chr20:44763896-44764285 -aggtttaggagtttacgggttccctgtccatccattcactacatgctcacctatccatcc -atccatccatttatccatccatccatccacctatcacttcatccatccatccatttatcc -atccatccatttatccatccatccatccatttatccatccatccatccatttatccatcc -atccatccatccatccacccatccatccgtccatccatttatccatccatccatccatcc -atttatccatccatttatccatccatccatccatccatccatccatccatccatttatcc -----atccatccatccatccacccatccatccatccgtccatccatttatccatccatcc -atccatccatccatccatccatccatttatccatccgtccatttatccatccatccatcc -acccacccatccatccatccatccacttatccatccacccatccatccatccgtccatcc -attcatccatccatccatcctcccacaaactcaccaagcctacaatacaa ->syndip_2_chr20:44763896-44764285 -aggtttaggagtttacgggttccctgtccatccattcactacatgctcacctatccatcc -atccatccatttatccatccatccatccacctatcacttcatccatccatccatttatcc -atccatccatttatccatccatccatccatttatccatccatccatccatttatccatcc -atccatccatccatccacccatccatccgtccatccatttatccatccatccatccatcc -atttatccatccatttatccatccatccatccatccatccatccatccatccatccatcc -atttatccatccatccatccatccacccatccatccatccgtccatccatttatccatcc -atccatccatccatccatccatccatttatccatccgtccatttatccatccatccatcc -acccacccatccatccatccatccatttatccatccacccatccatccatccgtccatcc -attcatccatccatccatcctcccacaaactcaccaagcctacaatacaa ->p:HG002_1_chr20:44763896-44764285 -aggtttaggagtttacgggttccctgtccatccattcactacatgctcacctatccatcc -atccatccatttatccatccatccatccacctatcacttcatccatccatccatttatcc -atccatccatttatccatccatccatccatttatccatccatccatccatttatccatcc -atccatccatccatccacccatccatccgtccatccatttatccatccatccatccatcc -atttatccatccatttatccatccatccatccatccatccatccatccatccatccatcc -atttatccatccatccatccatccacccatccatccatccgtccatccatttatccatcc -atccatccatccatccatccatccatttatccatccgtccatttatccatccatccatcc -acccacccatccatccatccatccatttatccatccacccatccatccatccgtccatcc -attcatccatccatccatcctcccacaaactcaccaagcctacaatacaa ->p:HG002_2_chr20:44763896-44764285 -aggtttaggagtttacgggttccctgtccatccattcactacatgctcacctatccatcc -atccatccatttatccatccatccatccacctatcacttcatccatccatccatttatcc -atccatccatttatccatccatccatccatttatccatccatccatccatttatccatcc -atccatccatccatccacccatccatccgtccatccatttatccatccatccatccatcc -atttatccatccatttatccatccatccatccatccatccatccatccatccatttatcc -----atccatccatccatccacccatccatccatccgtccatccatttatccatccatcc -atccatccatccatccatccatccatttatccatccgtccatttatccatccatccatcc -acccacccatccatccatccatccacttatccatccacccatccatccatccgtccatcc -attcatccatccatccatcctcccacaaactcaccaagcctacaatacaa ->ref_chr20:44763896-44764285 -aggtttaggagtttacgggttccctgtccatccattcactacatgctcacctatccatcc -atccatccatttatccatccatccatccacctatcacttcatccatccatccatttatcc -atccatccatttatccatccatccatccatttatccatccatccatccatttatccatcc -atccatccatccatccacccatccatccgtccatccatttatccatccatccatccatcc -atttatgcatccatttatccatccatccatccatccatccatccatccatccatttatcc -----atccatccatccatccacccatccatccatccgtccatccattcatccatccatcc -atcctcccacaaactcaccaagcctacaatgca--------------------------- ------------------------------------------------------------- --------------------------------------------------a diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_3c46aa76090bff6875247fdf2448bd2a.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_3c46aa76090bff6875247fdf2448bd2a.msa deleted file mode 100644 index e3abd738..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_3c46aa76090bff6875247fdf2448bd2a.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:34235688-34236191 -gtgggaggattgctagagcccaggaagtcgtggctgaagtgggctcatgataatgccact -gcactccagcctgtgtgacagagtgagactctgagaaagaagaaagaaagaaagaaagaa -agaaagaaagaaagaaagaaagaaagaaagaaagaaggaaggaaggaaggaaggaaggaa -aggaaggaaggaaggaaggaaggaaggaaggaaggaagcgggagggagggaagaaggaag -gaaggaggagggagggaagaatgaaggaaggaaggaaggaaggaaggaaggaaggaagcg -ggagggagggaagaaggaaggaaggaaggaaggagggagggagggaagaaggaaggagga -gggagggagggaagcaggaaagaaggaaggaaggagaaagagagaaagagagagagaaga -agaaagagaaagaaacagaaaaggaaggaaggagagagagaaagaaagagaaagagaagg -aaggaaggaaggagaaagaaaggaaaggaaaggagtggaaaggaaaggagaggaaaggag -aaaggagggagggagggaaaagaaagaaagaaagaaaaggctaaa ->syndip_2_chr20:34235688-34236191 -gtgggaggattgctagagcccaggaagtcgtggctgaagtgggctcatgataatgccact -gcactccagcctgtgtgacagagtgagactctgagaaagaagaaagaaagaaagaaagaa -agaaagaaagaaagaaagaaagaaagaaagaaagaaggaaggaaggaaggaaggaaggaa -aggaaggaaggaaggaaggaaggaaggaaggaaggaagcgggagggagggaagaaggaag -gaaggaggagggagggaagaatgaaggaaggaaggaaggaaggaaggaaggaaggaagcg -ggagggagggaagaaggaaggaaggaaggaaggagggagggagggaagaaggaaggagga -gggagggagggaagcaggaaagaaggaaggaaggagaaagagagaaagagagagagaaga -agaaagagaaagaaacagaaaaggaaggaaggagagagagaaagaaagagaaagagaagg -aaggaaggaaggagaaagaaaggaaaggaaaggagtggaaaggaaaggagaggaaaggag -aaaggagggagggagggaaaagaaagaaagaaagaaaaggctaaa ->p:HG002_1_chr20:34235688-34236191 -gtgggaggattgctagagcccaggaagtcgtggctgaagtgggctcatgataatgccact -gcactccagcctgtgtgacagagtgagactctgagaaagaagaaagaaagaaagaaagaa -agaaagaaagaaagaaagaaagaaagaaagaaagaaggaaggaaggaaggaaggaaggaa -aggaaggaaggaaggaaggaaggaaggaaggaaaggaa-ggaaggaaggaaggaaggaag -gaagcgggagggagggaagaaggaaggaaggaaggaaggagggaaggaaggaaggaagcg -ggagggagggaagaaggaaggaaggaaggaaggagggagggagggaagaaggaaggagga -gggagggagggaagaaggaaagaaggaaggaaggagaaagagagaaagagagagagaaga -agaaagagaaagaaacagaaaaggaaggaaggagagagagaaagaaagagaaagagaagg -aaggaaggaaggagaaagaaaggaaaggaaaggagtggaaaggaaaggagaggaaaggag -aaaggagggagggagggaaaagaaagaaagaaagaaaaggctaaa ->p:HG002_2_chr20:34235688-34236191 -gtgggaggattgctagagcccaggaagtcgtggctgaagtgggctcatgataatgccact -gcactccagcctgtgtgacagagtgagactctgagaaagaagaaagaaagaaagaaagaa -agaaagaaagaaagaaagaaagaaagaaagaaagaaggaaggaaggaaggaaggaaggaa -aggaaggaaggaaggaaggaaggaaggaaggaaaggaa-ggaaggaaggaaggaaggaag -gaagcgggagggagggaagaaggaaggaaggaaggaaggagggaaggaaggaaggaagcg -ggagggagggaagaaggaaggaaggaaggaaggagggagggagggaagaaggaaggagga -gggagggagggaagaaggaaagaaggaaggaaggagaaagagagaaagagagagagaaga -agaaagagaaagaaacagaaaaggaaggaaggagagagagaaagaaagagaaagagaagg -aaggaaggaaggagaaagaaaggaaaggaaaggagtggaaaggaaaggagaggaaaggag -aaaggagggagggagggaaaagaaagaaagaaagaaaaggctaaa ->ref_chr20:34235688-34236191 -gtgggaggattgctagagcccaggaagtcgtggctgaagtgggctcatgataatgccact -gcactccagcctgtgtgacagagtgagactctgagaaagaagaaagaaagaaagaaagaa -agaaagaaagaaagaaagaaagaaagaaagaaagaaggaaggaaggaaggaaggaaggaa -aggaaggaaggaaggaaggaaggaaggaaggaaaggaa---------------------- ----------------------------------ggaaggaaggaaggaaggaaggaagcg -ggagggagggaagaaggaaggaaggaaggaaggagggagggagggaaga----------- ----------------aggaaagaaggaaggaaggagaaagagagaaagagagagagaaga -agaaagagaaagaaacagaaaaggaaggaaggagagagagaaagaaagagaaagagaagg -aaggaaggaaggagaaagaaaggaaaggaaaggagtggaaaggaaaggagaggaaaggag -aaaggagggagggagggaaaagaaagaaagaaagaaaaggctaaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_3f5a43abd13ceb7f5864bdfd3c62d54f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_3f5a43abd13ceb7f5864bdfd3c62d54f.msa deleted file mode 100644 index eee286d9..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_3f5a43abd13ceb7f5864bdfd3c62d54f.msa +++ /dev/null @@ -1,80 +0,0 @@ ->syndip_1_chr20:62830412-62831038 -aggtgggtgaggttggggcaagggcctggcat-ggggggcggcacacccagacgggccag -acccgacagggtatgggcactgacgagccaggacctccttccccagggccagaagggcag -catgggagaccccggccttccaggcccccagggcctccgaggtgacgtgggcgaccgggt -aagtggccctctcagcaggaagctcccctgcaccccctctacccatgtaccacagtcccc -caccccccaccgtgctccacc--------------------------------------- ----ccccaccacagtcccccaccccccaccccagtccccaaacccctaccacagtccccc -aa-ccccaccacagtcccccaccccctaccacagtcccccaccccctaccacagtccccc -aacccccaccacagtcccccacccccaccacagtccgccaacccccatgacagtccctca ---------------------acccccaccacagtcccccaacccccatgacagtccccca -acccccaccacagtcccccaacccccaccacagtccccaccccctaccacagtcccccaa -cccccaccacagtcccccaccccctaccacaatccccca-cccccaccacagtcccctgg -gacgcagacagggagaggcccttgcagctcccagtgggaaatctggccatgggcagtgtc -tccctgcgtggcggaggcagtggcatcagggccccgactgtggcgcctttggcccctctg -accttccacgtggtgttccttgtgggtgggaggctgcgggagcctgggccgctctgcctc -ctgccctgcgtagacgcctggcgggacctgcacacggtcagtgttca ->syndip_2_chr20:62830412-62831038 -aggtgggtgaggttggggcaagggcctggcat-ggggggcggcacacccagacgggccag -acccgacagggtatgggcactgacgagccaggacctccttccccagggccagaagggcag -catgggagaccccggccttccaggcccccagggcctccgaggtgacgtgggcgaccgggt -aagtggccctctcagcaggaagctcccctgcaccccctctacccatgtaccacagtcccc -caccccccaccacagtcccccaccccccaccccagtccccaaacccctaccacagtcccc -caaccccaccacagtcccccaccccctaccacagtcccccaacccctaccacagtccccc -aacccccaccacagtcccccaccccc-accacagtccgccaacccccatgacagtccccc -aacccccaccacagtcccccacccccaccacagtccgccaacccccatgacagtccccca -acccccaccacagtcccccaacccccatgacagtcccccaacccccaccacagtccccca -acccctaccacagtcccccaacccccaccacagtccccaccccctaccacagtcccccaa -cccccaccacagtcccccaccccctaccacaatcccccaccccccaccacagtcccctgg -gacgcagacagggagaggcccttgcagctcccagtgggaaatctggccatgggcagtgtc -tccctgcgtggcggaggcagtggcatcagggccccgactgtggcgcctttggcccctctg -accttccacgtggtgttccttgtgggtgggaggctgcgggagcctgggccgctctgcctc -ctgccctgcgtagacgcctggcgggacctgcacacggtcagtgttca ->p:HG002_1_chr20:62830412-62831038 -aggtgggtgaggttggggcaagggcctggcat-ggggggcggcacacccagacgggccag -acccgacagggtatgggcactgacgagccaggacctccttccccagggccagaagggcag -catgggagaccccggccttccaggcccccagggcctccgaggtgacgtgggcgaccgggt -aagtggccctctcagcaggaagctcccctgcaccccctctacccatgtaccacagtcccc -caccccccaccacagtcccccaccccccaccccagtccccaaacccctaccacagtcccc -caaccccaccacagtcccccaccccctaccacagtcccccaacccctaccacagtccccc -aacccccaccacagtcccccaccccc-accacagtccgccaacccccatgacagtccccc -aacccccaccacagtcccccacccccaccacagtccgccaacccccatgacagtccccca -acccccaccacagtcccccaacccccatgacagtcccccaacccccaccacagtccccca -acccctaccacagtcccccaacccccaccacagtccccaccccctaccacagtcccccaa -cccccaccacagtcccccaccccctaccacaatcccccaccccccaccacagtcccctgg -gacgcagacagggagaggcccttgcagctcccagtgggaaatctggccatgggcagtgtc -tccctgcgtggcggaggcagtggcatcagggccccgactgtggcgcctttggcccctctg -accttccacgtggtgttccttgtgggtgggaggctgcgggagcctgggccgctctgcctc -ctgccctgcgtagacgcctggcgggacctgcacacggtcagtgttca ->p:HG002_2_chr20:62830412-62831038 -aggtgggtgaggttggggcaagggcctggcatgggggggcggcacacccagacgggccag -acccgacagggtatgggcactgacgagccaggacctccttccccagggccagaagggcag -catgggagaccccggccttccaggcccccagggcctccgaggtgacgtgggcgaccgggt -aagtggccctctcagcaggaagctcccctgcaccccctctacccatgtaccacagtcccc -caccccccaccgtgctccacc--------------------------------------- ----ccccaccacagtcccccaccccccaccccagtccccaaacccctaccacagtccccc -aa-ccccaccacagtcccccaccccctaccacagtcccccaccccctaccacagtccccc -aacccccaccacagtcccccacccccaccacagtccgccaacccccatgacagtccctca ---------------------acccccaccacagtcccccaacccccatgacagtccccca -acccccaccacagtcccccaacccccaccacagtccccaccccctaccacagtcccccaa -cccccaccacagtcccccaccccctaccacaatccccca-cccccaccacagtcccctgg -gacgcagacagggagaggcccttgcagctcccagtgggaaatctggccatgggcagtgtc -tccctgcgtggcggaggcagtggcatcagggccccgactgtggcgcctttggcccctctg -accttccacgtggtgttccttgtgggtgggaggctgcgggagcctgggccgctctgcctc -ctgccctgcgtagacgcctggcgggacctgcacacggtcagtgttca ->ref_chr20:62830412-62831038 -aggtgggtgaggttggggcaagggcctggcat-ggggggcggcacacccagacgggccag -acccgacagggtatgggcactgacgagccaggacctccttccccagggccagaagggcag -catgggagaccccggccttccaggcccccagggcctccgaggtgacgtgggcgaccgggt -aagtggccctctcagcaggaagctcccctgcaccccctctacccatgtaccacagtcccc -c----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------acccccatgacagtcccccaacccccaccacagtccccca -acccctaccacagtcccccaacccccaccacagtccccaccccctaccacagtcccccaa -cccccaccacagtcccccaccccctaccacaatcccccaccccccaccacagtcccctgg -gacgcagacagggagaggcccttgcagctcccagtgggaaatctggccatgggcagtgtc -tccctgcgtggcggaggcagtggcatcagggccccgactgtggcgcctttggcccctctg -accttccacgtggtgttccttgtgggtgggaggctgcgggagcctgggccgctctgcctc -ctgccctgcgtagacgcctggcgggacctgcacacggtcagtgttca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_3f90779dcd8c05402fb060d819c516f1.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_3f90779dcd8c05402fb060d819c516f1.msa deleted file mode 100644 index 4170dc40..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_3f90779dcd8c05402fb060d819c516f1.msa +++ /dev/null @@ -1,135 +0,0 @@ ->syndip_1_chr20:4032257-4033328 -cccggccgccaccccgtctgggaagtgaggagcgtctctgcttggccacccatcgtctgg -gatatgaggagcccctctgcctggctgcccagtctggaaagt------------------ -----------------------gaggagcgtctctgcccggccgccatcccatctaggaa -gcgaggagcgcctcttcccggctgccatcccatctaggaactgaggagcgtctctgcccg -gccgcccatcgtctgagatgtggggagcacctctgccccaccgccctgtctgggatgtga -ggagcgcctctgctgggccgcaaccctgtctgggaggtgaggagcgtctctgccccgccg -ctccgtctgagaagtgaggaaaccctctgcctggcaaccgccccgtctgagaagtgagga -gcccctccgtccggcaaccaccccgt---------------------------------- ------------------------------------------------------ctgggaa -gtgaggagcgtctccgcccggcagccaccccgtccgggagggaggtggggggggtcagcc -ccccgcccggccagccgccccgtccgggaggtgaggggctcctctgcccggccgccccta -ctgggaagtgaggagcccctctgcccggccagccgccccgtccgggagggaggcgggggg -gggggtcggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggcc -ggccgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgag -gacccctctgcccggccagccgccccgtccgggagggaggtgggggggtcagccccccgc -ccggccggctgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactggga -agtgaggagcccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagc -cccccgcctggccagccgccccatccgggagggaggtgggggggtcagccccccgcccgg -ccagccgccccgtccgggaggggggagggggggtcagccccctgcccggccagccgcccc -gtccgggagggaggt-gggggggggtcagccccccgcccggcca-gccgccccgtccggg -agggaggtggggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggc -gcctctgcccggccacccctactgggaagtgaggagcccctctgcccggccagccgcccc -gtccgggagggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggg -gggtcagccccctttccggcc--gccgcctgtccgggaggtgaggggcgcctctgcctgg -ccgcccctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggag -gtggggg ->syndip_2_chr20:4032257-4033328 -cccggccgccaccccgtctgggaagtgaggagcgtctctgcttggccacccatcgtctgg -gatatgaggagcccctctgcctggctgcccagtctggaaagtgaggagcgtctctgcccg -gccgccatcccatctaggaagcgaggagcgtctctgcccggccgccatcccatctaggaa -gcgaggagcgcctcttcccggctgccatcccatctaggaactgaggagcgtctctgcccg -gccgcccatcgtctgagatgtggggagcacctctgccccaccgccctgtctgggatgtga -ggagcgcctctgctgggccgcaaccctgtctgggaggtgaggagcgtctctgccccgccg -ctccgtctgagaagtgaggaaaccctctgcctggcaaccgccccgtctgagaagtgagga -gcccctccgtccggcaaccaccccgt---------------------------------- ------------------------------------------------------ctgggaa -gtgaggagcgtctccgcccggcagccaccccgtccgggagggaggt-------------- ------------------------------------------------------------- -------------------------------------------------------gggggg -gggggtcggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggcc -ggccgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgag -gacccctctgcccggccagccgccccgtccgggagggaggtgggggggtcagccccccgc -ccggccggctgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactggga -agtgaggagcccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagc -cccccgcctggccagccgccccatccgggagggaggtgggggggtcagccccccgcccgg -ccagccgccccgtccgggaggggggagggggggtcagccccctgcccggccagccgcccc -gtccgggagggaggtgggggggggggtcagccccccgcccggccagccgccccgtccggg -agggaggtggggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggc -gcctctgcccggccacccctactgggaagtgaggagcccctctgcccggccagccgcccc -gtccgggagggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggg -gggtcagccccctttccggcc--gccgcctgtccgggaggtgaggggcgcctctgcctgg -ccgcccctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggag -gtggggg ->p:HG002_1_chr20:4032257-4033328 -cccggccgccaccccgtctgggaagtgaggagcgtctctgcttggccacccatcgtctgg -gatatgaggagcccctctgcctggctgcccagtctggaaagtgaggagcgtctctgcccg -gccgccatcccatctaggaagcgaggagcgtctctgcccggccgccatcccatctaggaa -gcgaggagcgcctcttcccggctgccatcccatctaggaactgaggagcgtctctgcccg -gccgcccatcgtctgagatgtggggagcacctctgccccaccgccctgtctgggatgtga -ggagcgcctctgctgggccgcaaccctgtctgggaggtgaggagcgtctctgccccgccg -ctccgtctgagaagtgaggaaaccctctgcctggcaaccgccccgtctgagaagtgagga -gcccctccgtccggcaaccaccccgt---------------------------------- ------------------------------------------------------ctgggaa -gtgaggagcgtctccgcccggcagccaccccgtccgggagggaggt-------------- ------------------------------------------------------------- -------------------------------------------------------gggggg -gggggtcggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggcc -ggccgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgag -gacccctctgcccggccagccgccccgtccgggagggaggtgggggggtcagccccccgc -ccggccggctgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactggga -agtgaggagcccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagc -cccccgcctggccagccgccccatccgggagggaggtgggggggtcagccccccgcccgg -ccagccgccccgtccgggaggggggagggggggtcagccccctgcccggccagccgcccc -gtccgggagggaggtggggggggggtcagccccctttccggcccagccgccccgtccggg -agggaggtggggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggc -gcctctgcccggccacccctactgggaagtgaggagcccctctgcccggccagccgcccc -gtccgggagggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggg -gggtcagccccccttccggccgggccgcctgtccgggaggtgaggggcgcctctgcctgg -ccgcccctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggag -gtggggg ->p:HG002_2_chr20:4032257-4033328 -cccggccgccaccccgtctgggaagtgaggagcgtctctgcttggccacccatcgtctgg -gatatgaggagcccctctgcctggctgcccagtctggaaagtgaggagcgtctctgcccg -gccgccatcccatctaggaagcgaggagcgtctctgcccggccgccatcccatctaggaa -gcgaggagcgcctcttcccggctgccatcccatctaggaactgaggagcgtctctgcccg -gccgcccatcgtctgagatgtggggagcacctctgccccaccgccctgtctgggatgtga -ggagcgcctctgctgggccgcaaccctgtctgggaggtgaggagcgtctctgccccgccg -ctccgtctgagaagtgaggaaaccctctgcctggcaaccgccccgtctgagaagtgagga -gcccctccgtccggcaaccaccccgtccgggagggaggtggggggggtcagccccccgcc -cggccagccgccccgtccgggaggtgaggggctcctctgcccggccgcccctactgggaa -gtgaggagcgtctccgcccggcagccaccccgtccgggagggaggt-------------- ------------------------------------------------------------- -------------------------------------------------------gggggg -gggggtcggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggcc -ggccgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgag -gacccctctgcccggccagccgccccgtccgggagggaggtgggggggtcagccccccgc -ccggccggctgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactggga -agtgaggagcccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagc -cccccgcctggccagccgccccatccgggagggaggtgggggggtcagccccccgcccgg -ccagccgccccgtccgggaggggggagggggggtcagccccctgcccggccagccgcccc -gtccgggagggaggt-ggggggggggtcagccccctttccggcc-gccgccccgtccggg -agggaggtggggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggc -gcctctgcccggccacccctactgggaagtgaggagcccctctgcccggccagccgcccc -gtccgggagggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggg -gggtcagccccccttccggccggccgccctgtccgggaggtgaggggcgcctctgcctgg -ccgcccctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggag -gtggggg ->ref_chr20:4032257-4033328 -cccggccgccaccccgtctgggaagtgaggagcgtctctgcttggccacccatcgtctgg -gatatgaggagcccctctgcctggctgcccagtctggaaagtgaggagcgtctctgcccg -gccgccatcccatctaggaagcgaggagcgtctctgcccggccgccatcccatctaggaa -gcgaggagcgcctcttcccggctgccatcccatctaggaactgaggagcgtctctgcccg -gccgcccatcgtctgagatgtggggagcacctctgccccaccgccctgtctgggatgtga -ggagcgcctctgctgggccgcaaccctgtctgggaggtgaggagcgtctctgccccgccg -ctccgtctgagaagtgaggaaaccctctgcctggcaaccgccccgtctgagaagtgagga -gcccctccgtccggcaaccaccccgt---------------------------------- ------------------------------------------------------ctgggaa -gtgaggagcgtctccgcccggcagccaccccgtccgggagggaggt-------------- ------------------------------------------------------------- -------------------------------------------------------gggggg -gggggtcggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggcc -ggccgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgag -gacccctctgcccggccagccgccccgtccgggagggaggtgggggggtcagccccccgc -ccggccggctgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactggga -agtgaggagcccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagc -cccccgcctggccagccgccccatccgggagggaggtgggggggtcagccccccgcccgg -ccagccgccccgtccgggaggggggagggggggtcagccccctgcccggccagccgcccc -gtccgggagggaggt-ggggggggggtcagccccctttccggcc-gccg----------- ----------------------------------------cctgtccgggaggtgaggggc -gcctctgcctggccgcccctactgggaagtgagga-cccctctgcccggccagccgcccc -gtccgggagggaggtggggg---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_42e0cb6dab56dba4b2b1bfa60d340a7c.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_42e0cb6dab56dba4b2b1bfa60d340a7c.msa deleted file mode 100644 index a9c3ebec..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_42e0cb6dab56dba4b2b1bfa60d340a7c.msa +++ /dev/null @@ -1,90 +0,0 @@ ->syndip_1_chr20:62321031-62321873 -gaggtcccagagttctggcagagtcatagggtcaggtaggagtcagatgggagtgaaggg -catggggtcacccagggagaaggtagggccagcacaaggggttggggccggaggtggggc -cagtgaaggggcggggccggtggaggcagggtcagtgaaggggtggggccagtggaggaa -gagggggccagtggaggaggcggggcctgtggaggggtggggccagtggaggcagggtca -gtgaaggggtggggccggtggaggaagagggggccagtgaaggtgtggggccagtggagg -aggtgcagccagtggaagaggtggggccagtgggggtggggtcagtggaggggtggggtc -agaggacaggtgggttcagaggacgggtgggttcagaggacgggtgggttcagaggacgg -gtggggtcagtggaggggtggggtcagtggaggggtagggtcagaggacgggtagggtca -gtggaggggtagggccagcagaggggtggggtcagcggaggggtggggtcagtggagggg -tggggtcagtggaggggtggggtcagtggaggcagggtcagtgaaagggtggcgccagtg -gaggaagagggcgccagtggaggaagagggcgccagtggaggaagagggggccagtggag -gcagggcctgtggaggggtggggccagtggaggtggggtcagtgaaggggtggggccagc -ggaggaggtgcagccagtggaagaggtggggccaatgggggtggggtcagtggaggggtg -gggtcagtgggggaggcagggccagcagaggggtggggccagt----------------- -ggaggggtggggccagcggaggggtggggtcagtgggggaggaagggccagcagatgggg -tggggccagggcacacaggaaggctagggacagtagaggggtgcagccagcagtggagct -gcagcgctcctcagcgtggttgg ->syndip_2_chr20:62321031-62321873 -gaggtcccagagttctggcagagtcatagggtcaggtaggagtcagatgggagtgaaggg -catggggtcacccagggagaaggtagggccagcacaaggggttggggccggaggtggggc -cagtgaaggggcggggccggtggaggcagggtcagtgaaggggtggggccagtggaggaa -gagggggccagtggaggaggcggggcctgtggaggggtggggccagtggaggcagggtca -gtgaaggggtggggccggtggaggaagagggggccagtgaaggtgtggggccagtggagg -aggtgcagccagtggcagaggtggggccagtgggggtggggtcagtggaggggtggggtc -agaggac----------------------------------------------------- ------------------------------------------------------------- -------gggtagggtcagtggaggggtagggccagcagaggggtggggtcagtggagggg -tggggtcagtggaggggtggggtcagtggaggcagggtcagtgaaagggt---------- ----------ggcgccagtggaggaagagggcgccagtggaggaagagggggccagtggag -gcagggcctgtggaggggtggggccagtggaggtggggtcagtgaaggggtggggccagc -ggaggaggtgcagccagtggaagaggtggggccaatgggggtggggtcagtggaggggtg -gggtcagtgggggaggcagggccagcagaggggtggggccagtggaggggtggggccagc -ggaggggtggggccagcggaggggtggggtcagtgggggaggaagggccagcagatgggg -tggggccagggcacacaggaaggctagggacagtagaggggtgcagccagcagtggagct -gcagcgctcctcagcgtggttgg ->p:HG002_1_chr20:62321031-62321873 -gaggtcccagagttctggcagagtcatagggtcaggtaggagtcagatgggagtgaaggg -catggggtcacccagggagaaggtagggccagcacaaggggttggggccggaggtggggc -cagtgaaggggcggggccggtggaggcagggtcagtgaaggggtggggccagtggaggaa -gagggggccagtggaggaggcggggcctgtggaggggtggggccagtggaggcagggtca -gtgaaggggtggggccggtggaggaagagggggccagtgaaggtgtggggccagtggagg -aggtgcagccagtggcagaggtggggccagtgggggtggggtcagtggaggggtggggtc -agaggac----------------------------------------------------- ------------------------------------------------------------- -------gggtagggtcagtggaggggtagggccagcagaggggtggggtcagtggagggg -tggggtcagtggaggggtggggtcagtggaggcagggtcagtgaaagggt---------- ----------ggcgccagtggaggaagagggcgccagtggaggaagagggggccagtggag -gcagggcctgtggaggggtggggccagtggaggtggggtcagtgaaggggtggggccagc -ggaggaggtgcagccagtggaagaggtggggccaatgggggtggggtcagtggaggggtg -gggtcagtgggggaggcagggccagcagaggggtggggccagtggaggggtggggccagc -ggaggggtggggccagcggaggggtggggtcagtgggggaggaagggccagcagatgggg -tggggccagggcacacaggaaggctagggacagtagaggggtgcagccagcagtggagct -gcagcgctcctcagcgtggttgg ->p:HG002_2_chr20:62321031-62321873 -gaggtcccagagttctggcagagtcatagggtcaggtaggagtcagatgggagtgaaggg -catggggtcacccagggagaaggtagggccagcacaaggggttggggccggaggtggggc -cagtgaaggggcggggccggtggaggcagggtcagtgaaggggtggggccagtggaggaa -gagggggccagtggaggaggcggggcctgtggaggggtggggccagtggaggcagggtca -gtgaaggggtggggccggtggaggaagagggggccagtgaaggtgtggggccagtggagg -aggtgcagccagtggaagaggtggggccagtgggggtggggtcagtggaggggtggggtc -agaggacaggtgggttcagaggacgggtgggttcagaggacgggtgggttcagaggacgg -gtggggtcagtggaggggtggggtcagtggaggggtagggtcagaggacgggtagggtca -gtggaggggtagggccagcagaggggtggggtcagcggaggggtggggtcagtggagggg -tggggtcagtggaggggtggggtcagtggaggcagggtcagtgaaagggtggcgccagtg -gaggaagagggcgccagtggaggaagagggcgccagtggaggaagagggggccagtggag -gcagggcctgtggaggggtggggccagtggaggtggggtcagtgaaggggtggggccagc -ggaggaggtgcagccagtggaagaggtggggccaatgggggtggggtcagtggaggggtg -gggtcagtgggggaggcagggccagcagaggggtggggccagt----------------- -ggaggggtggggccagcggaggggtggggtcagtgggggaggaagggccagcagatgggg -tggggccagggcacacaggaaggctagggacagtagaggggtgcagccagcagtggagct -gcagcgctcctcagcgtggttgg ->ref_chr20:62321031-62321873 -gaggtcccagagttctggcagagtcatagggtcaggtaggagtcagatgggagtgaaggg -catggggtcacccagggagaaggtagggccagcacaaggggttggggccggaggtggggc -cagtgaaggggcggggccggtggaggcagggtcagtgaaggggtggggccagtggaggaa -gagggggccagtggaggaggcggggcctgtggaggggtggggccagtggaggcagggtca -gtgaaggggtggggccggtggaggaagagggggccagtgaaggtgtggggccagtggagg -aggtgcagccagtggaagaggtggggccagtgggggtggggtcagtggaggggtggggtc -agaggacgggtgggt--------------------------------------------- -----------------------------------------tcagaggacgggtagggtca -gtggaggggtagggccagcagaggggtagggccagcagaggggtggggtcagtggagggg -tggggtcagtggaggggtggggtcagtggaggcagggtcagtgaaagggt---------- -----------------------------ggcgccagtggaggaagagggggccagtggag -gcagggcctgtggaggggtggggccagtggaggtggggtcagtgaaggggtggggccagc -ggaggaggtgcagccagtggaagaggtggggccaatgggggtggggtcagtggaggggtg -gggtcagtgggggaggcagggccagcagaggggtggggtcagt----------------- -ggaggggtggggccagtggaggggtggggtcagtgggggaggaagggccagcagatgggg -tggggccagggcacacaggaaggctagggacagtagaggggtgcagccagcagtggagct -gcagcgctcctcagcgtggttgg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_42fae7a80da28fb57afe9f85370908c2.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_42fae7a80da28fb57afe9f85370908c2.msa deleted file mode 100644 index e5af0dc2..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_42fae7a80da28fb57afe9f85370908c2.msa +++ /dev/null @@ -1,345 +0,0 @@ ->syndip_1_chr20:64173409-64176529 -gagcaggagggagcccataccccagtgcctgtagttgtgtccatttcccctccctgactt -ctcctcctgcagcatccttccctttagttgtgtccatttcccctccctgacttctcctcc -tgcagcatctttcctagttgtgtccatttcccctccctgacttctcctcctgcagcatct -ttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttcctag -ttgtgtccatttcccctccctgacttctcctcctgcagcatccttccctgtagttgtgtc -catttcccctccctgacttctcctcctgcagcatctttccctgtagttgtgtccatttcc -cctccctgacttctcctcctgcagcatctttccttgtagttgtgtccatttcccctccct -ggcttctcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttct -cctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcat -ctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgt -agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc -atttcccctccctggctt---ctcctgcagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggct -tctcctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcag -catctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccc -tgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtg -tccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctc -cctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcaactt -tcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtc -catttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagca -tctttcc---tagttgtgtccatttcccctccctggcttctcctgtagcatctttcctag -ttgtgtccattccccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -ttcccctccctgg------cttctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcc -tgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctttc -ctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgt -ccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccc -tccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggctt -ctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtcca -tttcccctccctggcgtctcctcctgcagcatctttcctagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctcctcctgc -agcatctttccctgtagttgtgtccatttcccctccctggcttctcctcctgcagcatct -ttccctgtagttgtgtccattccccctccctggcttctcctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgt -gtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgt -agttgtgtccattccccctccctggcttctcctcctgcagcatctttccctgtagttgtg -tccatttcccctccctggctt---ctgcagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcat -ctttccctg--------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------t -agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc -atttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctc -cctgg--------------------------------------------------cttct -cctgtagcatctttccctgtagttgtgttcatttcccctccctggctt------------ ---------------------------------------------ctcctgcagcatcttt -ccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagtt -gtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccattt -cccctccctgg------------------------------------------------- ------------------------------------------------------------- -cttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgc -agcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttc -cctgtagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgctcc -ctggtagcctcttgggagc ->syndip_2_chr20:64173409-64176529 -gagcaggagggagcccataccccagtgcctgtagttgtgtccatttcccctccctgactt -ctcctcctgcagcatccttccctttagttgtgtccatttcccctccctgacttctcctcc -tgcagcatctttcctagttgtgtccatttcccctccctgacttctcctcctgcagcatct -ttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttcctag -ttgtgtccatttcccctccctgacttctcctcctgcagcatccttccctgtagttgtgtc -catttcccctccctgacttctcctcctgcagcatctttccctgtagttgtgtccatttcc -cctccctgacttctcctcctgcagcatctttccttgtagttgtgtccatttcccctccct -ggcttctcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttct -cctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcat -ctttccctgtagttgtgtccatttcccctccctggcttctc------------------- -----------------------------ctcctgcagcatctttccctgtagttgtgtcc -atttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggct -tctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcag -catctttccctgtagttgtgtccatttcccctccctggctt------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------ctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctt -tcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgtagcatctttcc------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------tagttgtgtccatttcccctccctggctt -ctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcca -tttcccctccctgg---------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------cttctcctacagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgtagcatctttcc---tagttgtgtccatttcccctccct -ggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggctt---ct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctt -tcc--------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------tagttgtgtccatttccc -ctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcat -ctttccctg--------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------tagttgtgtccatttcccctccctggcttctcctgtag -catctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgt -agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc -atttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctc -cctggcgtctcctcctgcagcatctttcctagttgtgtccatttcccctccctggcttct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctcctgcag -catctttccctgtagttgtgtccattccccctccctggcttctcctcctgcagcatcttt -ccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagtt -gtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccattt -cccctccctgg------------------------------------------------- ------------------------------------------------------------- -cttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgc -agcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttc -cctgtagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgctcc -ctggtagcctcttgggagc ->p:HG002_1_chr20:64173409-64176529 -gagcaggagggagcccataccccagtgcctgtagttgtgtccatttcccctccctgactt -ctcctcctgcagcatccttccctttagttgtgtccatttcccctccctgacttctcctcc -tgcagcatctttcctagttgtgtccatttcccctccctgacttctcctcctgcagcatct -ttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttcctag -ttgtgtccatttcccctccctgacttctcctcctgcagcatccttccctgtagttgtgtc -catttcccctccctgacttctcctcctgcagcatctttccctgtagttgtgtccatttcc -cctccctgacttctcctcctgcagcatctttccttgtagttgtgtccatttcccctccct -ggcttctcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttct -cctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcat -ctttccctgtagttgtgtccatttcccctccctggcttctc------------------- -----------------------------ctcctgcagcatctttccctgtagttgtgtcc -atttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggct -tctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcag -catctttccctgtagttgtgtccatttcccctccctggctt------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------ctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctt -tcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgtagcatctttcc------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------tagttgtgtccatttcccctccctggctt -ctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcca -tttcccctccctgg---------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------cttctcctacagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgtagcatctttcc---tagttgtgtccatttcccctccct -ggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggctt---ct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctt -tcc--------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------tagttgtgtccatttccc -ctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcat -ctttccctg--------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------tagttgtgtccatttcccctccctggcttctcctgtag -catctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgt -agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc -atttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctc -cctggcgtctcctcctgcagcatctttcctagttgtgtccatttcccctccctggcttct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctcctgcag -catctttccctgtagttgtgtccattccccctccctggcttctcctcctgcagcatcttt -ccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagtt -gtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccattt -cccctccctgg------------------------------------------------- ------------------------------------------------------------- -cttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgc -agcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttc -cctgtagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgctcc -ctggtagcctcttgggagc ->p:HG002_2_chr20:64173409-64176529 -gagcaggagggagcccataccccagtgcctgtagttgtgtccatttcccctccctgactt -ctcctcctgcagcatccttccctttagttgtgtccatttcccctccctgacttctcctcc -tgcagcatctttcctagttgtgtccatttcccctccctgacttctcctcctgcagcatct -ttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttcctag -ttgtgtccatttcccctccctgacttctcctcctgcagcatccttccctgtagttgtgtc -catttcccctccctgacttctcctcctgcagcatctttccctgtagttgtgtccatttcc -cctccctgacttctcctcctgcagcatctttccttgtagttgtgtccatttcccctccct -ggcttctcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttct -cctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcat -ctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgt -agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc -atttcccctccctggctt---ctcctgcagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggct -tctcctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcag -catctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccc -tgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtg -tccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctc -cctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcaactt -tcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtc -catttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagca -tctttcc---tagttgtgtccatttcccctccctggcttctcctgtagcatctttcctag -ttgtgtccattccccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -ttcccctccctgg------cttctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcc -tgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctttc -ctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgt -ccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccc -tccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggctt -ctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtcca -tttcccctccctggcgtctcctcctgcagcatctttcctagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctcctcctgc -agcatctttccctgtagttgtgtccatttcccctccctggcttctcctcctgcagcatct -ttccctgtagttgtgtccattccccctccctggcttctcctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgt -gtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgt -agttgtgtccattccccctccctggcttctcctcctgcagcatctttccctgtagttgtg -tccatttcccctccctggctt---ctgcagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcat -ctttccctg--------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------t -agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc -atttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctc -cctgg--------------------------------------------------cttct -cctgtagcatctttccctgtagttgtgttcatttcccctccctggctt------------ ---------------------------------------------ctcctgcagcatcttt -ccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagtt -gtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccattt -cccctccctgg------------------------------------------------- ------------------------------------------------------------- -cttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgc -agcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttc -cctgtagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgctcc -ctggtagcctcttgggagc ->ref_chr20:64173409-64176529 -gagcaggagggagcccataccccagtgcctgtagttgtgtccatttcccctccctgactt -ctcctcctgcagcatccttccctt------------------------------------ ---------------tagttgtgtccatttcccctccctgacttctcctcctgcagcatcc -ttccctttagttgtgtccatttcccctccctgacttctcctcctgcagcatctttcctag -ttgtgtccatttcccctccctgacttctcctcctgcagcatctttccttgtagttgtgtc -catttcccctccctggcttctcctcctgcagcatctttccttgtagttgtgtccatttcc -cctccctgacttctcctcctgcagcatccttccctgtagttgtgtccatttcccctccct -ggctt------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------ctcctgcagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggct -tctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtag -catctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttcc- ---tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtg -tccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctc -cctggcttctc--------------------------------------------ctcct -gcagcatctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctt -tcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagca -tctttccctgtagttgtgtccattccccctccctgacttctc------------------ ---------------------------ctcctgcagcatctttccctgtagttgtgtccat -ttcccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctc- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------ctcctgcagcatctttccctgtagttgtgtccattccccc -tccctggcttctcctgtagcatctttcc---tagttgtgtccatttcccctccctggctt -ctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtcca -tttcccctccctgg---------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------cttctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctt -tccctgtagttgtgtccattccccctccctggcgtctcctcctgcagcatctttccctgt -agttgtgtccattccccctccctggctt---ctcctgcagcatctttccctgtagttgtg -tccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcat -ctttccctgtagttgtgtccattccccctccctgacttctcctcctgcagcatctttccc -tgtagttgtgtccatttcccctccctggcgtctcctcctgcagcatctttccctgtagtt -gtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatttccc -ctccctggcttctcctcctgcagcatctttccctgtagttgtgtccattccccctccctg -gcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtag -catctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgt -agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc -atttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctc -cctgg---cttctcctgcagcatctttcctagttgtgtccatttcccctccctggcttct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggctt---ctcctgtag -catctttccctgtagttgtgtccattccccctccctggcgtctcctcctgcagcatcttt -ccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagtt -gtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccattc -cccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctcctgcagcatctttccctgtagttgtgtccattccccctccctggctt -ctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgc -agcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttc -cctgtagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgctcc -ctggtagcctcttgggagc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_43661afecfb4af36939766c89e8d0e19.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_43661afecfb4af36939766c89e8d0e19.msa deleted file mode 100644 index ae2b5d2e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_43661afecfb4af36939766c89e8d0e19.msa +++ /dev/null @@ -1,145 +0,0 @@ ->syndip_1_chr20:61201683-61202474 -aacctaagctttcaccgttagagaaggaatttcctcactcaggaccctctgcggatgtca -cctccatcctcatcaggaccctccatggtgtcacctccatcctcactcaggacactccat -ggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatcctcactcagga -ccctccatgagtgccacctccatcctcactcaggatcccctgtaagtgtcacctccatcc -tcaccaggaccctccatg-gtgtcaccgccatcctcactcaggaccctccatgagtgcca -cctccatcctcaccaggatcccctgtaagtgtcacctccatcctcac-caggaccctcca -tgagtgtcacctccatc----ctcaggaccctccatgagtgtcacctccatcctcactca -ggaccctccat-ggtgtcacctccatcctcactcaggaccctccat-ggtgtcacctcca -tcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgt -cacctccatcctca----------------------------ccaggaccctccatgagt -gtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccc -tccatgggtgtcacctccatcctcactcaggaccctccat-ggtgtcaccgccatcctca --------------------------------ctcaggaccctccatgagtgtcacctcca -tcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgt -cacctccatcctcaccaggatcccctgtaagtgtcacctccatcctcaccaggaccctcc -atgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactca -ggaccctccatg-gtgtcacctccatcctcaccaggatcccctgtaagtgtcacctccat -cctcac-caggaccctccatgagtgtcacctccatcctca-------------------- -------ctcaggaccctccatg-gtgtcacctccatcctcactcaggaccctccatggtg -tcacctccatcctcactcaggaccctccat-ggtgtcacctccatcctcactcaggaccc -tccatgggtgtcacctccatcctcactcaggaccctccatg-gtgtcacctccatcctca -ccaggaccctccatgagtgtcacctccatc----ctcaggaccctccatgagtgtcacct -ccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatgg -tgtcacctccatcctcactcaggaccctccatg--------------------------- ---------gtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca -ccaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctc -catcctcactcaggaccctccgtgagtgccagctctgtctaccctcgggaccctccatga -gtgtctcctctatctaccctcaggaccctctgtgaatgtcctcgccatccatactccccc ->syndip_2_chr20:61201683-61202474 -aacctaagctttcaccattagagaaggaatttcctcactcaggaccctctgcggatgtcg -cctccatcctcatcaggaccctccatggtgtcacctccatcctcactcaggacactccat -ggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatcctcactcagga -ccctccatgggtgtcacctccatcctcac-caggatcccctgtaagtgtcacctccatcc -tcaccaggaccctccatgagtgtcacctccatcctcactcaggaccctccatg-gtgtca -cctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctcca -tgggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactca -ggaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgccacctcca -tcctcaccaggatcccctgtaagtgtcacctccatcctcaccaggaccctccatgagtgt -cacctccatcctcaggaccctccatgagtgtcacctccatcctcaggaccctccatgagt -gtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccc -tccat-ggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctca -ctcaggaccctccatgagtgtcacctccatcctcaggaccctccatgagtgtcacctcca -tcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgt -cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggacactc -catggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatcctcactca -ggaccctccatgagtgccacctccatcctcaccaggatcccctgtaagtgtcacctccat -cctcactcaggaccctccatgagtgtcacctccatcctcaggaccctccatggtgtcacc -tccatcctcaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtg -tcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccc -tccatgggtgtcacctccatcctcactcaggaccctccatgagtgtcacctccatcctca -ctcaggaccctccatggtgtcacctccatcctcactcaggaccctccatg-gtgtcacct -ccatcctcactcaggacactccatggtgtcacctccatccttactcaggaccctccatgg -tgtcaccgccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggatc -ccctgtaagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca -ctcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctc -catcctcactcaggaccctccgtgagtgccagctctgtctaccctcgggaccctccatga -gtgtctcctctatctaccctaaggaccctctgtgaatgtcctcgccatccatactccccc ->p:HG002_1_chr20:61201683-61202474 -aacctaagctttcaccattagagaaggaatttcctcactcaggaccctctgcggatgtcg -cctccatcctcatcaggaccctccatggtgtcacctccatcctcactcaggacactccat -ggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatcctcactcagga -ccctccatgggtgtcacctccatcctcac-caggatcccctgtaagtgtcacctccatcc -tcaccaggaccctccatgagtgtcacctccatcctcactcaggaccctccatg-gtgtca -cctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctcca -tgggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactca -ggaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgccacctcca -tcctcaccaggatcccctgtaagtgtcacctccatcctcaccaggaccctccatgagtgt -cacctccatcctcaggaccctccatgagtgtcacctccatcctcaggaccctccatgagt -gtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccc -tccat-ggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctca -ctcaggaccctccatgagtgtcacctccatcctcaggaccctccatgagtgtcacctcca -tcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgt -cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggacactc -catggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatcctcactca -ggaccctccatgagtgccacctccatcctcaccaggatcccctgtaagtgtcacctccat -cctcactcaggaccctccatgagtgtcacctccatcctcaggaccctccatggtgtcacc -tccatcctcaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtg -tcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccc -tccatgggtgtcacctccatcctcactcaggaccctccatgagtgtcacctccatcctca -ctcaggaccctccatggtgtcacctccatcctcactcaggaccctccatg-gtgtcacct -ccatcctcactcaggacactccatggtgtcacctccatccttactcaggaccctccatgg -tgtcaccgccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggatc -ccctgtaagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca -ctcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctc -catcctcactcaggaccctccgtgagtgccagctctgtctaccctcgggaccctccatga -gtgtctcctctatctaccctaaggaccctctgtgaatgtcctcgccatccatactccccc ->p:HG002_2_chr20:61201683-61202474 -aacctaagctttcaccgttagagaaggaatttcctcactcaggaccctctgcggatgtca -cctccatcctcatcaggaccctccatggtgtcacctccatcctcactcaggacactccat -ggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatcctcactcagga -ccctccatgagtgccacctccatcctcactcaggatcccctgtaagtgtcacctccatcc -tcaccaggaccctccatg-gtgtcaccgccatcctcactcaggaccctccatgagtgcca -cctccatcctcaccaggatcccctgtaagtgtcacctccatcctcac-caggaccctcca -tgagtgtcacctccatc----ctcaggaccctccatgagtgtcacctccatcctcactca -ggaccctccat-ggtgtcacctccatcctcactcaggaccctccat-ggtgtcacctcca -tcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgt -cacctccatcctca----------------------------ccaggaccctccatgagt -gtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccc -tccatgggtgtcacctccatcctcactcaggaccctccat-ggtgtcaccgccatcctca --------------------------------ctcaggaccctccatgagtgtcacctcca -tcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgt -cacctccatcctcaccaggatcccctgtaagtgtcacctccatcctcaccaggaccctcc -atgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactca -ggaccctccatg-gtgtcacctccatcctcaccaggatcccctgtaagtgtcacctccat -cctcac-caggaccctccatgagtgtcacctccatcctca-------------------- -------ctcaggaccctccatg-gtgtcacctccatcctcactcaggaccctccatggtg -tcacctccatcctcactcaggaccctccat-ggtgtcacctccatcctcactcaggaccc -tccatgggtgtcacctccatcctcactcaggaccctccatg-gtgtcacctccatcctca -ccaggaccctccatgagtgtcacctccatc----ctcaggaccctccatgagtgtcacct -ccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatgg -tgtcacctccatcctcactcaggaccctccatg--------------------------- ---------gtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca -ccaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctc -catcctcactcaggaccctccgtgagtgccagctctgtctaccctcgggaccctccatga -gtgtctcctctatctaccctcaggaccctctgtgaatgtcctcgccatccatactccccc ->ref_chr20:61201683-61202474 -aacctaagctttcaccattagagaaggaatttcctcactcaggaccctctgcggatgtcg -cctccatcctcatcaggaccctccatggtgtcacctccatcctcactcaggacactccat -ggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatcctcactcagga -ccctccatgagtgccacctccatcctcac-caggatcccctgtaagtgtcacctccatcc -tcaccaggaccctccatgagtgtcacctccatcct------------------------- -------------------------------------------------caggaccctcca -tgagtgtcacctccatc------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------ctcactcaggaccctccat-ggtgtcaccgccatcctcactcaggaccc -tccatgagtgccacctccatcctcaccaggatcccctgtaa-gtgtcacctccatcctca -ccaggaccctccatgagtgtcacctccatc----ctcaggaccctccatgagtgtcacct -ccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatgg -tgtcacctccatcctcactcaggaccctccatg--------------------------- --------ggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca -ctcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctc -catcctcactcaggaccctccgtgagtgccagctctgtctaccctcgggaccctccatga -gtgtctcctctatctaccctcaggaccctctgtgaatgtcctcgccatccatactccccc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_448275ede2855814c5aa2db2165078ff.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_448275ede2855814c5aa2db2165078ff.msa deleted file mode 100644 index 4bf003ef..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_448275ede2855814c5aa2db2165078ff.msa +++ /dev/null @@ -1,85 +0,0 @@ ->syndip_1_chr20:278900-279186 ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------gggaaaggcaggagagggcgcgcgagtgcgcggagggagg -gcgggacggag----ggagggagggcgggagggagggacggagggaggaagggcgggacg -gagggagggagggcgggagggacggagggcgggacggcgggagggcgggacggagggacg -gagggagggcgggacggagggcgggagggcgggacggagggagggag---ggagggaggg -cgggacggagggagggagggagggagggacggagggcgggacggagggagggagggcgga -g-ggagggagggcgggacggagggagggagggcgggacggagggtgggagggagggaggg -atggaggga----gggagggagggacggagggcgggacggagggacggagggagggaggg -agggacggaggttgggacggagggacggagggcgggcggatgccgcgggtctcaccgcca -aggtgtcctg ->syndip_2_chr20:278900-279186 -gggaaaggcaggagagggcgcgcgagtgcgcggagggagggcgggacggagggagggagg -gcgggacggagggagggagggagggcgggacggagggagggagggcgggacggagggagg -gagggagggacggagggcgggacggcgggagggcgggacggagggacggagggagggcgg -gacggagggcgggagggcgggacggagggagggagggagggagggcgggacggagggagg -gagggcgggacggagggagggagggagggacggagggcgggacggcgggagggcgggacg -gagggacggagggagggcgggacggagggcgggagggcgggacggagggagggagggcgg -gacggagggacggagggagggagggcgggacggagggagggagggcgggacggagggacg -gagggagggagggcgggacggagggagggagggagggacggagggcgggacggcgggagg -gcgggacggagggacggagggagggcgggacggagggcgggagggagggagggcgggacg -gagggagggagggagggagggcgggacggagggagggagggagggagggacggagggacg -gagggagggagggagggagggacggagggcgggacggagggagggagggcggagggaggg -agggcgggacggagggagggagggagggacggagggcgggacggagggagggagggcgga -g-ggagggagggcgggacggagggagggagggcgggagggatggagggagggagggcggg -acggagggagggcgggagggagggacggagggcgggacggagggacggagggagggaggg -agggacggaggttgggacggagggacggagggcgggcggatgccgcgggtctcaccgcca -aggtgtcctg ->p:HG002_1_chr20:278900-279186 -gggaaaggcaggagagggcgcgcgagtgcgcggagggagggcgggacggagggagggagg -gcgggacggagggagggagggagggcgggacggagggagggagggcgggacggagggagg -gagggagggacggagggcgggacggcgggagggcgggacggagggacggagggagggcgg -gacggagggcgggagggcgggacggagggagggagggagggagggcgggacggagggagg -gagggcgggacggagggagggagggagggacggagggcgggacggcgggagggcgggacg -gagggacggagggagggcgggacggagggcgggagggcgggacggagggagggagggcgg -gacggagggacggagggagggagggcgggacggagggagggagggcgggacggagggacg -gagggagggagggcgggacggagggagggagggagggacggagggcgggacggcgggagg -gcgggacggagggacggagggagggcgggacggagggcgggagggagggagggcgggacg -gagggagggagggagggagggcgggacggagggagggagggagggagggacggagggacg -gagggagggagggagggagggacggagggcgggacggagggagggagggcggagggaggg -agggcgggacggagggagggagggagggacggagggcgggacggagggagggagggcgga -g-ggagggagggcgggacggagggagggagggcgggagggatggagggagggagggcggg -acggagggagggcgggagggagggacggagggcgggacggagggacggagggagggaggg -agggacggaggttgggacggagggacggagggcgggcggatgccgcgggtctcaccgcca -aggtgtcctg ->p:HG002_2_chr20:278900-279186 ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------gggaaaggcaggagagggcgcgcgagtgcgcggagggagg -gcgggacggag----ggagggagggcgggagggagggacggagggaggaagggcgggacg -gagggagggagggcgggagggacggagggcgggacggcgggagggcgggacggagggacg -gagggagggcgggacggagggcgggagggcgggacggagggagggag---ggagggaggg -cgggacggagggagggagggagggagggacggagggcgggacggagggagggagggcgga -g-ggagggagggcgggacggagggagggagggcgggacggagggtgggagggagggaggg -atggaggga----gggagggagggacggagggcgggacggagggacggagggagggaggg -agggacggaggttgggacggagggacggagggcgggcggatgccgcgggtctcaccgcca -aggtgtcctg ->ref_chr20:278900-279186 ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------gggaaaggcaggagagggcgcgcgagtgcgcggaggg -agggcgggacggagggagggagggcgggacggagggagggagggagggacggagggcggg -acggcgggagggcgggacggagggacggagggagggcgggacggagggcgggagggcggg -acggagggagggagggagggagggacggagggcgggacggagggacggagggagggaggg -agggacggaggttgggacggagggacggagggcgggcggatgccgcgggtctcaccgcca -gggtgtcctg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_45f1dc1c7a33a6a5fbb511967c1352d7.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_45f1dc1c7a33a6a5fbb511967c1352d7.msa deleted file mode 100644 index 867d45f9..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_45f1dc1c7a33a6a5fbb511967c1352d7.msa +++ /dev/null @@ -1,125 +0,0 @@ ->syndip_1_chr20:8661844-8662219 -atttaataaatcttcagtgaaaggcaagaggctacacacagtgacagacccagagataaa -ccctgtgcccctagagatttgcactcctcttaaaagtgtatatatatataattatataat -tatttattatataattatatataattatataattatttattatataattatatataatta -tataattatttattatataattatatataa-tatacaattatttattatataattatata -taattatatatttattatatttat-----tatacagttatataataaataattatataat -tatatataattatat-atatataattatatataattatatataattatataattatatat -aattg-tatataattatttattatataattatatatta-tttattat--ataattatata -attatatatta-tttattat---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------atattatataattata -taattatatattatttattatata-----atatataattatatat-------tatttatt -atataattatatattatttatta---------tatatattatttattatata-------- ---------------attatatattatgtattatataattatataattatatattatgtat -tatataat----------------tatatattatgtattatataattatataattatata -ttatgtattatataattatatattatttattatataattatataattatatattatttat -tatataattatataattatatattatttattatataat---------------------t -atataattatatattatttattatataattatataattatatattattt--------att -atataattatatattatttattatataattatatattatttattacataaatatatatta -tttattacataagtatatatcacttattatataattgcatataattatttattatataat -tgcatataa----ttattatataattgtatatagttatttattatataattg-------- ------------------tatatagttatttattatataattctatata-------attat -ttattatctaattctatattaaatataattatttattatctaattctatattatatataa -ttatttattatataattctatattatatataatta ->syndip_2_chr20:8661844-8662219 -atttaataaatcttcagtgaaaggcaagaggctacacacagtgacagacccagagataaa -ccctgtgcccctagagatttgcactcctcttaaaagtgtatatatatataattatataat -tatttattatataattatatataattatat------------------------------ ----aattatttattatataatgatatataattatataattatttattatataattatata -taattatataattatttattatataattatatataattatataattatttattatataat -tatatataattatataattatttattatataattatat---------------------- --ataattatataattatttattatataattatatataattatataattatttattatata -attatatataattatataattatttattatataattatatataattatataattatttat -tatataattatatataattatataattatttattatataattatatataatatacaatta -tttattatataattatatataatatacaattatttattatataattatatataattatat -atttattatatttattatacagttatataataaataattatataattatatataattata -taattatatataattatatatatataattatatgtaattatatataattatataattatt -atataattgtatataatatataattatataattatatattatttattatataatatataa -ttatataattatatattatttattatataatatataattatataattatatattatttat -tatataattatatattatttattatatatattatttattatataattatataattatata -ttatttattatataattatatattatttattatataa-tatataattatatattatttat -tatataa-tatataattatatattatttattatataattatatattatgtattatataat -atataattatatattatgtattatataattatataattatatattatttattatataatt -atataattatatattatttattacataattatatattatttattacataagtatatatta -tttattacataagtatatatcacttattatataattgtatataattatttattatataat -tgcatataattatttattatataattgtatatagttatttattatataattctatatagt -tatttattatataattctatataattatttattatctaattctatattatatataattat -ttattatctaattctatattaaatataattatttattatctaattctatattatatataa -ttatttattatataattctatattatatataatta ->p:HG002_1_chr20:8661844-8662219 -atttaataaatcttcagtgaaaggcaagaggctacacacagtgacagacccagagataaa -ccctgtgcccctagagatttgcactcctcttaaaagtgtatatatatataattatataat -tatttattatataattatatataattatat------------------------------ ----aattatttattatataattatatataa-tatacaattatttattatataattatata -taattatatatttatttattatataattatatataattatataattatttattatataat -tatatataattatataattatttattatataattatat---------------------- --ataattatataattatttattatataattatatataattatataattatttattatata -attatatataattatataattatttattatataattatatataattatataattatttat -tatataattatatataattatataattatttattatataattatatataatatacaatta -tttattatataattatatataatatacaattatttattatataattatatataattatat -atttattatatttattatacagttatataataaa----tatataattatatataaatata -taattatatataattatatatatataattatatgtaattatatataattatataattatt -atataattgtatataatatataattatataattatatattatttattatataatatataa -ttatataattatatattatttattatataatatataattatataattatatattatttat -tatataattatatattatttattatatatattatttattatataattatataattatata -ttatttattatataattatatattatttattatataa-tatataattatatattatttat -tatataa-tatataattatatattatttattatataattatatattatgtattatataat -atataattatatattatgtattatataattatataattatatattatttattatataatt -atataattatatattatttattacataattatatattatttattacataagtatatatta -tttattacataagtatatatcacttattatataattgtatataattatttattatataat -tgcatataattatttattatataattgtatatagttatttattatataattctatatagt -tatatttattatacagttatataataaataattatataattatatataattatatattat -ttattatctaattctatattaaatataattatttattatctaattctatattatatataa -ttatttattatataattctatattatatataatta ->p:HG002_2_chr20:8661844-8662219 -atttaataaatcttcagtgaaaggcaagaggctacacacagtgacagacccagagataaa -ccctgtgcccctagagatttgcactcctcttaaaagtgtatatatatataattatataat -tatttattatataattatatataattatataattatttattatataattatatataa-ta -tacaattatttattatataattatatataa-tatacaattatttattatataattatata -taattatatatttattatatttat-----tatacagttatataataaataattatataat -tatatataattatat-atatataattatatataattatatataattatataattatatat -aattg-tatataattatttattatataattatatatta-tttattat--ataattatata -attatatatta-tttattat---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------atattatataattata -taattatatattatttattatata-----atatataattatatat-------tatttatt -atataattatatattatttatta---------tatatattatttattatata-------- ---------------attatatattatgtattatataattatataattatatattatgtat -tatataat----------------tatatattatgtattatataattatataattatata -ttatgtattatataattatatattatttattatataattatataattatatattatttat -tatataattatataattatatattatttattatataat---------------------t -atataattatatattatttattatataattatataattatatattattt--------att -atataattatatattatttattatataattatatattatttattacataaatatatatta -tttattacataagtatatatcacttattatataattgcatataattatttattatataat -tgcatataa----ttattatatatttat-----tatatttattatacagt---------- ------------------tatataataaataattatataattatatataattatatattat -ttattatctaattctatattaaatataattatttattatctaattctatattatatataa -ttatttattatataattctatattatatataatta ->ref_chr20:8661844-8662219 -atttaataaatcttcagtgaaaggcaagaggctacacacagtgacagacccagagataaa -ccctgtgcccctagagatttgcactcctcttaaaagtgtatatatatataattatataat -tatttattatataattatatataattatat------------------------------ ----aattatttattatataattatatataa-tatacaattatttattatataattatata -taattatatatttattatatttat-----tatacagttatataataaataattatataat -tatatataattatat-attatttattatctaattctat---------------------- --atta-aatataattatttattatctaattctatatta-tatataattatttattatata -attctatatta-tatataatta-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------ diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_46284ada8ba275934db54af7d309b8ae.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_46284ada8ba275934db54af7d309b8ae.msa deleted file mode 100644 index 35f3a458..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_46284ada8ba275934db54af7d309b8ae.msa +++ /dev/null @@ -1,245 +0,0 @@ ->syndip_1_chr20:64125109-64127974 -atgatccacccaccttggcctcccaaagtgctgggattacaggtgtgagccactgcgccc -ggacacactttgctagttttttttttttgttttgtttttttagtagcagtgctgggatta -caggtgtcagccaccatgcctggctcaaatactacactgtcttgattactacagctttat -actcaaatactacaccatcttgattactacagctttatactcaaataccacaccgtcttg -attaccacagctgtatactcaaataccacaccgtcttgattaccacagctttatactcaa -ataccacaccgtcttgattaccaaagctttatactcaaataccacactgtcttgattacc -acagctttatactcaaataacacaccgtcttgattaccacagctttatactcaaatacta -caccgtcttgattaccacagctttatactcaaataccacactgtcttgattaccacagct -ttatactcaaataccacactgtcttgattcctatagctttatactcaaataccacactgt -cttgattaccacagctttatactcaaatactacactgtcttgattactatagctttatac -tcaaatactacactgtcttgattactatagctttatactcaaatactacactgtc-tgat -tactacagctttatactcaaataccaccctgtcttgattaccacagctttatactcaaat -accacaccgtcttgattaccacagctgtatactcaaatactacaccgtcttgattaccac -agctgtatactcaaatactacactgtcttgattaccacagctttatactcaaataccaca -ctgtcttgattaccaccgctttatactcaaataccacactgtcttgattactatagcttt -atactcaaatactacactgtctgattactacagctttatactcaaataccacactgtctt -gattaccacagctttatactcaaatactacactgtcttgattactatagctttatactca -aatactacactgtctgattactacagctttatactcaaataccacactatcttgattact -acagctttatactcaaatactacactgtctgattactacagctttatactcaaataccac -accgtcttgattaccacagctttatactcaaatactacactgtcttgattactacagctt -tatactcaaataccacaccgtcttgattaccacagctgtatactcaaatactacaccgtc -ttgattaccacagctttatactcaaatactacaccgtcttgattaccacagctttatact -caaataccacactgtcttgattactatagctttatactcaaatactacactgtctgatta -ctacagctttatactcaaataccacactgtcttgattaccacagctttatactcaaatac -tacactgtctgattactacagctttatactcaaataccacactgtcttgattaccacagc -tttatactcaaatactacactgtcttgattaccacagctttatactcaaataccacaccg -tcttgattaccacagctgtatactcaaataccacactgtcttgattaccacagctgtata -ctcaaataccacactgtcttgattaccac------------------------------- --------agctttatactcaaataccacactgtcttgattaccacagctttatacgcaaa -taccacactgtcttgattactatagctttatactcaaataccacactgtcttgattacta -cagctttatactcaaataccacactgtcttgattactacagctttatactcaaatactac -actgtcttgattaacacagctttatactcaaatactacactgtcttgattaccacagctt -tatactcaaatactacactgtcttgattactatagctttatactcaaataccacactgtc -ttgattactatagctttatactcaaatactacactgtcttgattaccacagctttatact -caaatactacactgtcttgattactatagctttatactcaaataccacactgtcttgatt -accacagctttatactcaaataccacactgtcttgattaccacagctttatactcaaata -ctacactgtcttgattactacagctttatactcaaataccacactgtcttgattactata -gctttatactcaaataccacactgtcttgattactatagctttatactc----------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------tgttttgaggtcaggtagtgtcagtccctc ->syndip_2_chr20:64125109-64127974 -atgatccacccaccttggcctcccaaagtgctgggattacaggtgtgagccactgcgccc -ggacacactttgctagttttttttttttgttttgtttttttagtagcagtgctgggatta -caggtgtcagccaccatgcctggctcaaatactacactgtcttgattactacagctttat -actcaaatactacaccatcttgattactacagctttatactcaaataccacaccgtcttg -attaccacagctgtatactcaaataccacaccgtcttgattaccacagctttatactcaa -ataccacaccgtcttgattaccaaagctttatactcaaataccacactgtcttgattacc -acagctttatactcaaataacacaccgtcttgattaccacagctttatactcaaatacta -caccgtcttgattaccacagctttatactcaaataccacactgtcttgattaccacagct -ttatactcaaataccacactgtcttgattcctatagctttatactcaaataccacactgt -cttgattaccacagctttatactcaaatactacactgtcttgattactatagctttatac -tcaaatactacactgtcttgattactatagctttatactcaaatactacactgtc-tgat -tactacagctttatactcaaataccaccctgtcttgattaccacagctttatactcaaat -accacaccgtcttgattaccacagctgtatactcaaatactacaccgtcttgattaccac -agctgtatactcaaatactacactgtcttgattaccacagctttatactcaaataccaca -ctgtcttgattaccaccgctttatactcaaataccacactgtcttgattactatagcttt -atactcaaatactacactgtctgattactacagctttatactcaaataccacactgtctt -gattaccacagctttatactcaaatactacactgtcttgattactatagctttatactca -aatactacactgtctgattactacagctttatactcaaataccacactatcttgattact -acagctttatactcaaatactacactgtctgattactacagctttatactcaaataccac -accgtcttgattaccacagctttatactcaaatactacactgtcttgattactacagctt -tatactcaaataccacaccgtcttgattaccacagctgtatactcaaatactacaccgtc -ttgattaccacagctttatactcaaatactacaccgtcttgattaccacagctttatact -caaataccacactgtcttgattactatagctttatactcaaatactacactgtctgatta -ctacagctttatactcaaataccacactgtcttgattaccacagctttatactcaaatac -tacactgtctgattactacagctttatactcaaataccacactgtcttgattaccacagc -tttatactcaaatactacactgtcttgattaccacagctttatactcaaataccacaccg -tcttgattaccacagctgtatactcaaataccacactgtcttgattaccacagctgtata -ctcaaataccacactgtcttgattaccac------------------------------- --------agctttatactcaaataccacactgtcttgattaccacagctttatacgcaaa -taccacactgtcttgattactatagctttatactcaaataccacactgtcttgattacta -cagctttatactcaaataccacactgtcttgattactacagctttatactcaaatactac -actgtcttgattaacacagctttatactcaaatactacactgtcttgattaccacagctt -tatactcaaatactacactgtcttgattactatagctttatactcaaataccacactgtc -ttgattactatagctttatactcaaatactacactgtcttgattaccacagctttatact -caaatactacactgtcttgattactatagctttatactcaaataccacactgtcttgatt -accacagctttatactcaaataccacactgtcttgattaccacagctttatactcaaata -ccacactgtcttgattactacagctttatactcaaataccacactgtcttgattactata -gctttatactcaaataccacactgtcttgattactatagctttatactc----------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------tgttttgaggtcaggtagtgtcagtccctc ->p:HG002_1_chr20:64125109-64127974 -atgatccacccaccttggcctcccaaagtgctgggattacaggtgtgagccactgcgccc -ggacacactttgctagttttttttttttgttttgtttttttagtagcagtgctgggatta -caggtgtcagccaccatgcctggctcaaatactacactgtcttgattactacagctttat -actcaaatactacaccatcttgattactacagctttatactcaaataccacaccgtcttg -attaccacagctgtatactcaaataccacaccgtcttgattaccacagctttatactcaa -ataccacaccgtcttgattaccaaagctttatactcaaataccacactgtcttgattacc -acagctttatactcaaataacacaccgtcttgattaccacagctttatactcaaatacta -caccgtcttgattaccacagctttatactcaaataccacactgtcttgattaccacagct -ttatactcaaataccacactgtcttgattcctatagctttatactcaaataccacactgt -cttgattaccacagctttatactcaaatactacactgtcttgattactatagctttatac -tcaaatactacactgtcttgattactatagctttatactcaaatactacactgtc-tgat -tactacagctttatactcaaataccaccctgtcttgattaccacagctttatactcaaat -accacaccgtcttgattaccacagctgtatactcaaatactacaccgtcttgattaccac -agctgtatactcaaatactacactgtcttgattaccacagctttatactcaaataccaca -ctgtcttgattaccaccgctttatactcaaataccacactgtcttgattactatagcttt -atactcaaatactacactgtctgattactacagctttatactcaaataccacactgtctt -gattaccacagctttatactcaaatactacactgtcttgattactatagctttatactca -aatactacactgtctgattactacagctttatactcaaataccacactatcttgattact -acagctttatactcaaatactacactgtctgattactacagctttatactcaaataccac -accgtcttgattaccacagctttatactcaaatactacactgtcttgattactacagctt -tatactcaaataccacaccgtcttgattaccacagctgtatactcaaatactacaccgtc -ttgattaccacagctttatactcaaatactacaccgtcttgattaccacagctttatact -caaataccacactgtcttgattactatagctttatactcaaatactacactgtctgatta -ctacagctttatactcaaataccacactgtcttgattaccacagctttatactcaaatac -tacactgtctgattactacagctttatactcaaataccacactgtcttgattaccacagc -tttatactcaaatactacactgtcttgattaccacagctttatactcaaataccacaccg -tcttgattaccacagctgtatactcaaataccacactgtcttgattaccacagctgtata -ctcaaataccacactgtcttgattaccac------------------------------- --------agctttatactcaaataccacactgtcttgattaccacagctttatacgcaaa -taccacactgtcttgattactatagctttatactcaaataccacactgtcttgattacta -cagctttatactcaaataccacactgtcttgattactacagctttatactcaaatactac -actgtcttgattaacacagctttatactcaaatactacactgtcttgattaccacagctt -tatactcaaatactacactgtcttgattactatagctttatactcaaataccacactgtc -ttgattactatagctttatactcaaatactacactgtcttgattaccacagctttatact -caaatactacactgtcttgattactatagctttatactcaaataccacactgtcttgatt -accacagctttatactcaaataccacactgtcttgattaccacagctttatactcaaata -ccacactgtcttgattactacagctttatactcaaataccacactgtcttgattactata -gctttatactcaaataccacactgtcttgattactatagctttatactc----------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------tgttttgaggtcaggtagtgtcagtccctc ->p:HG002_2_chr20:64125109-64127974 -atgatccacccaccttggcctcccaaagtgctgggattacaggtgtgagccactgcgccc -ggacacactttgctagttttttttttttgttttgtttttttagtagcagtgctgggatta -caggtgtcagccaccatgcctggctcaaatactacactgtcttgattactacagctttat -actcaaatactacaccatcttgattactacagctttatactcaaataccacaccgtcttg -attaccacagctgtatactcaaataccacaccgtcttgattaccacagctttatactcaa -ataccacaccgtcttgattaccaaagctttatactcaaataccacactgtcttgattacc -acagctttatactcaaataacacaccgtcttgattaccacagctttatactcaaatacta -caccgtcttgattaccacagctttatactcaaataccacactgtcttgattaccacagct -ttatactcaaataccacactgtcttgattcctatagctttatactcaaataccacactgt -cttgattaccacagctttatactcaaatactacactgtcttgattactatagctttatac -tcaaatactacactgtcttgattactatagctttatactcaaatactacactgtc-tgat -tactacagctttatactcaaataccaccctgtcttgattaccacagctttatactcaaat -accacaccgtcttgattaccacagctgtatactcaaatactacaccgtcttgattaccac -agctgtatactcaaatactacactgtcttgattaccacagctttatactcaaataccaca -ctgtcttgattaccaccgctttatactcaaataccacactgtcttgattactatagcttt -atactcaaatactacactgtctgattactacagctttatactcaaataccacactgtctt -gattaccacagctttatactcaaatactacactgtcttgattactatagctttatactca -aatactacactgtctgattactacagctttatactcaaataccacactatcttgattact -acagctttatactcaaatactacactgtctgattactacagctttatactcaaataccac -accgtcttgattaccacagctttatactcaaatactacactgtcttgattactacagctt -tatactcaaataccacaccgtcttgattaccacagctgtatactcaaatactacaccgtc -ttgattaccacagctttatactcaaatactacaccgtcttgattaccacagctttatact -caaataccacactgtcttgattactatagctttatactcaaatactacactgtctgatta -ctacagctttatactcaaataccacactgtcttgattaccacagctttatactcaaatac -tacactgtctgattactacagctttatactcaaataccacactgtcttgattaccacagc -tttatactcaaatactacactgtcttgattaccacagctttatactcaaataccacaccg -tcttgattaccacagctgtatactcaaataccacactgtcttgattaccacagctgtata -ctcaaataccacactgtcttgattaccac------------------------------- --------agctttatactcaaataccacactgtcttgattaccacagctttatacgcaaa -taccacactgtcttgattactatagctttatactcaaataccacactgtcttgattacta -cagctttatactcaaataccacactgtcttgattactacagctttatactcaaatactac -actgtcttgattaacacagctttatactcaaatactacactgtcttgattaccacagctt -tatactcaaatactacactgtcttgattactatagctttatactcaaataccacactgtc -ttgattactatagctttatactcaaatactacactgtcttgattaccacagctttatact -caaatactacactgtcttgattactatagctttatactcaaataccacactgtcttgatt -accacagctttatactcaaataccacactgtcttgattaccacagctttatactcaaata -ctacactgtcttgattactacagctttatactcaaataccacactgtcttgattactata -gctttatactcaaataccacactgtcttgattactatagctttatactc----------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------tgttttgaggtcaggtagtgtcagtccctc ->ref_chr20:64125109-64127974 -atgatccacccaccttggcctcccaaagtgctgggattacaggtgtgagccactgcgccc -ggacacactttgctagttttttttttttgttttgtttttttagtagcagtgctgggatta -caggtgtcagccaccatgcctggctcaaatactacactgtcttgattactacagctttat -actcaaatactacaccatcttgattactacagctttatactcaaataccacaccgtcttg -attaccacagctgtatactcaaataccacaccgtcttgattaccaaagctttatactcaa -ataccacactgtcttgattaccacagctttatactcaaataacacaccgtcttgattacc -acagctttatactcaaatactacaccgtcttgattaccacagctttatactcaaatacca -cactgtcttgattaccacagctttatactcaaatactacactgtcttgattcctatagct -ttatactcaaataccacactgtcttgattaccacagctttatactcaaatactacactgt -cttgattactatagctttatactcaaatactacactgtcttgattactatagctttatac -tcaaatactacactgtc-tgattactacagctttatactcaaataccaccctgtcttgat -taccacagctttatactcaaataccacaccgtcttgattaccacagctgtatactcaaat -ac--tactgtcctgattactacagctttatactcaaataccacaccgtcttgattaccac -agctgtatactcaaatactacaccgtcttgattaccacagctttatactcaaatactaca -ccgtcttgattaccacagctttatactcaaataccacactgtcttgattactatagcttt -atactcaaatactacactgtctgattactacagctttatactcaaataccacactgtctt -gattaccacagctttatactcaaatactacactgtcttgattactatagctttatactca -aatactacactgtctgattactacagctttatactcaaataccacactatcttgattact -acagctttatactcaaatactacactgtctgattactacagctttatactcaaataccac -accgtcttgattaccacagctttatactcaaatactacactgtcttgattactacagctt -tatactcaaataccacaccgtcttgattaccacagctgtatactcaaatactacaccgtc -ttgattaccacagctttatactcaaatactacaccgtcttgattaccacagctttatact -caaataacacactgtcttgattactatagctttatactcaaatactacactgtctgatta -ctacagctttatactcaaataccacactgtcttgattaccacagctttatactcaaatac -tacactgtctgattactacagctttatactcaaataccacactgtcttgattaccacagc -tttatactcaaatactacactgtcttgattaccacagctttatactcaaataccacaccg -tcttgattaccacagctgtatactcaaataccacactgtcttgattaccacagctgtata -ctcaaataccacactgtcttgattaccacagctttatactcaaataccacactgtcttga -ttactatagctttatactcaaataccacactgtcttgattaccacagctttatacgcaaa -taccacactgtcttgattactatagctttatactcaaataccacactgtcttgattacta -cagctttatactcaaataccacactgtcttgattactacagctttatactcaaatactac -actgtcttgattaacacagctttatactcaaatactacactgtcttgattaccacagctt -tatactcaaatactacactgtcttgattactatagctttatactcaaataccacactgtc -ttgattactatagctttatactcaaatactacactgtcttgattaccacagctttatact -caaatactacactgtcttgattactatagctttatactcaaataccacactgtcttgatt -accacagctttatactcaaataccacactgtcttgattaccacagctttatactcaaata -ccacactgtcttgattaccacagctttatactcaaataccacactgtcttgattactata -gctttatactcaaataccacactgtcttgattactacagctttatactcaaataccacac -tgtcttgattaacacagctttatactcaaatactacactgtcttgattaccacagcttta -tactcaaatactacactgtcttgattactatagctttatactcaaataccacactgtctt -gattactatagctttatactcaaatactacactgtcttgattaccacagctttatactca -aatactacactgtcttgattactatagctttgtactcaaataccacactgtcttgattac -cacagctttatactcaaataccacactgtcttgattaccacagctttatactcaaatacc -acactgtcttgattactatagctttatactcaaataccacactgtcttgattactacagc -tttatactcaaataccacactgtcttgattactacagctttatactcaaatactacactg -tcttgattaacacagctttatactcaaatactacactgtcttgattaccacagctttata -ctcaaatactacactgtcttgattactatagctttatactcaaataccacactgtcttga -ttactatagctttatactctgttttgaggtcaggtagtgtcagtccctc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_47dd2373cb7a299cd7298bc9bec38ccb.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_47dd2373cb7a299cd7298bc9bec38ccb.msa deleted file mode 100644 index 4fd8aa9e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_47dd2373cb7a299cd7298bc9bec38ccb.msa +++ /dev/null @@ -1,35 +0,0 @@ ->syndip_1_chr20:24681988-24682277 -aggctaaggaggtcagcatgcagcaggaggcaaactgtgaagtacctctctggcctggcc -tttgtgaattaccacagtgc---------------------------------------- ------------------------------------------------------------- -----------------ggggtccacccaggaaactgtgaagtacctctctgggcgttgtg -aattaccacagttaggggtttacccaggaaactgtgaagtatctctctggcctttgtgaa -tcaccacagttaggggtctatgcaggagtactggtcattcacagactc ->syndip_2_chr20:24681988-24682277 -aggctaaggaggtcagcatgcagcaggaggcaaactgtgaagtacctctctggcctggcc -tttgtgaattaccacagtcaggggtctacccaggaaactgtgaagtacctctctggcctt -tgtgaattaccacagtcaggggtccacccaggaaactgtgaagtacctctctggcctttg -tgaattaccacagtcaggggtccacccaggaaactgtgaagtacctctctgggcgttgtg -aattaccacagttaggggtttacccaggaaactgtgaagtatctctctggcctttgtgaa -tcaccacagttaggggtctatgcaggagtactggtcattcacagactc ->p:HG002_1_chr20:24681988-24682277 -aggctaaggaggtcagcatgcagcaggaggcaaactgtgaagtacctctctggcctggcc -tttgtgaattaccacagtcaggggtccacccaggaaactgtgaagtacctctctggcctt -tgtgaattaccacagtcaggggtccacccaggaaactgtgaagtacctctctggcctttg -tgaattaccacagtcaggggtccacccaggaaactgtgaagtacctctctgggcgttgtg -aattaccacagttaggggtttacccaggaaactgtgaagtatctctctggcctttgtgaa -tcaccacagttaggggtctatgcaggagtactggtcattcacagactc ->p:HG002_2_chr20:24681988-24682277 -aggctaaggaggtcagcatgcagcaggaggcaaactgtgaagtacctctctggcctggcc -tttgtgaattaccacagtgc---------------------------------------- ------------------------------------------------------------- -----------------ggggtccacccaggaaactgtgaagtacctctctgggcgttgtg -aattaccacagttaggggtttacccaggaaactgtgaagtatctctctggcctttgtgaa -tcaccacagttaggggtctatgcaggagtactggtcattcacagactc ->ref_chr20:24681988-24682277 -aggctaaggaggtcagcatgcagcaggaggcaaactgtgaagtacctctctggcctggcc -tttgtgaattaccacagtgc---------------------------------------- -------------------ggggtccacccaggaaactgtgaagtacctctgtggcctttg -tgaattaccacagtcaggggtccacccaggaaactgtgaagtacctctctgggcgttgtg -aattaccacagttaggggtttacccaggaaactgtgaagtatctctctggcctttgtgaa -tcaccacagttaggggtctatgcaggagtactggtcattcacagactc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_484b3ccb263a028be8e244603dc44725.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_484b3ccb263a028be8e244603dc44725.msa deleted file mode 100644 index 4b55aa27..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_484b3ccb263a028be8e244603dc44725.msa +++ /dev/null @@ -1,110 +0,0 @@ ->syndip_1_chr20:62270079-62271294 -cccaggcagagcgcgtccttgtggtgctgtgcacaccccgcccaccctccgtccaccctg -cgcatgcagtgcctgtggtgtcctgaggccttggtggggccgtcctagtccctggtgcag -acgaggagcctgagaggcttagcagctcatgtgtgtgtcagctgggaacccacagcaagt -ggattccaaagcctgccatgtccctgttgccactagcacctcctcctccactccctcctg -gcctctctgggtcctctccttgtccctcctggcctctctgggtcctctccttgtccctcc -ctgacctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtcc -ctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctc-c -tggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcc -tctctgggtcctctct---gacctctctgagtcctctccttgtc---------------- --------------cctctctgggtcctctccttgtccctctctgggtcctctccttgtcc -ctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctc -tggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcc -tctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctct -gggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctggcct -ctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctg -ggtcctctccttgtccctctctggcctctctgggtcctttccttgtccctttctggtctc -tctggtcctctccttctctccttgtccctctccctctgcctctgctttgcccaccccaga -ccctgctccttcctgaagagcctgccctgaggtgacagctgtgtttccctggaatgccta -ctgcccttgggatccctttcctggaagcccggtgggaagagtggcccctgtgggcactcg -tccccttggcaccttcccagcttcccccactaagccatgcgccc------tgccgtccag -ggcctgggagcagacacctgaga ->syndip_2_chr20:62270079-62271294 -cccaggcagagcgcgtccttgtggtgctgtgcacaccccgcccaccctccgtccaccctg -cgcatgcagtgcctgtggtgtcctgaggccttggtggggccgtcctagtccctggtgcag -acgaggagcctgagaggcttagcagctcatgtgtgtgtcagctgggaacccacagcaagt -ggattccaaagcctgccatgtccctgttgccactagcacctcctcctccactccctcctg -gcctctctgggtcctctccttgtccctcctggcctctctgggtcctctccttgtccctcc -ctgacctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtcc -ctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctctc -tggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctc------- ---------------ct---ggcctctctgggtcctctccttgtc---------------- ------------------------------------------------------------- --------------------------------cctctctgggtcctctccttgtccctctc -tgacctctctgggtcctctccttgtccctctctgggtcctctccttgtc----------- -------------------------------cctctctgggtcctctccttgtccctctct -gggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctggcct -ctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctg -ggtcctctccttgtccctctctggcctctctgggtcctttccttgtccctttctggtctc -tctggtcctctccttctctccttgtccctctccctctgcctctgctttgcccaccccaga -ccctgctccttcctgaagagcctgccctgaggtgacagctgtgtttccctggaatgccta -ctgcccttgggatccctttcctggaagcccggtgggaagagtggcccctgtgggcactcg -tccccttggcaccttcccagcttcccccactaagccatgcgccc------tgccgtccag -ggcctgggagcagacacctgaga ->p:HG002_1_chr20:62270079-62271294 -cccaggcagagcgcgtccttgtggtgctgtgcacaccccgcccaccctccgtccaccctg -cgcatgcagtgcctgtggtgtcctgaggccttggtggggccgtcctagtccctggtgcag -acgaggagcctgagaggcttagcagctcatgtgtgtgtcagctgggaacccacagcaagt -ggattccaaagcctgccatgtccctgttgccactagcacctcctcctccactccctcctg -gcctctctgggtcctctccttgtccctcctggcctctctgggtcctctccttgtccctcc -ctgacctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtcc -ctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctctc -tggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctc------- ---------------ct---ggcctctctgggtcctctccttgtc---------------- ------------------------------------------------------------- --------------------------------cctctctgggtcctctccttgtccctctc -tgacctctctgggtcctctccttgtccctctctgggtcctctccttgtc----------- -------------------------------cctctctgggtcctctccttgtccctctct -gggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctggcct -ctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctg -ggtcctctccttgtccctctctggcctctctgggtcctttccttgtccctttctggtctc -tctggtcctctccttctctccttgtccctctccctctgcctctgctttgcccaccccaga -ccctgctccttcctgaagagcctgccctgaggtgacagctgtgtttccctggaatgccta -ctgcccttgggatccctttcctggaagcccggtgggaagagtggcccctgtgggcactcg -tccccttggcaccttcccagcttcccccactaagccatgcgccctctctgtgccgtccag -ggcctgggagcagacacctgaga ->p:HG002_2_chr20:62270079-62271294 -cccaggcagagcgcgtccttgtggtgctgtgcacaccccgcccaccctccgtccaccctg -cgcatgcagtgcctgtggtgtcctgaggccttggtggggccgtcctagtccctggtgcag -acgaggagcctgagaggcttagcagctcatgtgtgtgtcagctgggaacccacagcaagt -ggattccaaagcctgccatgtccctgttgccactagcacctcctcctccactccctcctg -gcctctctgggtcctctccttgtccctcctggcctctctgggtcctctccttgtccctcc -ctgacctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtcc -ctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctc-c -tggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcc -tctctgggtcctctct---gacctctctgagtcctctccttgtc---------------- --------------cctctctgggtcctctccttgtccctctctgggtcctctccttgtcc -ctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctc -tggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcc -tctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctct -gggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctggcct -ctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctg -ggtcctctccttgtccctctctggcctctctgggtcctttccttgtccctttctggtctc -tctggtcctctccttctctccttgtccctctccctctgcctctgctttgcccaccccaga -ccctgctccttcctgaagagcctgccctgaggtgacagctgtgtttccctggaatgccta -ctgcccttgggatccctttcctggaagcccggtgagaagagtggcccctgtgggcactcg -tccccttggcaccttcccagcttcccccactaagccatgcgccctctctgtgccgtccag -ggcctgggagcagacacctgaga ->ref_chr20:62270079-62271294 -cccaggcagagcgcgtccttgtggtgctgtgcacaccccgcccaccctccgtccaccctg -cgcatgcagtgcctgtggtgtcctgaggccttggtggggccgtcctagtccctggtgcag -acgaggagcctgagaggcttagcagctcatgtgtgtgtcagctgggaacccacagcaagt -ggattccaaagcctgccatgtccctgttgccactagcacctcctcctccactccctcctg -gcctctctgggtcctctccttgtccctcctggcctctctgggtcctctccttgtccctcc -ctgacctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtcc -ctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctctc -tggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctc-ctggcc -tctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctct -gggtcctctctgacctctctgggtcctctccttgtccctctctgggtcctctccttgtcc -ctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctc -tggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcc -tctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctct -gggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctggcct -ctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctg -ggtcctctccttgtccctctctggcctctctgggtcctttccttgtccctttctggtctc -tctggtcctctccttctctccttgtccctctccctctgcctctgctttgcccaccccaga -ccctgctccttcctgaagagcctgccctgaggtgacagctgtgtttccctggaatgccta -ctgcccttgggatccctttcctggaagcccggtgggaagagtggcccctgtgggcactcg -tccccttggcaccttcccagcttcccccactaagccatgcgccc------tgccgtccag -ggcctgggagcagacacctgaga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_499b9b66e7735f3d7b3af193f2b77110.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_499b9b66e7735f3d7b3af193f2b77110.msa deleted file mode 100644 index c3fc335d..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_499b9b66e7735f3d7b3af193f2b77110.msa +++ /dev/null @@ -1,410 +0,0 @@ ->syndip_1_chr20:64131813-64133956 -tcccagacttctcctggcctctctcatgtcctatgagaccccctcactgtccaccctcat -gtcctgtagagaccccctcactgtccactctcatggcctatagagaccccctcactgtca -actctcatgtcctatg-agaccccctcactgtccactctcatggcctgtagagaccccct -cactgtccaccctcatgt------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------cctatagagaccccctcactgt -ccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctat-gagacccc -ctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcat -ggcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtcca -ccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctc -actgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctgtagag -accccctcactgtccaccctcatgtcctat------------------------------ ------------------------------------------------------------- -----------------------------------------------gagaccccctcact -gtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagacc -ccctcactgtccaccctcatgtcctatgagaccccctcactgtccactctcatgtcctat --gagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctca -tgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtc -caccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccct -cactgtccactctcatgtcctatgagaccccctcactgtccactctcatggcctgtagag -accccctcactgtccaccctcatgtcctgtagagaccccctcactgtccaccctcgtgtc -ctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccacc -ctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcact -gtccactctcatgtcctatagagaccccctcactgtccaccctcatggcctatagagacc -ccctcactgtccaccctcatggcctgtagagaccccctcactgtccactctcatggccta -tagagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctc -atggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctat-gagacccc -ctcactgtccactctcatggcctgtagagaccccctcactgtccaccctcatgtcctatg -agaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcgtg -tcctata---------------------------------gagaccccctcactgtccac -cctcatgtcctatagagaccccctcactgtccgccctcatgtcctat-gagaccccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagaga -ccccctcactgtccaccctcgtgtcctat------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------agagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccgc -cctcatgtccta------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------tgagaccccctcactgtccaccctc -atgtcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatgtcctatg------------------------------------------ --------------------------agaccccctcactgtccaccctcatgtcctatgag -accccctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctcgtgtc -ctatagagaccccctcactgtcaactctcatgtcctatagagaccccctcactgtccacc -ctcgtgtcctat-gagaccccctcactgtccaccctcatgtcctatagagaccccctcac -tgtcca----------------------------------ccctcatgtcctat-gagac -cccctcactgtccaccctcatgtcctat-gagaccccctcactgtccactctcatgtcct -atgagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtcaactctc -atgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcact-- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------gtccaccctcatgtcctatagagaccccctcactgtccaccctcat -ggcctgtagagaccccctcactgtcaactctcatgtcctat-gagaccccctcactgtcc -accctcatgtcctatagagaccccctcactgtccaccctcatgtcc-aaagagaccccct -cactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtaga -gaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgt -cc-aaagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccac -cctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctca -ctgtccaccctcatgtccaaagagaccccctcactgtccaccctcatggcctg------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------tagagaccccctcactgtccaccctcatgtcctatgagaccccc -tcactgtccactctcatgtcctatgagaccccctcactgtccaccctcatggcctgtaga -gaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcgtgtc -ctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccc -tcatgtcctatagagaccccctcactgtccactctcatgtcctatgagaccccctcactg -tccaccctcatgtcctatgagaccccctcactgtccacccatatggcctgtagagacccc -ctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgta -gagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcat -ggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcc -acccatatggcctgtagagaccccctcactgtccaccctcaggaccctctgcatttgctc -cttgggttcccg ->syndip_2_chr20:64131813-64133956 -tcccagacttctcctggcctctctcatgtcctatgagaccccctcactgtccaccctcat -gtcctgtagagaccccctcactgtccactctcatggcctatagagaccccctcactgtcc -accctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccct -cactgtccaccctcatgtcctatagagacccctcactgtccaccctcatgg--------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------cctat-gagaccccctcactgt -ccactctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagacccc -ctcactgtccaccctcatgtcctatagaga-cccctcactgtccaccctcatggcctat- -gagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcat -ggcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtcca -ccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctc -actgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctgtagag -accccctcactgtccaccctcatgtcctat------------------------------ ------------------------------------------------------------- -----------------------------------------------gagaccccctcact -gtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagacc -ccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctat -agagaccccctcactgtccactctcatgtcctatagagaccccctcactgtccaccctca -tggcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtc -cactctcatggcctatagagaccccctcactgtccaccctcatggcctata--------- ------------------------gagaccccctcactgtccaccctcatggcctgtagag -accccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggc -ctgtagagaccccctcactgtccaccctcatggcctat-gagaccccctcactgtccacc -ctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcact -gtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagacc -ccctcactgtccgccctcatgtcctat-gagaccccctcactgtccaccctcatgtccta -tagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctc -atgtcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctat-gagacccc -ctcactgtccaccctcatgtcctatgaga--cccctcactgtccaccctcatgtcctatg -agaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtccactctcatg -tcctat----------------------------------gagaccccctcactgtccac -cctcatggcctgtagagaccccctcactgtccaccctcgtgtcctatagagaccccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagaga -ccccctcactgtcaactctcatgtcctat------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccac -cctcatgtccaa------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------agagaccccctcactgtccaccctc -atggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgt -ccaccctcatggcctata------------------------------------------ -------------------------gagaccccctcactgtccaccctcatgtccaaagag -accccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggc -ctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccacc -ctcatggcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcac -tgtcca----------------------------------ccctcgtgtcctatagagac -cccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcct -atgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctc -atgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcact-- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------gtccaccctcgtgtcctatagagaccccctcactgtccaccctcat -ggcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtcc -accctcgtgtcctatagagaccccctcactgtccaccctcatggcctatagagaccccct -cactgtccaccctcat-gtccaaagagaccccctcactgtccaccctcatggcctgtaga -gaccccctcactgtccacccatatggcctgtagagaccccctcactgtccaccctcatgt -cctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccac -cctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctca -ctgtccaccctcatggcctatgagaccccctcactgtccaccctcatggcctg------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------tagagaccccctcactgtccaccctcatgtcctatagagacccc -tcactgtccaccctcatgtcctata----------------------------------- --------------------------------gagaccccctcactgtccaccctcgtgtc -ctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccc -tcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactg -tccaccctcatgtccta---------------------------------tagagacccc -ctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcgt -gtcctatagagaccccctcactgtccacccatatggcctgtagagaccccctcactgtcc -acccatatggcctgtagagaccccctcactgtccaccctcaggaccctctgcatttgctc -cttgggttcccg ->p:HG002_1_chr20:64131813-64133956 -tcccagacttctcctggcctctctcatgtcctatgagaccccctcactgtccaccctcat -gtcctgtagagaccccctcactgtccactctcatggcctatagagaccccctcactgtcc -accctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccct -cactgtccaccctcatgtcctatagagacccctcactgtccaccctcatggcctatgaga -ccccctcactgtccactctcatgtcctatagagaccccctcactgtccaccctcgtgtcc -tatagagaccccctcactgtccaccctcatgtcctatagagacccctcactgtccaccct -catggcctatgagaccccctcactgtccaccctcatggcctatagagaccccctcactgt -ccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctat-gagacccc -ctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcat -gtcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtcca -ccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctc -actgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatagag -accccctcactgtccactctcatgtcctatagagaccccctcactgtccaccctcatggc -ctatgagaccccctcactgtccactctcatggcctatagagaccccctcactgtccaccc -tcatggcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcact -gtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagacc -ccctcactgtccaccctcatggcctatgagaccccctcactgtccaccctcatgtcctat --gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcg -tgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtc -cgccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctata--------- ------------------------gagaccccctcactgtccaccctcatggcctgtagag -accccctcactgtccgccctcatgtcctat-gagaccccctcactgtccaccctcatgtc -ctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccacc -ctcatgtcctatgagaccccctcactgtccaccctcatgtcctat-gagaccccctcact -gtccaccctcatgtcctatgaga--cccctcactgtccaccctcatgtcctat-gagacc -ccctcactgtccaccctcatgtcctat-gagaccccctcactgtccactctcatgtccta -tgaga------------------------------------------------------- ----------------cccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatggcctgtagagaccccctcactgtcaactctcatgtcctat-gagacccc -ctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtccaaag -agaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatg -gcctgta---------------------------------gagaccccctcactgtccac -cctcatggcctatagagaccccctcactgtccaccctcatgtcc---------------- --------------------aaagagaccccctcactgtccaccctcatggcctgtagaga -ccccctcactgtccaccctcatggcctgt------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------agagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccac -cctcatgtccaa------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------agagaccccctcactgtccaccctc -atggcctgtagagaccccctcactgtccacccatatggcctgtagagaccccctcactgt -ccaccctcatgtcctata------------------------------------------ ------------------------------------------------------------- --------------------------------gagaccccctcactgtccaccctcatggc -ctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccacc -ctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatagagaccccctcac -tgtcca----------------------------------ccctcatgtcctatagagac -cccctcactgtccaccctcgtgtcctat-------------------------------- --agagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctc -atggcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcact-- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------gtccaccctcgtgtcctatagagaccccctcactgtccaccctcat -ggcctatagagaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtcc -accctcatgtcctatagagaccccctcactgtccaccctcatgtcc-------------- ------------------------------------------------------------- -----------------------------tatagagaccccctcactgtccaccctcatgt -cctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccac -cctcatgtcctgtagagaccccctcactgtccaccctcatggcctatagagaccccctca -ctgtccaccctcatggcctatgagaccccctcactgtccaccctcatggcctg------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------tagagaccccctcactgtccaccctcatgtcctatagagacccc -tcactgtccaccctcatgtcctata----------------------------------- --------------------------------gagaccccctcactgtccaccctcgtgtc -ctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccc -tcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactg -tccaccctcatgtccta---------------------------------tagagacccc -ctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcgt -ggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcc -acccatatggcctgtagagaccccctcactgtccaccctcaggaccctctgcatttgctc -cttgggttcccg ->p:HG002_2_chr20:64131813-64133956 -tcccagacttctcctggcctctctcatgtcctatgagaccccctcactgtccaccctcat -gtcctgtagagaccccctcactgtccactctcatggcctatagagaccccctcactgtcc -accctcatggcctgta-------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------gagacc -ccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtccta -tagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctc -atgtcctat-gagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgt -ccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagacccc -ctcactgtccaccctcatgtcctgtagagaccccctcactgtccaccctcatgtcctatg -agaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatg -tcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccac -cctcatgtcctatagagaccccctcactgtccaccctcatgtcctat-gagaccccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagaga -ccccctcactgtccaccctcatgtcctatgagaccccctcactgtccactctcatgtcct -atgagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctc -atgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgt -ccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccc -tcactgtccactctcatgtcctatgagaccccctcactgtccactctcatggcctgtaga -gaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtccaccctcgtgt -cctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccac -cctcatgtcctatgagaccccctcactgtccactctcatgtcctatagagaccccctcac -tgtccaccctcatggcctatgagaccccctcactgtccactctcatggcctatagagacc -ccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatggcctg -tagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctc -atggcctgtagagaccccctcactgtccaccctcatggcctatagagaccccctcactgt -ccaccctcatgtcctatgagaccccctcactgtccactctcatgtcctatgagaccccct -cactgtccactctcatggcctgtagagaccccctcactgtccaccctcatgtcctatgag -accccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtc -ctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccgcc -ctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatagagaccccctcac -tgtccaccctcatggcctgtagagaccccctcactgtccgccctcatgtcctatagagac -cccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcct -atgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctc -atgtcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatgagaccccct -cactgtccaccctcatgtcctatgagacccctcactgtccaccctcatgtcctatgagac -cccctcactgtccaccctcatgtcctatgagaccccctcactgtccactctcatgtccta -tgagacccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcat -ggcctgtagagaccccctcactgtcaactctcatgtcctat-gagaccccctcactgtcc -accctcatgtcctatagagaccccctcactgtccaccctcatgtcc-aaagagaccccct -cactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtaga -gaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgt -cc-aaagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccac -cctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctca -ctgtccaccctcatgtccaaagagaccccctcactgtccaccctcatggcctgtagagac -cccctcactgtccacccatatggcctgtagagaccccctcactgtccaccctcatgtcct -atagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccct -catggcctatagagaccccctcactgtccactctcatgtcctatgagaccccctcactgt -ccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctatgagaccccc -tcactgtccactctcatgtcctatgagaccccctcactgtccaccctcatggcctgtaga -gaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcgtgtc -ctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccc -tcatgtcctatagagaccccctcactgtccactctcatgtcctatgagaccccctcactg -tccaccctcatgtcctatgagaccccctcactgtccaccctcatggcctatagagacccc -ctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtccaccctcat -ggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcc -acccatatggcctgtagagaccccctcactgtccaccctcaggaccctctgcatttgctc -cttgggttcccg ->ref_chr20:64131813-64133956 -tcccagacttctcctggcctctctcatgtcctatgagaccccctcactgtccaccctcat -gtcctgtagagaccccctcactgtccactctcatggcctatagagaccccctcactgtcc -accctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccct -cactgtccaccctcatgt------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------cctatagagaccccctcactgt -ccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctat-gagacccc -ctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcat -gtcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtcca -ccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctc -actgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatagag -accccctcactgtccactctcatgtcctatagagaccccctcactgtccaccctcatggc -ctatgagaccccctcactgtccactctcatggcctatagagaccccctcactgtccaccc -tcatggcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcact -gtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagacc -ccctcactgtccaccctcatggcctatgagaccccctcactgtccaccctcatgtcctat --gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcg -tgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtc -cgccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctata--------- ------------------------gagaccccctcactgtccaccctcatggcctgtagag -accccctcactgtccgccctcatgtcctat-gagaccccctcactgtccaccctcatgtc -ctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccacc -ctcatgtcctatgagaccccctcactgtccaccctcatgtcctat-gagaccccctcact -gtccaccctcatgtcctatgaga--cccctcactgtccaccctcatgtcctat-gagacc -ccctcactgtccaccctcatgtcctat-gagaccccctcactgtccactctcatgtccta -tgaga------------------------------------------------------- ----------------cccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatggcctgtagagaccccctcactgtcaactctcatgtcctat-gagacccc -ctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtccaaag -agaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatg -gcctgta---------------------------------gagaccccctcactgtccac -cctcatggcctatagagaccccctcactgtccaccctcatgtcc---------------- --------------------aaagagaccccctcactgtccaccctcatggcctgtagaga -ccccctcactgtccaccctcatggcctgt------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------agagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccac -cctcatgtccaa------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------agagaccccctcactgtccaccctc -atggcctgtagagaccccctcactgtccacccatatggcctgtagagaccccctcactgt -ccaccctcatgtcctata------------------------------------------ ------------------------------------------------------------- --------------------------------gagaccccctcactgtccaccctcatggc -ctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccacc -ctca-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------t -ggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcc -acccatatggcctgtagagaccccctcactgtccaccctcaggaccctctgcatttgctc -cttgggttcccg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_4bc2ea84b87f661189678979f79a7384.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_4bc2ea84b87f661189678979f79a7384.msa deleted file mode 100644 index efd1537d..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_4bc2ea84b87f661189678979f79a7384.msa +++ /dev/null @@ -1,110 +0,0 @@ ->syndip_1_chr20:641836-642465 -gagcctccctctgggggtgccccccaatctggttgcctgggaggggggcccagcgggggt -ggagttgcctgggggggggggcccagcgggggtggagttgcctgggggggg-ggcccagc -gggggtggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggg-- -gcccagcgggggtggagttgcctggg-----------------------------ggggg -gaggcccagcgggggtggagttgcctgggggggggcccagcgggggtggagttgcctggg -ggggg-ggcccagcgggggtggagttgcctgggggggggaggcccagcgggggtggagtt -gcctgggggggg--gcccagcgggggtggagttgcctgggg------------------- -----------gggggaggcccagcgggggtggagttgcctgggggggg------------ --------------------ggcccagcgggggtggagttgcctggggggg---ggcccag -cgggggtggagttgcctgggggggg---cccagcgggggtggagttgcctggggggggcc -cagcgggggtggagttgcctggggggggccccagcgggggtggagttgcctggggggg-- -ggcccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagttgcctggg -gggggcccagcgggggtggagttgcctggggggggccccagcgggggtggagttgcctgg -gggggggcccagcgggggtggagttgcctggggggggggcccagcgggggtggagttgcc -tggggggggggcccagcgggggtggagttgcctgggggggggggcccagcgggggtggag -ttgcctgggggggggcccagcgggggtggagttgcctg-gggggggggcccagcgggggt -ggagttgcct-ggggggggcccagcgggggtggagttgcct-gggggggggcccagcggg -ggtggagttgcctg-gggggggggcccagcgggggtggagttgcctg-gggggggcccag -cgggggtggagttgcctgtgggggggggcccagcgggggtggagttgcctggggggggcc -cagcgggggtggagttgcctgggggggggcccagcgggggtggagcaccctggacggccc -cgcggagccccctgc ->syndip_2_chr20:641836-642465 -gagcctccctctgggggtgccccccaatctggttgcctgggacgggggcccagcgggggt -ggagttgcct-ggggggggggcccagcgggggtggagttgcctggggggggaggcccagc -gggggtggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggggt -gcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcctgtggggg -gaggcccagcgggggtggagttgcct-ggggggggcccagcgggggtggggttgcctggg -gggggaggcccagcgggggtggagttgcctgggggggggaggcccagcgggggtggagtt -gcctgggggggggtgcccagcgggggtggagttgcctgggggggggcccagcgggggtgg -agttgcc--tggggggggcccagcgggggtggggttgcctggggggggcccagcgggggt -ggggttgcctggggggggaggcccagcgggggtggagttgcctgggggggggaggcccag -cgggggtggagttgcctgggggggggtgcccagcgggggtggagttgcctggggggggcc -cagcgggggtggggttgcctgggggggg-cccagcgggggtggggttgcctgggggggga -ggcccagcaggggtggagttgcctgggggggggtgcccagcgggggtggagttgcctggg -gggggcccagcgggggtggagttgcctgggggggg-cccagcgggggtggagttgcctgg -gggggggcccagcggggatggggttgcct-gggggggggcccagcgggggtggggttgcc -t-gggggggggcccagcgggggtggagttgcct--gggggggggcccagcgggggtggag -ttgcct-ggggggggcccagcgggggtggagttgcctgtgggggggggcccagcgggggt -ggagttgcctgggggggggcccagcgggggtggagttgcctggggggggggcccagcggg -ggtggagttgcctgtggtggggggcccagcgggggtggagttgcctgtgggggggcccag -cgggggtggagttgcctgtgggggggggcccagcgggggtggagttgcctggggggggcc -cagcgggggtggagttgcct-ggggggggcccagcgggggtggagcaccctggacggccc -cgcggagccccctgc ->p:HG002_1_chr20:641836-642465 -gagcctccctctgggggtgccccccaatctggttgcctgggacgggggcccagcgggggt -ggagttgcct-ggggggggggcccagcgggggtggagttgcctggggggggaggcccagc -gggggtggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggggt -gcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcctgtggggg -gaggcccagcgggggtggagttgcct-ggggggggcccagcgggggtggggttgcctggg -gggggaggcccagcgggggtggagttgcctgggggggggaggcccagcgggggtggagtt -gcctgggggggggtgcccagcgggggtggagttgcctgggggggggcccagcgggggtgg -agttgcc--tggggggggcccagcgggggtggggttgcctggggggggcccagcgggggt -ggggttgcctggggggggaggcccagcgggggtggagttgcctgggggggggaggcccag -cgggggtggagttgcctgggggggggtgcccagcgggggtggagttgcctggggggggcc -cagcgggggtggggttgcctgggggggg-cccagcgggggtggggttgcctgggggggga -ggcccagcaggggtggagttgcctgggggggggtgcccagcgggggtggagttgcctggg -gggggcccagcgggggtggagttgcctgggggggg-cccagcgggggtggagttgcctgg -gggggggcccagcggggatggggttgcct-gggggggggcccagcgggggtggggttgcc -t-gggggggggcccagcgggggtggagttgcct--gggggggggcccagcgggggtggag -ttgcct-ggggggggcccagcgggggtggagttgcctgtgggggggggcccagcgggggt -ggagttgcctgggggggggcccagcgggggtggagttgcctggggggggggcccagcggg -ggtggagttgcctgtggtggggggcccagcgggggtggagttgcctgtgggggggcccag -cgggggtggagttgcctgtgggggggggcccagcgggggtggagttgcctggggggggcc -cagcgggggtggagttgcct-ggggggggcccagcgggggtggagcaccctggacggccc -cgcggagccccctgc ->p:HG002_2_chr20:641836-642465 -gagcctccctctgggggtgccccccaatctggttgcctgggaggggggcccagcgggggt -ggagttgcctgggggggggggcccagcgggggtggagttgcctgggggggg-ggcccagc -gggggtggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggg-- -gcccagcgggggtggagttgcctggg-----------------------------ggggg -gaggcccagcgggggtggagttgcctgggggggggcccagcgggggtggagttgcctggg -ggggg-ggcccagcgggggtggagttgcctgggggggggaggcccagcgggggtggagtt -gcctgggggggg--gcccagcgggggtggagttgcctgggg------------------- -----------gggggaggcccagcgggggtggagttgcctgggggggg------------ --------------------ggcccagcgggggtggagttgcctggggggg---ggcccag -cgggggtggagttgcctgggggggg---cccagcgggggtggagttgcctggggggggcc -cagcgggggtggagttgcctggggggggccccagcgggggtggagttgcctggggggg-- -ggcccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagttgcctggg -gggggcccagcgggggtggagttgcctggggggggccccagcgggggtggagttgcctgg -gggggggcccagcgggggtggagttgcctggggggggggcccagcgggggtggagttgcc -tggggggggggcccagcgggggtggagttgcctgggggggggggcccagcgggggtggag -ttgcctgggggggggcccagcgggggtggagttgcctg-gggggggggcccagcgggggt -ggagttgcct-ggggggggcccagcgggggtggagttgcct-gggggggggcccagcggg -ggtggagttgcctg-gggggggggcccagcgggggtggagttgcctg-gggggggcccag -cgggggtggagttgcctgtgggggggggcccagcgggggtggagttgcctggggggggcc -cagcgggggtggagttgcctgggggggggcccagcgggggtggagcaccctggacggccc -cgcggagccccctgc ->ref_chr20:641836-642465 -gagcctccctctgggggtgccccccaatctggttgcctgggacgggggcccagcgggggt -ggagttgcct-ggggggggggcccagcgggggtggagttgcctggggggggaggcccagc -gggggtggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggggt -gcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcctgtggggg -gaggcccagcgggggtggagttgcct-ggggggggcccagcgggggtggggttgcctggg -gggggaggcccagcgggggtggagttgcctgggggggggaggcccagcgggggtggagtt -gcctgggggggggtgcccagcgggggtggagttgcct-ggggggggcccagcgggggtgg -agttgcctgtggtggggggccagcgggggtgaagttgcctgggggggg-ccagcgggggt -ggagttgcctggggggggg---ccagcgggggtggagttgcctgtggggggggg--ccag -cgggggtggagttgcctgggggggg----ccagcgggggtggagttgcctgggggggg-c -cagcgggggtggagcaccctggacggcc-cc----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --gcggagccccctgc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_4c58cd890a178b3db2bef2c0c3e3b462.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_4c58cd890a178b3db2bef2c0c3e3b462.msa deleted file mode 100644 index 7d816edb..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_4c58cd890a178b3db2bef2c0c3e3b462.msa +++ /dev/null @@ -1,65 +0,0 @@ ->syndip_1_chr20:23155504-23155975 -ctgcagaagtaaattttgccctgcagcacaaaagaggaaggaaagcaagggaagggaagg -ggaggggaggaagggaaggggaggggaggaagggaaggggaggggaggaaggcgaggtga -ggggaggagaggtgaggggagggggggaggggaggggagggagagtgaggaagagagaga -gaaagggagagaggaaggaaagaagaaaggaaggaaggaaagaaggaaggaagggaggga -gggagggaggaaagaaggaaggaaaggagggaggaagggagggaaagagagagagaggaa -aagagagagaaagagaaagagagaaagagaggaaggaaggaaggaaggagagagagaaag -aaagaaggaaagaggaaggaaggaagaaagaaaagaaagaaagaaaaaagaaagaaagga -aggagagaaagaaatgaaagagaaagaaagaaagaaagaaagaaagaaagaaaggagaga -aaaaggaaaaacaaagaaagagaaaagaaggagagaaggaaaggaaaaagaaagaaagaa -ggaaagaaagaaaaaagaaggaaagaaagaagaaagaaagaaagaaagaaagaaagaaag -aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaaaagaaagag -aaaggaaggaaggaaggaaggtcttaacaccttggtaatttttgtgctctt ->syndip_2_chr20:23155504-23155975 -ctgcagaagtaaattttgccctgcagcacaaaagaggaaggaaagcaag----------- ---------ggaagggaaggggaggggaggaagggaaggggaggggaggaaggcgaggtga -ggggaggagaggtgaggggagggggggaggggaggggagggagagtgaggaagagagaga -gaaagggagagaggaaggaaagaagaaaggaaggaaggaaagaaggaaggaagggaggga -gggagggaggaaagaaggaaggaaaggagggaggaagggagggaaagagagagagaggaa -aagagagagaaagagaaagagagaaagagaggaaggaaggaaggaaggagagagagaaag -aaagaaggaaagaggaaggaaggaagaaagaaaagaaagaaagaaaaaagaaagaaagga -aggagagaaagaaatgaaag----agaaagaaagaaagaaagaaagaaagaaaggagaga -aaaaggaaaaacaaagaaagagaaaagaaggagagaaggaaaggaaaaagaaagaaagaa -ggaaagaaagaaaaaagaaggaaagaaag------------------------aagaaag -aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaaaagaaagag -aaaggaaggaaggaaggaaggtcttaacaccttggtaatttttgtgctctt ->p:HG002_1_chr20:23155504-23155975 -ctgcagaagtaaattttgccctgcagcacaaaagaggaaggaaagcaag----------- ---------ggaagggaaggggaggggaggaagggaaggggaggggaggaaggcgaggtga -ggggaggagaggtgaggggagggggggaggggaggggagggagagtgaggaagagagaga -gaaagggagagaggaaggaaagaagaaaggaaggaaggaaagaaggaaggaagggaggga -gggagggaggaaagaaggaaggaaaggagggaggaagggagggaaagagagagagaggaa -aagagagagaaagagaaagagagaaagagaggaaggaaggaaggaaggagagagagaaag -aaagaaggaaagaggaaggaaggaagaaagaaaagaaagaaagaaaaaagaaagaaagga -aggagagaaagaaatgaaag----agaaagaaagaaagaaagaaagaaagaaaggagaga -aaaaggaaaaacaaagaaagagaaaagaaggagagaaggaaaggaaaaagaaagaaagaa -ggaaagaaagaaaaaagaaggaaagaaag------------------------aagaaag -aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaaaagaaagag -aaaggaaggaaggaaggaaggtcttaacaccttggtaatttttgtgctctt ->p:HG002_2_chr20:23155504-23155975 -ctgcagaagtaaattttgccctgcagcacaaaagaggaaggaaagcaagggaagggaagg -ggaggggaggaagggaaggggaggggaggaagggaaggggaggggaggaaggcgaggtga -ggggaggagaggtgaggggagggggggaggggaggggagggagagtgaggaagagagaga -gaaagggagagaggaaggaaagaagaaaggaaggaaggaaagaaggaaggaagggaggga -gggagggaggaaagaaggaaggaaaggagggaggaagggagggaaagagagagagaggaa -aagagagagaaagagaaagagagaaagagaggaaggaaggaaggaaggagagagagaaag -aaagaaggaaagaggaaggaaggaagaaagaaaagaaagaaagaaaaaagaaagaaagga -aggagagaaagaaatgaaagagaaagaaagaaagaaagaaagaaagaaagaaaggagaga -aaaaggaaaaacaaagaaagagaaaagaaggagagaaggaaaggaaaaagaaagaaagaa -ggaaagaaagaaaaaagaaggaaagaaagaagaaagaaagaaagaaagaaagaaagaaag -aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaaaagaaagag -aaaggaaggaaggaaggaaggtcttaacaccttggtaatttttgtgctctt ->ref_chr20:23155504-23155975 -ctgcagaagtaaattttgccctgcagcac------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------aaaagaggaaggaaagcaagggaagggaaggggagggga--ggaagggaaggaa -aagagagagaaagagaaagagagaaagagaggaaggaaggaaggaaggagagagagaaag -aaagaaggaaagaggaaggaaggaagaaagaaaagaaagaaagaaaaaagaaagaaagga -aggagagaaagaaatgaaag--------agaaagaaagaaagaaagaaagaaaggagaga -aaaaggaaaaacaaagaaagagaaaagaaggagagaaggaaaggaaaaagaaagaaagaa -ggaaagaaagaaaaaagaaggaaagaaag------------aagaaagaaagaaagaaag -aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaaaagaaagag -aaaggaaggaaggaaggaaggtcttaacaccttggtaatttttgtgctctt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_4cdf28703764613af970b6a20a9d76f8.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_4cdf28703764613af970b6a20a9d76f8.msa deleted file mode 100644 index 7d784ca0..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_4cdf28703764613af970b6a20a9d76f8.msa +++ /dev/null @@ -1,135 +0,0 @@ ->syndip_1_chr20:61201722-61202342 -caggaccctctgcggatgtcgcctccatcctcatcaggaccctccatggtgtcacctcca -tcctcactcaggacactccatggtgtcacctccatccttactcaggaccctccatggtgt -caccgccatcctcactcaggaccctccatgagtgccacctccatcctcactcaggatccc -ctgtaagtgtcacctccatcctcaccaggaccctccatg-gtgtcaccgccatcctcact -caggaccctccatgagtgccacctccatcctcaccaggatcccctgtaagtgtcacctcc -atcctcac-caggaccctccatgagtgtcacctccatc----ctcaggaccctccatgag -tgtcacctccatcctcactcaggaccctccat-ggtgtcaccgccatcctcactcaggac -cctccatg-gtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctc -actcaggaccctccatggtgtcacctccatcctca------------------------- ----ccaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcac -ctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctcca -t-ggtgtcaccgccatcctca-------------------------------ctcaggac -cctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctc -actcaggaccctccatggtgtcacctccatcctcaccaggatcccctgtaagtgtcacct -ccatcctcaccaggaccctccatgagtgtcacctccatcctcactcaggaccctccatgg -tgtcacctccatcctcactcaggaccctccata-gtgccacctccatcctcac-caggat -cccctgtaagtgtcacctccatcctcac-caggaccctccatgagtgtcacctccatcct -cactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgtcacc -tccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatg -ggtgtcacctccatcctcac-tcaggaccctccatggtgtcacctccatcctcac-cagg -accctccatgagtgtcacctccatc----ctcaggaccctccatg--------------- -----------------------------------------------------agtgtcac -ctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccat -g-gtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcag -gaccctccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcc -tcactcaggaccctcca ->syndip_2_chr20:61201722-61202342 -caggaccctctgcggatgtcgcctccatcctcatcaggaccctccatggtgtcacctcca -tcctcactcaggacactccatggtgtcacctccatccttactcaggaccctccatggtgt -caccgccatcctcactcaggaccctccatgagtgccacctccatcctcac-caggatccc -ctgtaagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcctcact -caggaccctccatg-gtgtcacctccatcctcactcaggaccctccatggtgtcacctcc -atcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgag -tgtcacctccatcctcactcaggaccctccat-ggtgtcaccgccatcctcactcaggac -cctccatgagtgccacctccatcctcaccaggatcccctgtaagtgtcacctccatcctc -accaggaccctccatgagtgtcacctccatcctcaggaccctccatgagtgtcacctcca -tcctcaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcac -ctccatcctcactcaggaccctccat-ggtgtcacctccatcctcactcaggaccctcca -tgggtgtcacctccatcctcactcaggaccctccatgagtgtcacctccatcctcaggac -cctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctc -actcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgtcacct -ccatcctcactcaggacactccatggtgtcacctccatccttactcaggaccctccatgg -tgtcaccgccatcctcactcaggaccctccatgagtgccacctccatcctcac-caggat -cccctgtaagtgtcacctccatcctcactcaggaccctccatgagtgtcacctccatcct -ca----ggaccctccatggtgtcacctccatcctca---ggaccctccatgagtgtcacc -tccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatg -ggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcagg -accctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcc -tcactcaggaccctccatggtgtcacctccatcctcactcaggacactccatggtgtcac -ctccatccttactcaggaccctccatggtgtcaccgccatcctcactcaggaccctccat -gagtgccacctccatcctcac-caggatcccctgtaagtgtcacctccatcctcactcag -gaccctccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcc -tcactcaggaccctcca ->p:HG002_1_chr20:61201722-61202342 -caggaccctctgcggatgtcgcctccatcctcatcaggaccctccatggtgtcacctcca -tcctcactcaggacactccatggtgtcacctccatccttactcaggaccctccatggtgt -caccgccatcctcactcaggaccctccatgagtgccacctccatcctcac-caggatccc -ctgtaagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcctcact -caggaccctccatg-gtgtcacctccatcctcactcaggaccctccatggtgtcacctcc -atcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatggg -tgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcaggac -cctccatgggtgccacctccatcctcaccaggatcccctgtaagtgtcacctccatcctc -accaggaccctccatgagtgtcacctccatcctcaggaccctccatgagtgtcacctcca -tcctcaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcac -ctccatcctcactcaggaccctccat-ggtgtcacctccatcctcactcaggaccctcca -tgggtgtcacctccatcctcactcaggaccctccatgagtgtcacctccatcctcaggac -cctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctc -actcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgtcacct -ccatcctcactcggaccctccatgagtgtcacctccatcctcactcaggaccctccatgg -tgtcaccgccatcctcactcaggaccctccatgagtgccacctccatcctcac-caggat -cccctgtaagtgtcacctccatcctcac-caggaccctccatgagtgtcacctccatcct -ca----ggaccctccatggtgtcacctccatcctca---ggaccctccatgagtgtcacc -tccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatg -ggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcagg -accctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcc -tcactcaggaccctccatggtgtcacctccatcctcactcaggacactccatagtgtcac -ctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccat -g-gtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcag -gaccctccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcc -tcactcaggaccctcca ->p:HG002_2_chr20:61201722-61202342 -caggaccctctgcggatgtcgcctccatcctcatcaggaccctccatggtgtcacctcca -tcctcactcaggacactccatggtgtcacctccatccttactcaggaccctccatggtgt -caccgccatcctcactcaggaccctccatgagtgccacctccatcctcac-caggatccc -ctgtaagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcctcact -caggaccctccatgagtgccacctccatcctcaccaggatcccctgtaagtgtcacctcc -atcctcac-caggaccctccatgagtgtcacctccatc----ctcaggaccctccatgag -tgtcacctccatcctcactcaggaccctccat-ggtgtcacctccatcctcactcaggac -cctccatg-gtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctc -actcaggaccctccatggtgtcacctccatcctca------------------------- ----ccaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcac -ctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctcca -t-ggtgtcaccgccatcctca-------------------------------ctcaggac -cctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctc -actcaggaccctccatggtgtcacctccatcctcaccaggatcccctgtaagtgtcacct -ccatcctcaccaggaccctccatgagtgtcacctccatcctcactcaggaccctccatgg -tgtcacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcac-caggat -cccctgtaagtgtcacctccatcctcac-caggaccctccatgagtgtcacctccatcct -cactcaggaccctccatggtgtcacctccatcctcactcggaccctccatgagtgtcacc -tccatcctcactcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatg -agtgccacctccatcctcac-caggatcccctgtaagtgtcacctccatcctcac-cagg -accctccatgagtgtcacctccatc----ctcaggaccctccatg--------------- -----------------------------------------------------agtgtcac -ctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccat -g-gtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcag -gaccctccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcc -tcactcaggaccctcca ->ref_chr20:61201722-61202342 -caggaccctctgcggatgtcgcctccatcctcatcaggaccctccatg------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------gtgtcacctccatcctcactcaggacactccatgg -tgtcacctccatccttactcaggaccctccatg-gtgtcaccgccatcctcactcaggac -cctccatgagtgccacctccatcctcac-caggatcccctgtaagtgtcacctccatcct -caccaggaccctccatgagtgtcacctccatcctca---ggaccctccatgagtgtcacc -tccatcctcactcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatg -agtgccacctccatcctcac-caggatcccctgtaagtgtcacctccatcctcac-cagg -accctccatgagtgtcacctccatc----ctcaggaccctccatg--------------- -----------------------------------------------------agtgtcac -ctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccat -g-gtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcag -gaccctccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcc -tcactcaggaccctcca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_4db311fc47aae6446b8b9b636f4647d0.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_4db311fc47aae6446b8b9b636f4647d0.msa deleted file mode 100644 index 7a0491d2..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_4db311fc47aae6446b8b9b636f4647d0.msa +++ /dev/null @@ -1,180 +0,0 @@ ->syndip_1_chr20:61100792-61102687 -tatttaaaacaaaaccccactgacaagtcctgtgactggagagaccccgagtgaaggcag -acctccatgtcctctacatcctgtgccacatctggagagacccctgtgagggcagagagc -tacctcctcttcttcctgtgtcacacctggagagaccccgagtgagggcggatggccacg -tcttctacttcctgtgtcacacctggagagaccccgagtgagggcagatggccacatcct -ctacttcctgtgtcacacctggggagaccctgagtgagggcagacagccatgtcctctac -gtcctgtgccacatccggagagaccccaagagagggcagacagccacctcctctacttcc -tgtgtcacacctggagagaccccgagtgagggcggatggccacgtcttctacttcctgtg -tcacacctggagagaccccgagtgagggcagatggccacatcctctacttcctgtgtcac -acct-------------------------------------------------------- ---------------------------------------------------------gggg -agaccctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccggagagac -cccaagagagggcagacagccacctcctctacttcctgtgtcacacctggagagactcca -agtgaggagagacggccacgtcttctacttcctgtgtcacacctggagagaccccgagtg -agggtggatggccacatcctctaattcctgtgtcatacctggagagaccccgagtgaggg -cagatggccacctcctctacttcctgtgtcacacctggagagaccccgagtgagggcaga -ctgccacctcctctacttcctgtgtcacacctagagagaccccgagtgaggacagccagc -catgtcctctacttcctgtgccacatccggagagatcccgagtgagggcagacagccatg -tcctctacttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcct -ctaattcctgtgtcacacctggagagaccccgagtgagggcagacggccacctcctctac -ttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattcc -tgtgtcatgcctggagagaccccgagtgagggcagatggccacatcctctaattcctatg -tcacacctggagagaccccgagtgagggtggatggccacatcctctaattcctgtgtcat -acctggagagaccccgagtgagggcagatggccacctcctctacttcctgtgtcacacct -ggagagaccccgagtgagggcagatggccacctcctctacttcctgtgtcacacctggag -agaccccaagtgagggcagacagccatgtcctctacgtcctgtgccacatccggagagac -cccga-tgagggcagacagctaccccctctacttcctgtgtcacacctgcagagacccca -agtgagggcagatggccacctcttctacttcctgtgtcacacctggagaggccccgagtg -agggcagacggccacctcctctacttcctgtgtcacacctggagagaccccgagtgaggg -cagacggccacatcctctatttcctgtgtcacacctggagagaccccgagtgagggcaga -cggccacatcctctaattcctgtgtcacacatggagagaccccgagtgagggcagaaggc -cacatcctctacttcctgtgtcacacctagagagaccccgagtgagggcggatggccaca -tcctctaattcctgtgtcacacctggggagaccccgagtgagggcagatggccacatcct -ctaattcctgtgtcacacctggagacacacagagtaaaggtggacagccacctcctctac -gtcctgtgccacacctggagacaccctgagttaaggcagatggccacctcctctaattat -ttttaagaacttttttggggtataa ->syndip_2_chr20:61100792-61102687 -tatttaaaacaaaaccccactgacaagtcctgtgactggagagaccccgagtgaaggcag -acctccatgtcctctacatcctgtgccacatctggagagacccctgtgagggcagagagc -tacctcctcttcttcctgtgtcacacctggagagaccccgagtgagggcggatggccacg -tcttctacttcctgtgtcacacctggagagaccccgagtgagggcagatggccacatcct -ctacttcctgtgtcacacctggggagaccctgagtgagggcagacagccatgtcctctac -gtcctgtgccacatccggagagaccccaagagagggcagacagccacctcctctacttcc -tgtgtcacacctggagagactccaagtgaggagagacggccacgtcttctacttcctgtg -tcacacctggagagacctcgagtgagggcagatggccacatcctctaattcctgtgtcac -acctggagaaaccccaagtgagggcagactgccacctcctctacttcctgtgtcacacct -agagagaccccgagtgaggacagccagccatgtcctctacttcctgtgccacatccggag -agatcccgagtgagggcagacagccatgtcctctacttcctgtgtcacacctggagagac -cccgagtgagggcagacagccacatcctctaattcctgtgtcacacctggagagaccccg -agtgagggcagacggctacatcctctaattcctgtgtcatgcctggagagaccccgagtg -agggcagatggccacatcctctaattcctatgtcacacctggagagaccccgagtgaggg -tggatggccacatcctctaattcctgtgtcatacctggagagaccccgagtgagggcaga -tggccacctcctctacttcctgtgtcacacctggagagaccccaagtgagggcagacagc -catgtcctctacgtcctgtgccacatccggagagaccccga-tgagggcagacagctacc -ccctctacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccacctctt -ctacttcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcctctac -ttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctatttcc -tgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattcctgtg -tcacacatggagagaccccgagtgaaggcagaaggccacatcctctacttcctgtgtcac -acctagagagaccccgagtgagggcggatggccacatcctctaattcctatgtcacacct -ggagagaccccgagtgagggtggatggccacatcctctaattcctgtgtcatacctggag -agaccccgagtgagggcagatggccacctcctctacttcctgtgtcacacctggagagac -cccaagtgagggcagacagccatgtcctctacgtcctgtgccacatccggagagaccccg -a-tgagggcagacagctaccccctctacttcctgtgtcacacctgcagagaccccaagtg -agggcagatggccacctcttctacttcctgtgtcacacctggagaggccccgagtgaggg -cagacggccacctcctctacttcctgtgtcacacctggagagaccccgagtgagggcaga -cggccacatcctctaattcctgtgtcacacatggagagaccctgagtgagggcagaaggc -cacatcctctacttcctgtgtcacacctagagagaccccgagtgagggcggatggccaca -tcctctaattcctgtgtcacacctggggagaccccgagtgagggcagacggccacatcct -ctaattcctgtgtcacacctggagacacacagagtaaaggtggacagccacctcctctac -gtcctgtgccacacctggagacaccctgagttaaggcagatggccacctcctctaattat -ttttaagaacttttttggggtataa ->p:HG002_1_chr20:61100792-61102687 -tatttaaaacaaaaccccactgacaagtcctgtgactggagagaccccgagtgaaggcag -acctccatgtcctctacatcctgtgccacatctggagagacccctgtgagggcagagagc -tacctcctcttcttcctgtgtcacacctggagagaccccgagtgagggcggatggccacg -tcttctacttcctgtgtcacacctggagagaccccgagtgagggcagatggccacatcct -ctacttcctgtgtcacacctggggagaccctgagtgagggcagacagccatgtcctctac -gtcctgtgccacatccggagagaccccaagagagggcagacagccacctcctctacttcc -tgtgtcacacctggagagactccaagtgaggagagacggccacgtcttctacttcctgtg -tcacacctggagagacctcgagtgagggcagatggccacatcctctaattcctgtgtcac -acctggagaaaccccaagtgagggcagactgccacctcctctacttcctgtgtcacacct -agagagaccccgagtgaggacagccagccatgtcctctacttcctgtgccacatccggag -agatcccgagtgagggcagacagccatgtcctctacttcctgtgtcacacctggagagac -cccgagtgagggcagacagccacatcctctaattcctgtgtcacacctggagagaccccg -agtgagggcagacggctacatcctctaattcctgtgtcatgcctggagagaccccgagtg -agggcagatggccacatcctctaattcctatgtcacacctggagagaccccgagtgaggg -tggatggccacatcctctaattcctgtgtcatacctggagagaccccgagtgagggcaga -tggccacctcctctacttcctgtgtcacacctggagagaccccaagtgagggcagacagc -catgtcctctacgtcctgtgccacatccggagagaccccga-tgagggcagacagctacc -ccctctacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccacctctt -ctacttcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcctctac -ttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctatttcc -tgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattcctgtg -tcacacatggagagaccccgagtgaaggcagaaggccacatcctctacttcctgtgtcac -acctagagagaccccgagtgagggcggatggccacatcctctaattcctatgtcacacct -ggagagaccccgagtgagggtggatggccacatcctctaattcctgtgtcatacctggag -agaccccgagtgagggcagatggccacctcctctacttcctgtgtcacacctggagagac -cccaagtgagggcagacagccatgtcctctacgtcctgtgccacatccggagagaccccg -a-tgagggcagacagctaccccctctacttcctgtgtcacacctgcagagaccccaagtg -agggcagatggccacctcttctacttcctgtgtcacacctggagaggccccgagtgaggg -cagacggccacctcctctacttcctgtgtcacacctggagagaccccgagtgagggcaga -cggccacatcctctaattcctgtgtcacacatggagagaccctgagtgagggcagaaggc -cacatcctctacttcctgtgtcacacctagagagaccccgagtgagggcggatggccaca -tcctctaattcctgtgtcacacctggggagaccccgagtgagggcagacggccacatcct -ctaattcctgtgtcacacctggagacacacagagtaaaggtggacagccacctcctctac -gtcctgtgccacacctggagacaccctgagttaaggcagatggccacctcctctaattat -ttttaagaacttttttggggtataa ->p:HG002_2_chr20:61100792-61102687 -tatttaaaacaaaaccccactgacaagtcctgtgactggagagaccccgagtgaaggcag -acctccatgtcctctacatcctgtgccacatctggagagacccctgtgagggcagagagc -tacctcctcttcttcctgtgtcacacctggagagaccccgagtgagggcggatggccacg -tcttctacttcctgtgtcacacctggagagaccccgagtgagggcagatggccacatcct -ctacttcctgtgtcacacctggggagaccctgagtgagggcagacagccatgtcctctac -gtcctgtgccacatccggagagaccccaagagagggcagacagccacctcctctacttcc -tgtgtcacacctggagagaccccgagtgagggcggatggccacgtcttctacttcctgtg -tcacacctggagagaccccgagtgagggcagatggccacatcctctacttcctgtgtcac -acct-------------------------------------------------------- ---------------------------------------------------------gggg -agaccctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccggagagac -cccaagagagggcagacagccacctcctctacttcctgtgtcacacctggagagactcca -agtgaggagagacggccacgtcttctacttcctgtgtcacacctggagagaccccgagtg -agggtggatggccacatcctctaattcctgtgtcatacctggagagaccccgagtgaggg -cagatggccacctcctctacttcctgtgtcacacctggagagaccccgagtgagggcaga -ctgccacctcctctacttcctgtgtcacacctagagagaccccgagtgaggacagccagc -catgtcctctacttcctgtgccacatccggagagatcccgagtgagggcagacagccatg -tcctctacttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcct -ctaattcctgtgtcacacctggagagaccccgagtgagggcagacggccacctcctctac -ttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattcc -tgtgtcatgcctggagagaccccgagtgagggcagatggccacatcctctaattcctatg -tcacacctggagagaccccgagtgagggtggatggccacatcctctaattcctgtgtcat -acctggagagaccccgagtgagggcagatggccacctcctctacttcctgtgtcacacct -ggagagaccccgagtgagggcagatggccacctcctctacttcctgtgtcacacctggag -agaccccaagtgagggcagacagccatgtcctctacgtcctgtgccacatccggagagac -cccga-tgagggcagacagctaccccctctacttcctgtgtcacacctgcagagacccca -agtgagggcagatggccacctcttctacttcctgtgtcacacctggagaggccccgagtg -agggcagacggccacctcctctacttcctgtgtcacacctggagagaccccgagtgaggg -cagacggccacatcctctatttcctgtgtcacacctggagagaccccgagtgagggcaga -cggccacatcctctaattcctgtgtcacacatggagagaccccgagtgagggcagaaggc -cacatcctctacttcctgtgtcacacctagagagaccccgagtgagggcggatggccaca -tcctctaattcctgtgtcacacctggggagaccccgagtgagggcagatggccacatcct -ctaattcctgtgtcacacctggagacacacagagtaaaggtggacagccacctcctctac -gtcctgtgccacacctggagacaccctgagttaaggcagatggccacctcctctaattat -ttttaagaacttttttggggtataa ->ref_chr20:61100792-61102687 -tatttaaaacaaaaccccactgacaagtcctgtgactggagagaccccgagtgaaggcag -acctccatgtcctctacatcctgtgccacatctggagagacccctgtgagggcagagagc -tacctcctcttcttcctgtgtcacacctggagagaccccgagtgagggcggatggccacg -tcttctacttcctgtgtcacacctggagagaccccgagtgagggcagatggccacatcct -ctacttcctgtgtcacacctggggagaccctgagtgagggcagacagccatgtcctctac -gtcctgtgccacatccggagagaccccaagagagggcagacagccacctcctctacttcc -tgtgtcacacctggagagaccccgagtgagggcggatggccacgtcttctacttcctgtg -tcacacctggagagaccccgagtgagggcagatggccacatcctctacttcctgtgtcac -acct-------------------------------------------------------- ---------------------------------------------------------gggg -agaccctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccggagagac -cccaagagagggcagacagccacctcctctacttcctgtgtcacacctggagagactcca -agtgaggagagacggccacatcttctacttcctgtgtcacacctggagagacctcgagtg -agggcagatggccacatcctctaa------------------------------------ ---------------------ttcctgtgtcacacctggagagaccccaagtgagggcaga -ctgccacctcctctacttcctgtgtcacacctagagagaccccgagtgaggacagccagc -catgtcctctacttcctgtgccacatccggagagatcccgagtgagggcagacagccatg -tcctctacttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcct -ctaattcctgtgtcacacctggagagaccccgagtgagggcagacggccacctcctctac -ttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattcc -tgtgtcatgcctggagagaccccgagtgagggcatatggccacatcctctaattcctatg -tcacacctggagagaccccgagtgagggtggatggccacatcctctaattcctgtgtcat -acctggagagaccccgagtgagggcagatggccacctcctctacttcctgtgtcacacct -ggagagaccccgagtgagggcagatggccacctcctctacttcctgtgtcacacctggag -agaccccaagtgagggcagacagccatgtcctctacgtcctgtgccacatccggagagac -cccga-tgagggcagacagctaccccctctacttcctgtgtcacacctgcagagacccca -agtgagggcagatggccacctcttctacttcctgtgtcacacctggagaggccccgagtg -agggcagacggccacctcctctacttcctgtgtcacacctggagagaccccgagtgaggg -cagacggccacatcctctatttcctgtgtcacacctggagagaccccgagtgagggcaga -cggccacatcctctaattcctgtgtcacacatggagagaccccgagtgagggcagaaggc -cacatcctctacttcctgtgtcacacctagagagaccccgagtgagggcggatggccaca -tcctctaattcctgtgtcacacctggggagaccccgagtgagggcagatggccacatcct -ctaattcctgtgtcacacctggagacacacagagtaaaggtggacagccacctcctctac -gtcctgtgccacacctggagacaccctgagttaaggcagatggccacctcctctaattat -ttttaagaacttttttggggtataa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_4dd440cbf3dc72b6795a77d7b5cfee58.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_4dd440cbf3dc72b6795a77d7b5cfee58.msa deleted file mode 100644 index 595da9c7..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_4dd440cbf3dc72b6795a77d7b5cfee58.msa +++ /dev/null @@ -1,35 +0,0 @@ ->syndip_1_chr20:57350808-57350987 -atgcccggctaatttttgtatttttagtactgacggggggacggggggacgggggacggg -ggacggggggcgggggggacgggggacggggggcggggggggcgggggggacggggggcg -gggggggcgggggccggggggggcggggggacgggggcggggggccggggggggcggggg -gacggggg-cgggggggcggggggggcggggggacgggggcggggggcgcgggggggcgg -ggggggcggcgcgggggggcgggggggggcggggggcggggcggttcacgatgttggcca -gacttg ->syndip_2_chr20:57350808-57350987 -atgcccggctaatttttgtatttttagtactgacgg------------------------ ------------------------------------------------------------- ---------------------------------ggggacgggggggcgggggggcgggggg -gcgggggg-acggggggcggggggggcggggggacgggggcggggggcg---------gg -ggggggcggcgcgggggggc-ggggggggcggggggcggggcggttcacgatgttggcca -gacttg ->p:HG002_1_chr20:57350808-57350987 -atgcccggctaatttttgtatttttagtactgacgg------------------------ ------------------------------------------------------------- ---------------------------------ggggacgggggggcgggggggcgggggg -gcgggggg-acggggggcggggggggcggggggacgggggcggggggcg---------gg -ggggggcggcgcgggggggc-ggggggggcggggggcggggcggttcacgatgttggcca -gacttg ->p:HG002_2_chr20:57350808-57350987 -atgcccggctaatttttgtatttttagtactgacggggggacggggggacgggggacggg -ggacggggggcgggggggacgggggacggggggcggggggggcgggggggacggggggcg -gggggggcgggggccggggggggcggggggacgggggcggggggccggggggggcggggg -gacggggg-cgggggggcggggggggcggggggacgggggcggggggcgcgggggggcgg -ggggggcggcgcgggggggcgggggggggcggggggcggggcggttcacgatgttggcca -gacttg ->ref_chr20:57350808-57350987 -atgcccggctaatttttgtatttttagtactgacgg------------------------ ------------------------------------------------------------- ---------------------------------ggggacgggggggcgggggggcgggggg -acggggggcggggggggcggggggggcggggggacgggggcggggggcg---------gg -ggggggcggcgcgggggggc-ggggggggcggggggcggggcggttcacgatgttggcca -gacttg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_517866b874e6b14b3aa8ccf0cf071b60.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_517866b874e6b14b3aa8ccf0cf071b60.msa deleted file mode 100644 index 34f51471..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_517866b874e6b14b3aa8ccf0cf071b60.msa +++ /dev/null @@ -1,115 +0,0 @@ ->syndip_1_chr20:278700-279386 -gaaccccctctgggacgggtgctatggtgccgcatttcacagagctcggggaggcaaagt -taactaaaagtctcccggccagtgagtgctggcgcgctgggatgaaacccatctcggtcc -tcttgcaaagcccaggtgaggggagtgaagggtgaagaaatgcgtcttccaggtggagga -agcaccacgtgcagtgggcggggaaaggcaggagagggcgcgcgagtgcgcggagggagg -gcgggacggagggagggagggcgggagggagggacggag------------ggaggaagg -gcgggacggagggagggagggcgggagggacggagggcgggacggcgggagggcgggacg -gagggacggagggagggcgggacggagggcgggagggcgggacggagggagggagggagg -gagggc------------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------gggacggagggagggagggagggagggacggagggcgggacggagg -gagggagggcggagggagggagggcgggacggagggagggagggcgggacggagggtggg -agggagggag-------------------------------------------------- ----------------------ggatggagggagggagggagggacggagggcgggacgga -gggacggagggagggagggagggacggaggttgggacggagggacggagggcgggcggat -gccgcgggtctcaccgccaaggtgtcctgctgctgcagcagggcccgcacgtgcagggtc -gtgctgttctccatctcctggatggtctcgatcagctcccggttgagcttgctgaggaag -ttctcacggcttcggagctctcgcagagcggccctcccgctcctgagcgaggtctgcggg -cggagggaagagcagagaggcggcgctgcgccctgcccggcctgagccc ->syndip_2_chr20:278700-279386 -gaaccccctctgggacgggtgctatggtgccgcatttcacagagctcggggaggcaaagt -taactaaaagtctcccggccagtgagtgctggcgcgctgggatgaaacccatctcggtcc -tcttgcaaagcccaggtgaggggagtgaagggtgaagaaatgcgtcttccaggtggagga -agcaccacgtgcagtgggcggggaaaggcaggagagggcgcgcgagtgcgcggagggagg -gcgggacggagggagggagggcgggacggagggagggagggagggcgggacggagggagg -gagggcgggacggagggagggagggagggacggagggcgggacggcgggagggcgggacg -gagggacggagggagggcgggacggagggcgggagggcgggacggagggagggagggagg -gagggcgggacggagggagggagggcgggacggagggagggagggagggacggagggcgg -gacggcgggagggcgggacggagggacggagggagggcgggacggagggcgggagggcgg -gacggagggagggagggcgggacggagggacggagggagggagggcgggacggagggagg -gagggcgggacggagggacggagggagggagggcgggacggagggagggagggagggacg -gagggcgggacggcgggagggcgggacggagggacggagggagggcgggacggagggcgg -gagggagggagggcgggacggagggagggagggagggagggcgggacggagggagggagg -gagggagggacggagggacggagggagggagggagggagggacggagggcgggacggagg -gagggagggcggagggagggagggcgggacggagggagggagggagggacggagggcggg -acggagggagggagggcggagggagggagggcgggacggagggagggagggcgggaggga -tggagggagggagggcgggacggagggagggcgggagggagggacggagggcgggacgga -gggacggagggagggagggagggacggaggttgggacggagggacggagggcgggcggat -gccgcgggtctcaccgccaaggtgtcctgctgctgcagcagggcccgcacgtgcagggtc -gtgctgttctccatctcctggatggtctcgatcagctcccggttgagcttgctgaggaag -ttctcacggcttcggagctctcgcagagcggccctcccgctcctgagcgaggtctgcggg -cggagggaagagcagagaggcggcgctgcgccctgcccggcctgagccc ->p:HG002_1_chr20:278700-279386 -gaaccccctctgggacgggtgctatggtgccgcatttcacagagctcggggaggcaaagt -taactaaaagtctcccggccagtgagtgctggcgcgctgggatgaaacccatctcggtcc -tcttgcaaagcccaggtgaggggagtgaagggtgaagaaatgcgtcttccaggtggagga -agcaccacgtgcagtgggcggggaaaggcaggagagggcgcgcgagtgcgcggagggagg -gcgggacggagggagggagggcgggacggagggagggagggagggcgggacggagggagg -gagggcgggacggagggagggagggagggacggagggcgggacggcgggagggcgggacg -gagggacggagggagggcgggacggagggcgggagggcgggacggagggagggagggagg -gagggcgggacggagggagggagggcgggacggagggagggagggagggacggagggcgg -gacggcgggagggcgggacggagggacggagggagggcgggacggagggcgggagggcgg -gacggagggagggagggcgggacggagggacggagggagggagggcgggacggagggagg -gagggcgggacggagggacggagggagggagggcgggacggagggagggagggagggacg -gagggcgggacggcgggagggcgggacggagggacggagggagggcgggacggagggcgg -gagggagggagggcgggacggagggagggagggagggagggcgggacggagggagggagg -gagggagggacggagggacggagggagggagggagggagggacggagggcgggacggagg -gagggagggcggagggagggagggcgggacggagggagggagggagggacggagggcggg -acggagggagggagggcggagggagggagggcgggacggagggagggagggcgggaggga -tggagggagggagggcgggacggagggagggcgggagggagggacggagggcgggacgga -gggacggagggagggagggagggacggaggttgggacggagggacggagggcgggcggat -gccgcgggtctcaccgccaaggtgtcctgctgctgcagcagggcccgcacgtgcagggtc -gtgctgttctccatctcctggatggtctcgatcagctcccggttgagcttgctgaggaag -ttctcacggcttcggagctctcgcagagcggccctcccgctcctgagcgaggtctgcggg -cggagggaagagcagagaggcggcgctgcgccctgcccggcctgagccc ->p:HG002_2_chr20:278700-279386 -gaaccccctctgggacgggtgctatggtgccgcatttcacagagctcggggaggcaaagt -taactaaaagtctcccggccagtgagtgctggcgcgctgggatgaaacccatctcggtcc -tcttgcaaagcccaggtgaggggagtgaagggtgaagaaatgcgtcttccaggtggagga -agcaccacgtgcagtgggcggggaaaggcaggagagggcgcgcgagtgcgcggagggagg -gcgggacggagggagggagggcgggagggagggacggag------------ggaggaagg -gcgggacggagggagggagggcgggagggacggagggcgggacggcgggagggcgggacg -gagggacggagggagggcgggacggagggcgggagggcgggacggagggagggagggagg -gagggc------------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------gggacggagggagggagggagggagggacggagggcgggacggagg -gagggagggcggagggagggagggcgggacggagggagggagggcgggacggagggtggg -agggagggag-------------------------------------------------- ----------------------ggatggagggagggagggagggacggagggcgggacgga -gggacggagggagggagggagggacggaggttgggacggagggacggagggcgggcggat -gccgcgggtctcaccgccaaggtgtcctgctgctgcagcagggcccgcacgtgcagggtc -gtgctgttctccatctcctggatggtctcgatcagctcccggttgagcttgctgaggaag -ttctcacggcttcggagctctcgcagagcggccctcccgctcctgagcgacgtctgcggg -cggagggaagagcagagaggcggcgctgcgccctgcccggcctgagccc ->ref_chr20:278700-279386 -gaaccccctctgggacgggtgctatggtgccgcatttcacagagctcggggaggcaaagt -taactaaaagtctcccggccagtgagtgctggcgcgctgggatgaaacccatctcggtcc -tcttgcaaagcccaggtgaggggagtgaagggtgaagaaatgcgtcttccaggtggagga -agcaccacgtgcagtgggcggggaaaggcaggagagggcgcgcgagtgcgcggagggagg -gcgggacggagggagggagggcg------------------------------------- --------ggacggagggagggagggagggacggagggcgggacggcgggagggcgggacg -gagggacggagggagggcgggacggagggcgggagggcgggacggag------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------ggagggagggagggagggacggagggcgggacgga -gggacggagggagggagggagggacggaggttgggacggagggacggagggcgggcggat -gccgcgggtctcaccgccagggtgtcctgctgctgcagcagggcccgcacgtgcagggtc -gtgctgttctccatctcctggatggtctcgatcagctcccggttgagcttgctgaggaag -ttctcacggcttcggagctctcgcagagcggccctcccgctcctgagcgaggtctgcggg -cggagggaagagcagagaggcggcgctgcgccctgcccggcctgagccc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_5185292921c42211a88ed41c2fdeac76.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_5185292921c42211a88ed41c2fdeac76.msa deleted file mode 100644 index 9297e52e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_5185292921c42211a88ed41c2fdeac76.msa +++ /dev/null @@ -1,70 +0,0 @@ ->syndip_1_chr20:16394949-16395621 -ttccccttagttcatgtttattagacgtctaagttccaggtatgctgctgtgcactgagt -aaacaacaaactagattctatgtctgttttctggaagtgtacagtcgtggacagcaaagc -taaggctcagtacaacaaagggcatacccctgtcatcggtgtcttcttactctctcccta -atgtgatgtattcatcctcccagtttagtcaaggcagaaaggagatgaggaaggggagag -gaggggagaggagggaagaggaggggaggggaggggagaggaggagaggggaggagaggg -gaggccaagggaggggaggggaggggaggagaggggaggccaagggaggggaggggaggg -gaggagaggggaggccaagggaggggaggggaggggaggagaggggaggccaagggaggg -gaggggaggagaggggaggccaagggaggggaggggaggggaggagaggggaggccaagg -gaggggaggggaggggaggagaggggaggccaagggagaagatatgaaagaaatagggaa -ggagtgggacacagggaggaaaacaaaactatttcctttcatataaatgttgtcatctgg -ggagaagccctcactatctccttggtgcctttggcttttggtattcaaatcccagaactc -tacatttggaatctagttctttcaagctttacattccagaaatccatttccattcttaat -ctgaaagcaccaggaaggcggatgctaa ->syndip_2_chr20:16394949-16395621 -ttccccttagttcatgtttattagacgtctaagttccaggtatgctgctgtgcactgagt -aaacaacaaactagattctatgtctgttttctggaagtgtacagtcgtggacagcaaagc -taaggctcagtacaacaaagggcatacccctgtcatcggtgtcttcttactctctcccta -atgtgatgtattcatcctcccagtttagtccaggcagaaaggagatgaggaaggggagag -gaggggagaggaggggag------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----gggaggggaggggagaggaggggaggccaagggagaagatatgaaagaaatagggaa -ggagtgggacacagggaggaaaacaaaactatttcctttcatataaatgttgtcatctgg -ggagaagccctcactatctccttggtgcctttggcttttggtattcaaatcccagaactc -tacatttggaatctagttctttcaagctttacattccagaaatccatttccattcttaat -ctgaaagcaccaggaaggcggatgctaa ->p:HG002_1_chr20:16394949-16395621 -ttccccttagttcatgtttattagacgtctaagttccaggtatgctgctgtgcactgagt -aaacaacaaactagattctatgtctgttttctggaagtgtacagtcatggacagcaaagc -taaggctcagtacaacaaagggcatacccctgtcattggtgtcttcttactctctcccta -atgtgatgtattcatcctcccagtttagtccaggcagaaaggagatgaggaaggggagag -gaggggagaggaggggag------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----gggaggggaggggagaggaggggaggccaagggagaagatatgaaagaaatagggaa -ggagtgggacacagggaggaaaacaaaactatttcctttcatataaatgttgtcatctgg -ggagaagccctcactatctccttggtgcctttggcttttggtattcaaatcccagaactc -tacatttggaatctagttctttccagctttacattccagaaatccatttccattcttaat -ctgaaagcaccaggaaggcggatgctaa ->p:HG002_2_chr20:16394949-16395621 -ttccccttagttcatgtttattagacgtctaagttccaggtatgctgctgtgcactgagt -aaacaacaaactagattctatgtctgttttctggaagtgtacagtcgtggacagcaaagc -taaggctcagtacaacaaagggcatacccctgtcatcggtgtcttcttactctctcccta -atgtgatgtattcatcctcccagtttagtcaaggcagaaaggagatgaggaaggggagag -gaggggagaggagggaagaggaggggaggggaggggagaggaggagaggggaggagaggg -gaggccaagggaggggaggggaggggaggagaggggaggccaagggaggggaggggaggg -gaggagaggggaggccaagggaggggaggggaggggaggagaggggaggccaagggaggg -gaggggaggagaggggaggccaagggaggggaggggaggggaggagaggggaggccaagg -gaggggaggggaggggaggagaggggaggccaagggagaagatatgaaagaaatagggaa -ggagtgggacacagggaggaaaacaaaactatttcctttcatataaatgttgtcatctgg -ggagaagccctcactatctccttggtgcctttggcttttggtattcaaatcccagaactc -tacatttggaatctagttctttcaagctttacattccagaaatccatttccattcttaat -ctgaaagcaccaggaaggcggatgctaa ->ref_chr20:16394949-16395621 -ttccccttagttcatgtttattagacgtctaagttccaggtatgctgctgtgcactgagt -aaacaacaaactagattctatgtctgttttctggaagtgtacagtcgtggacagcaaagc -taaggctcagtacaacaaagggcatacccctgtcatcggtgtcttcttactctctcccta -atgtgatgtattcatcctcccagtttagtcaaggcagaaaggagatgaggaaggggagag -gaggggagaggagggaagaggaggggaggggaggggagaggaggagaggggaggagaggg -gaggccaagggaggggaggggaggggaggagaggggaggccaa-----gggaggggaggg -gaggagaggggaggccaagggaggggaggggaggggaggagaggggaggccaa------- ------------------------------------------------------------- ----gggaggggaggggaggagaggggaggccaagggagaagatatgaaagaaatagggaa -ggagtgggacacagggaggaaaacaaaactatttcctttcatataaatgttgtcatctgg -ggagaagccctcactatctccttggtgcctttggcttttggtattcaaatcccagaactc -tacatttggaatctagttctttcaagctttacattccagaaatccatttccattcttaat -ctgaaagcaccaggaaggcggatgctaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_51e9064d5900eec876c35446dc62af52.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_51e9064d5900eec876c35446dc62af52.msa deleted file mode 100644 index a58ca059..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_51e9064d5900eec876c35446dc62af52.msa +++ /dev/null @@ -1,180 +0,0 @@ ->syndip_1_chr20:61201483-61202674 -tctctaaatatttggaaactaataatgtacttgtccgtaaaatgtggataaaatggaatt -atctgagaattaaaattcttttgaactgaatgacaataaaaatacagcatatcaaaatgt -atgggatgcagctaaagcagtgctcagaggacaatctatactactagaggcttatattag -aaaaaaaaatttaaatcaataacctaagctttcaccgttagagaaggaatttcctcactc -aggaccctctgcggatgtcacctccatcctcatcaggaccctccatggtgtcacctccat -cctcactcaggacactccatggtgtcacctccatccttactcaggaccctccatggtgtc -accgccatcctcactcaggaccctccatgagtgccacctccatcctcactcaggatcccc -tgtaagtgtcacctccatcctcaccaggaccctccatg-gtgtcaccgccatcctcactc -aggaccctccatgagtgccacctccatcctcaccaggatcccctgtaagtgtcacctcca -tcctcac-caggaccctccatgagtgtcacctccatc----ctcaggaccctccatgagt -gtcacctccatcctcactcaggaccctccat-ggtgtcacctccatcctcactcaggacc -ctccat-ggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca -ctcaggaccctccatggtgtcacctccatcctca-------------------------- ---ccaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacc -tccatcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccat --ggtgtcaccgccatcctca-------------------------------ctcaggacc -ctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca -ctcaggaccctccatggtgtcacctccatcctcaccaggatcccctgtaagtgtcacctc -catcctcaccaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggt -gtcacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcaccaggatcc -cctgtaagtgtcacctccatcctcac-caggaccctccatgagtgtcacctccatcctca ---------------------------ctcaggaccctccatg-gtgtcacctccatcctc -actcaggaccctccatggtgtcacctccatcctcactcaggaccctccat-ggtgtcacc -tccatcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccat -g-gtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatc----ctcagg -accctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcc -tcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatg------- -----------------------------gtgtcacctccatcctcactcaggaccctcca -tggtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcctcactcagg -accctccatggtgtcacctccatcctcactcaggaccctccgtgagtgccagctctgtct -accctcgggaccctccatgagtgtctcctctatctaccctcaggaccctctgtgaatgtc -ctcgccatccatactcccccctcttagacccagactgtttcagggttggacactgagctg -tggcccctgagcctagctcttctccgagcttctcttgggcacctctctctcagactaggc -tcagctccaacaccagttcccagagcccttcctgttcactgtctggtgtctcacactcac -acctgctcacatgcacactgactcactcacactcaaactc ->syndip_2_chr20:61201483-61202674 -tctctaaatatttggaaactaataatgtacttgtccgtaaaatgtggataaaatggaatt -atctgagaattaaaattcttttgaactgaatgacaataaaaatacagcatatcaaaatgt -atgggatgcagctaaagcagtgctcagaggacaatctatactactagaggcttatattag -aaaaaaaaatttaaatcaataacctaagctttcaccattagagaaggaatttcctcactc -aggaccctctgcggatgtcgcctccatcctcatcaggaccctccatggtgtcacctccat -cctcactcaggacactccatggtgtcacctccatccttactcaggaccctccatggtgtc -accgccatcctcactcaggaccctccatgggtgtcacctccatcctcac-caggatcccc -tgtaagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcctcactc -aggaccctccatg-gtgtcacctccatcctcactcaggaccctccatggtgtcacctcca -tcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgggt -gtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcaggacc -ctccatgggtgccacctccatcctcaccaggatcccctgtaagtgtcacctccatcctca -ccaggaccctccatgagtgtcacctccatcctcaggaccctccatgagtgtcacctccat -cctcaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacc -tccatcctcactcaggaccctccat-ggtgtcacctccatcctcactcaggaccctccat -gggtgtcacctccatcctcactcaggaccctccatgagtgtcacctccatcctcaggacc -ctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca -ctcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctc -catcctcactcaggacactccatggtgtcacctccatccttactcaggaccctccatggt -gtcaccgccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggatcc -cctgtaagtgtcacctccatcctcactcaggaccctccatgagtgtcacctccatcctca -ggaccctccatggtgtcacctccatcctcaggaccctccatgagtgtcacctccatcctc -actcaggaccctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacc -tccatcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccat -gagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg -accctccatg-gtgtcacctccatcctcactcaggacactccatggtgtcacctccatcc -ttactcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgcca -cctccatcctcaccaggatcccctgtaagtgtcacctccatcctcactcaggaccctcca -tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg -accctccatggtgtcacctccatcctcactcaggaccctccgtgagtgccagctctgtct -accctcgggaccctccatgagtgtctcctctatctaccctaaggaccctctgtgaatgtc -ctcgccatccatactcccccctcttagacccagactgtttcagggttggacactgagctg -tggcccctgagcctagctcttctccgagcttctcttgggcacctctctctcagactaggc -tcagctccaacaccagttcccagagcccttcctgttcactgtctggtgtctcacactcac -acctgctcacatgcacactgactcactcacactcaaactc ->p:HG002_1_chr20:61201483-61202674 -tctctaaatatttggaaactaataatgtacttgtccgtaaaatgtggataaaatggaatt -atctgagaattaaaattcttttgaactgaatgacaataaaaatacagcatatcaaaatgt -atgggatgcagctaaagcagtgctcagaggacaatctatactactagaggcttatattag -aaaaaaaaatttaaatcaataacctaagctttcaccattagagaaggaatttcctcactc -aggaccctctgcggatgtcgcctccatcctcatcaggaccctccatggtgtcacctccat -cctcactcaggacactccatggtgtcacctccatccttactcaggaccctccatggtgtc -accgccatcctcactcaggaccctccatgggtgtcacctccatcctcac-caggatcccc -tgtaagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcctcactc -aggaccctccatg-gtgtcacctccatcctcactcaggaccctccatggtgtcacctcca -tcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgggt -gtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcaggacc -ctccatgggtgccacctccatcctcaccaggatcccctgtaagtgtcacctccatcctca -ccaggaccctccatgagtgtcacctccatcctcaggaccctccatgagtgtcacctccat -cctcaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacc -tccatcctcactcaggaccctccat-ggtgtcacctccatcctcactcaggaccctccat -gggtgtcacctccatcctcactcaggaccctccatgagtgtcacctccatcctcaggacc -ctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca -ctcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctc -catcctcactcaggacactccatggtgtcacctccatccttactcaggaccctccatggt -gtcaccgccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggatcc -cctgtaagtgtcacctccatcctcactcaggaccctccatgagtgtcacctccatcctca -ggaccctccatggtgtcacctccatcctcaggaccctccatgagtgtcacctccatcctc -actcaggaccctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacc -tccatcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccat -gagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg -accctccatg-gtgtcacctccatcctcactcaggacactccatggtgtcacctccatcc -ttactcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgcca -cctccatcctcaccaggatcccctgtaagtgtcacctccatcctcactcaggaccctcca -tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg -accctccatggtgtcacctccatcctcactcaggaccctccgtgagtgccagctctgtct -accctcgggaccctccatgagtgtctcctctatctaccctaaggaccctctgtgaatgtc -ctcgccatccatactcccccctcttagacccagactgtttcagggttggacactgagctg -tggcccctgagcctagctcttctccgagcttctcttgggcacctctctctcagactaggc -tcagctccaacaccagttcccagagcccttcctgttcactgtctggtgtctcacactcac -acctgctcacatgcacactgactcactcacactcaaactc ->p:HG002_2_chr20:61201483-61202674 -tctctaaatatttggaaactaataatgtacttgtccgtaaaatgtggataaaatggaatt -atctgagaattaaaattcttttgaactgaatgacaataaaaatacagcatatcaaaatgt -atgggatgcagctaaagcagtgctcagaggacaatctatactactagaggcttatattag -aaaaaaaaatttaaatcaataacctaagctttcaccgttagagaaggaatttcctcactc -aggaccctctgcggatgtcacctccatcctcatcaggaccctccatggtgtcacctccat -cctcactcaggacactccatggtgtcacctccatccttactcaggaccctccatggtgtc -accgccatcctcactcaggaccctccatgagtgccacctccatcctcactcaggatcccc -tgtaagtgtcacctccatcctcaccaggaccctccatg-gtgtcaccgccatcctcactc -aggaccctccatgagtgccacctccatcctcaccaggatcccctgtaagtgtcacctcca -tcctcac-caggaccctccatgagtgtcacctccatc----ctcaggaccctccatgagt -gtcacctccatcctcactcaggaccctccat-ggtgtcacctccatcctcactcaggacc -ctccat-ggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca -ctcaggaccctccatggtgtcacctccatcctca-------------------------- ---ccaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacc -tccatcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccat --ggtgtcaccgccatcctca-------------------------------ctcaggacc -ctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca -ctcaggaccctccatggtgtcacctccatcctcaccaggatcccctgtaagtgtcacctc -catcctcaccaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggt -gtcacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcaccaggatcc -cctgtaagtgtcacctccatcctcac-caggaccctccatgagtgtcacctccatcctca ---------------------------ctcaggaccctccatg-gtgtcacctccatcctc -actcaggaccctccatggtgtcacctccatcctcactcaggaccctccat-ggtgtcacc -tccatcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccat -g-gtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatc----ctcagg -accctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcc -tcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatg------- -----------------------------gtgtcacctccatcctcactcaggaccctcca -tggtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcctcactcagg -accctccatggtgtcacctccatcctcactcaggaccctccgtgagtgccagctctgtct -accctcgggaccctccatgagtgtctcctctatctaccctcaggaccctctgtgaatgtc -ctcgccatccatactcccccctcttagacccagactgtttcagggttggacactgagctg -tggcccctgagcctagctcttctccgagcttctcttgggcacctctctctcagactaggc -tcagctccaacaccagttcccagagcccttcctgttcactgtctggtgtctcacactcac -acctgctcacatgcacactgactcactcacactcaaactc ->ref_chr20:61201483-61202674 -tctctaaatatttggaaactaataatgtacttgtccgtaaaatgtggataaaatggaatt -atctgagaattaaaattcttttgaactgaatgacaataaaaatacagcatatcaaaatgt -atgggatgcagctaaagcagtgctcagaggacaatctatactactagaggcttatattag -aaaaaaaaatttaaatcaataacctaagctttcaccattagagaaggaatttcctcactc -aggaccctctgcggatgtcgcctccatcctcatcaggaccctccatggtgtcacctccat -cctcactcaggacactccatggtgtcacctccatccttactcaggaccctccatggtgtc -accgccatcctcactcaggaccctccatgagtgccacctccatcctcac-caggatcccc -tgtaagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatc------- ------------------------------------------------------------- ------------------------------------------ctcaggaccctccatgagt -gtcacctccatcctcactcaggaccctccat-ggtgtcaccgccatcctcactcaggacc -ctccatgagtgc------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------cacctccatcctcaccaggatcccctgtaagtgtcacctc -catcctcaccaggaccctccatgagtgtcacctccatcct-------------------- ------------------------------------------------------------- ----------------------------caggaccctccatgagtgtcacctccatcctca ---------------------------ctcaggaccctccatg-gtgtcacctccatcctc -actcaggaccctccatggtgtcacctccatcctcactcaggaccctccat-gg------- ------------------------------------------------------------- ------------------------------------------------------------- ------------gtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcc -tcactcaggaccctccatg----------------------------------------- ------------------------------------------------------------- -------------------------------------gtgtcacctccatcctcactcagg -accctccatggtgtcacctccatcctcactcaggaccctccgtgagtgccagctctgtct -accctcgggaccctccatgagtgtctcctctatctaccctcaggaccctctgtgaatgtc -ctcgccatccatactcccccctcttagacccagactgtttcagggttggacactgagctg -tggcccctgagcctagctcttctccgagcttctcttgggcacctctctctcagactaggc -tcagctccaacaccagttcccagagcccttcctgttcactgtctggtgtctcacactcac -acctgctcacatgcacactgactcactcacactcaaactc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_523baa1f515a7e26709b1c4664aa2d56.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_523baa1f515a7e26709b1c4664aa2d56.msa deleted file mode 100644 index bf316328..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_523baa1f515a7e26709b1c4664aa2d56.msa +++ /dev/null @@ -1,290 +0,0 @@ ->syndip_1_chr20:64124909-64128174 -attgcccaggatggagtgcagtggcgctatctcggctcactgcaacctctgtctcctggg -ttcaagcgattctcctgcctcagcctcccaagtagctgggattacaggtgtgcaccacca -cacccagctaatttttttgtattttcagtagagatgaggtttcactgtgttagccaggat -ggtctcgatttcctgacctcatgatccacccaccttggcctcccaaagtgctgggattac -aggtgtgagccactgcgcccggacacactttgctagttttttttttttgttttgtttttt -tagtagcagtgctgggattacaggtgtcagccaccatgcctggctcaaatactacactgt -cttgattactacagctttatactcaaatactacaccatcttgattactacagctttatac -tcaaataccacaccgtcttgattaccacagctgtatactcaaataccacaccgtcttgat -taccacagctttatactcaaataccacaccgtcttgattaccaaagctttatactcaaat -accacact--------------------------------------gtcttgattaccac -agctttatactcaaataacacaccgtcttgattaccacagctttatactcaaatactaca -ccgtcttgattaccacagctttatactcaaataccacactgtcttgattaccacagcttt -atactcaaataccacactgtcttgattcctatagctttatac------------------ ----------------tcaaataccacactgtcttgattaccacagctttatactcaaata -ctacactgtcttgattactatagctttatactcaaatactacactgtcttgattactata -gctttatactcaaatactacactgtctgattactacagctttatactcaaataccaccct -gtcttgattaccacagctttatactcaaataccacaccgtcttgattaccacagctgtat -actcaaatact------------------------------------acaccgtcttgat -taccacagctgtatactcaaatactacactgtcttgattaccacagctttatactcaaat -accacactgtcttgattaccaccgctttatactcaaataccacactgtcttgattactat -agctttatactcaaatactacactgtctgattactacagctttatactcaaataccacac -tgtcttgattaccacagctttatactcaaatactacactgtcttgattactatagcttta -tactcaaatactacactgtctgattactacagctttatactcaaataccacactatcttg -attactacagctttatactcaaatactacactgtctgattactacagctttatactcaaa -taccacaccgtcttgattaccacagctttatactcaaatactacactgtcttgattacta -cagctttatactcaaataccacaccgtcttgattaccacagctgtatactcaaatactac -accgtcttgattaccacagctttatactcaaatactacaccgtcttgattaccacagctt -tatactcaaataccacactgtcttgattactatagctttatactcaaatactacactgtc -tgattactacagctttatactcaaataccacactgtcttgattaccacagctttatactc -aaatactacactgtctgattactacagctttatactcaaataccacactgtcttgattac -cacagctttatactcaaatactacactgtcttgattaccacagctttatactcaaatacc -acaccgtcttgattaccacagctgtatactcaaataccacactgtcttgattaccacagc -tgtatactcaaataccacactgtcttgattaccacagctttatactcaaatacc------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------acactgtcttgattaccacagctttatacgcaaataccac -actgtcttgattactatagctttatactcaaataccacactgtcttgattactacagctt -tatactcaaataccacactgtcttgattactacagctttatactcaaatactacactgtc -ttgattaacacagctttatactcaaatactacactg------------------------ -----------------------------------------------------tcttgatt -accacagctttatactcaaatactacactgtcttgattactatagctttatactcaaata -ccacactgtcttgattactatagctttatactcaaatactacactgtcttgattaccaca -gctttatactcaaatactacactgtcttgattactatagctttatactcaaataccacac -tgtcttgattaccacagctttatactcaaataccacactgtcttgattaccacagcttta -tactcaaatactacactgtcttgattactac----------------------------- ------------------------------------------------agctttatactca -aatacc------------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------acactg -tcttgattactatagctttatactcaaataccacactgtcttgattactatagctttata -ctctgttttgaggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggg -gattataggttctttgcaaatttctatgcaaattttggaatcagtttgttaatttccaga -aaaaagcctcttgcaattttaattgcattaaatctatagatgagtttgggtagaatcggc -atatggagttttctgatgcatgaacacagcataactcctatttacatctttaa ->syndip_2_chr20:64124909-64128174 -attgcccaggatggagtgcagtggcgctatctcggctcactgcaacctctgtctcctggg -ttcaagcgattctcctgcctcagcctcccaagtagctgggattacaggtgtgcaccacca -cacccagctaatttttttgtattttcagtagagatgaggtttcactgtgttagccaggat -ggtctcgatttcctgacctcatgatccacccaccttggcctcccaaagtgctgggattac -aggtgtgagccactgcgcccggacacactttgctagttttttttttttgttttgtttttt -tagtagcagtgctgggattacaggtgtcagccaccatgcctggctcaaatactacactgt -cttgattactacagctttatactcaaatactacaccatcttgattactacagctttatac -tcaaataccacaccgtcttgattaccacagctgtatactcaaataccacaccgtcttgat -taccacagctttatactcaaataccacaccgtcttgattaccaaagctttatactcaaat -accacact--------------------------------------gtcttgattaccac -agctttatactcaaataacacaccgtcttgattaccacagctttatactcaaatactaca -ccgtcttgattaccacagctttatactcaaataccacactgtcttgattaccacagcttt -atactcaaataccacactgtcttgattcctatagctttatac------------------ ----------------tcaaataccacactgtcttgattaccacagctttatactcaaata -ctacactgtcttgattactatagctttatactcaaatactacactgtcttgattactata -gctttatactcaaatactacactgtctgattactacagctttatactcaaataccaccct -gtcttgattaccacagctttatactcaaataccacaccgtcttgattaccacagctgtat -actcaaatact------------------------------------acaccgtcttgat -taccacagctgtatactcaaatactacactgtcttgattaccacagctttatactcaaat -accacactgtcttgattaccaccgctttatactcaaataccacactgtcttgattactat -agctttatactcaaatactacactgtctgattactacagctttatactcaaataccacac -tgtcttgattaccacagctttatactcaaatactacactgtcttgattactatagcttta -tactcaaatactacactgtctgattactacagctttatactcaaataccacactatcttg -attactacagctttatactcaaatactacactgtctgattactacagctttatactcaaa -taccacaccgtcttgattaccacagctttatactcaaatactacactgtcttgattacta -cagctttatactcaaataccacaccgtcttgattaccacagctgtatactcaaatactac -accgtcttgattaccacagctttatactcaaatactacaccgtcttgattaccacagctt -tatactcaaataccacactgtcttgattactatagctttatactcaaatactacactgtc -tgattactacagctttatactcaaataccacactgtcttgattaccacagctttatactc -aaatactacactgtctgattactacagctttatactcaaataccacactgtcttgattac -cacagctttatactcaaatactacactgtcttgattaccacagctttatactcaaatacc -acaccgtcttgattaccacagctgtatactcaaataccacactgtcttgattaccacagc -tgtatactcaaataccacactgtcttgattaccacagctttatactcaaatacc------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------acactgtcttgattaccacagctttatacgcaaataccac -actgtcttgattactatagctttatactcaaataccacactgtcttgattactacagctt -tatactcaaataccacactgtcttgattactacagctttatactcaaatactacactgtc -ttgattaacacagctttatactcaaatactacactg------------------------ -----------------------------------------------------tcttgatt -accacagctttatactcaaatactacactgtcttgattactatagctttatactcaaata -ccacactgtcttgattactatagctttatactcaaatactacactgtcttgattaccaca -gctttatactcaaatactacactgtcttgattactatagctttatactcaaataccacac -tgtcttgattaccacagctttatactcaaataccacactgtcttgattaccacagcttta -tactcaaataccacactgtcttgattactac----------------------------- ------------------------------------------------agctttatactca -aatacc------------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------acactg -tcttgattactatagctttatactcaaataccacactgtcttgattactatagctttata -ctctgttttgaggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggg -gattataggttctttgcaaatttctatgcaaattttggaatcagtttgttaatttccaga -aaaaagcctcttgcaattttaattgcattaaatctatagatgagtttgggtagaatcggc -atatggagttttctgatgcatgaacacagcataactcctatttacatctttaa ->p:HG002_1_chr20:64124909-64128174 -attgcccaggatggagtgcagtggtgctatctcggctcactgcaacctctgtctcctggg -ttcaagcgattctcctgcctcagcctcccaagtagctgggattacaggtgtgcaccacca -cacccagctaatttttttgtattttcagtagagatgaggtttcactgtgttagccaggat -ggtctcgatttcctgacctcatgatccacccaccttggcctcccaaagtgctgggattac -aggtgtgagccactgcgcccggacacactttgctagttttttttttttgttttgtttttt -tagtagcagtgctgggattacaggtgtcagccaccatgcctggctcaaatactacactgt -cttgattactacagctttatactcaaatactacaccatcttgattactacagctttatac -tcaaataccacaccgtcttgattaccacagctgtatactcaaataccacaccgtcttgat -taccacagctttatactcaaataccacaccgtcttgattaccaaagctttatactcaaat -accacact--------------------------------------gtcttgattaccac -agctttatactcaaataacacaccgtcttgattaccacagctttatactcaaatactaca -ccgtcttgattaccacagctttatactcaaataccacactgtcttgattaccacagcttt -atactcaaataccacactgtcttgattcctatagctttatac------------------ ----------------tcaaataccacactgtcttgattaccacagctttatactcaaata -ctacactgtcttgattactatagctttatactcaaatactacactgtcttgattactata -gctttatactcaaatactacactgtctgattactacagctttatactcaaataccaccct -gtcttgattaccacagctttatactcaaataccacaccgtcttgattaccacagctgtat -actcaaatact------------------------------------acaccgtcttgat -taccacagctgtatactcaaatactacactgtcttgattaccacagctttatactcaaat -accacactgtcttgattaccaccgctttatactcaaataccacactgtcttgattactat -agctttatactcaaatactacactgtctgattactacagctttatactcaaataccacac -tgtcttgattaccacagctttatactcaaatactacactgtcttgattactatagcttta -tactcaaatactacactgtctgattactacagctttatactcaaataccacactatcttg -attactacagctttatactcaaatactacactgtctgattactacagctttatactcaaa -taccacaccgtcttgattaccacagctttatactcaaatactacactgtcttgattacta -cagctttatactcaaataccacaccgtcttgattaccacagctgtatactcaaatactac -accgtcttgattaccacagctttatactcaaatactacaccgtcttgattaccacagctt -tatactcaaataccacactgtcttgattactatagctttatactcaaatactacactgtc -tgattactacagctttatactcaaataccacactgtcttgattaccacagctttatactc -aaatactacactgtctgattactacagctttatactcaaataccacactgtcttgattac -cacagctttatactcaaatactacactgtcttgattaccacagctttatactcaaatacc -acaccgtcttgattaccacagctgtatactcaaataccacactgtcttgattaccacagc -tgtatactcaaataccacactgtcttgattaccacagctttatactcaaatacc------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------acactgtcttgattaccacagctttatacgcaaataccac -actgtcttgattactatagctttatactcaaataccacactgtcttgattactacagctt -tatactcaaataccacactgtcttgattactacagctttatactcaaatactacactgtc -ttgattaacacagctttatactcaaatactacactg------------------------ -----------------------------------------------------tcttgatt -accacagctttatactcaaatactacactgtcttgattactatagctttatactcaaata -ccacactgtcttgattactatagctttatactcaaatactacactgtcttgattaccaca -gctttatactcaaatactacactgtcttgattactatagctttatactcaaataccacac -tgtcttgattaccacagctttatactcaaataccacactgtcttgattaccacagcttta -tactcaaataccacactgtcttgattactac----------------------------- ------------------------------------------------agctttatactca -aatacc------------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------acactg -tcttgattactatagctttatactcaaataccacactgtcttgattactatagctttata -ctctgttttgaggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggg -gattataggttctttgcaaatttctatgcaaattttggaatcagtttgttaatttccaga -aaaaagcctcttgcaattttaattgcattaaatctatagatgagtttgggtagaatcggc -atatggagttttctgatgcatgaacacagcataactcctatttacatctttaa ->p:HG002_2_chr20:64124909-64128174 -attgcccaggatggagtgcagtggtgctatctcggctcactgcaacctctgtctcctggg -ttcaagcgattctcctgcctcagcctcccaagtagctgggattacaggtgtgcaccacca -cacccagctaatttttttgtattttcagtagagatgaggtttcactgtgttagccaggat -ggtctcgatttcctgacctcatgatccacccaccttggcctcccaaagtgctgggattac -aggtgtgagccactgcgcccggacacactttgctagttttttttttttgttttgtttttt -tagtagcagtgctgggattacaggtgtcagccaccatgcctggctcaaatactacactgt -cttgattactacagctttatactcaaatactacaccatcttgattactacagctttatac -tcaaataccacaccgtcttgattaccacagctgtatactcaaataccacaccgtcttgat -taccacagctttatactcaaataccacaccgtcttgattaccaaagctttatactcaaat -accacact--------------------------------------gtcttgattaccac -agctttatactcaaataacacaccgtcttgattaccacagctttatactcaaatactaca -ccgtcttgattaccacagctttatactcaaataccacactgtcttgattaccacagcttt -atactcaaataccacactgtcttgattcctatagctttatac------------------ ----------------tcaaataccacactgtcttgattaccacagctttatactcaaata -ctacactgtcttgattactatagctttatactcaaatactacactgtcttgattactata -gctttatactcaaatactacactgtctgattactacagctttatactcaaataccaccct -gtcttgattaccacagctttatactcaaataccacaccgtcttgattaccacagctgtat -actcaaatact------------------------------------acaccgtcttgat -taccacagctgtatactcaaatactacactgtcttgattaccacagctttatactcaaat -accacactgtcttgattaccaccgctttatactcaaataccacactgtcttgattactat -agctttatactcaaatactacactgtctgattactacagctttatactcaaataccacac -tgtcttgattaccacagctttatactcaaatactacactgtcttgattactatagcttta -tactcaaatactacactgtctgattactacagctttatactcaaataccacactatcttg -attactacagctttatactcaaatactacactgtctgattactacagctttatactcaaa -taccacaccgtcttgattaccacagctttatactcaaatactacactgtcttgattacta -cagctttatactcaaataccacaccgtcttgattaccacagctgtatactcaaatactac -accgtcttgattaccacagctttatactcaaatactacaccgtcttgattaccacagctt -tatactcaaataccacactgtcttgattactatagctttatactcaaatactacactgtc -tgattactacagctttatactcaaataccacactgtcttgattaccacagctttatactc -aaatactacactgtctgattactacagctttatactcaaataccacactgtcttgattac -cacagctttatactcaaatactacactgtcttgattaccacagctttatactcaaatacc -acaccgtcttgattaccacagctgtatactcaaataccacactgtcttgattaccacagc -tgtatactcaaataccacactgtcttgattaccacagctttatactcaaatacc------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------acactgtcttgattaccacagctttatacgcaaataccac -actgtcttgattactatagctttatactcaaataccacactgtcttgattactacagctt -tatactcaaataccacactgtcttgattactacagctttatactcaaatactacactgtc -ttgattaacacagctttatactcaaatactacactg------------------------ -----------------------------------------------------tcttgatt -accacagctttatactcaaatactacactgtcttgattactatagctttatactcaaata -ccacactgtcttgattactatagctttatactcaaatactacactgtcttgattaccaca -gctttatactcaaatactacactgtcttgattactatagctttatactcaaataccacac -tgtcttgattaccacagctttatactcaaataccacactgtcttgattaccacagcttta -tactcaaatactacactgtcttgattactac----------------------------- ------------------------------------------------agctttatactca -aatacc------------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------acactg -tcttgattactatagctttatactcaaataccacactgtcttgattactatagctttata -ctctgttttgaggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggg -gattataggttctttgcaaatttctatgcaaattttggaatcagtttgttaatttccaga -aaaaagcctcttgcaattttaattgcattaaatctatagatgagtttgggtagaatcggc -atatggagttttctgatgcatgaacacagcataactcctatttacatctttaa ->ref_chr20:64124909-64128174 -attgcccaggatggagtgcagtggcgctatctcggctcactgcaacctctgtctcctggg -ttcaagcgattctcctgcctcagcctcccaagtagctgggattacaggtgtgcaccacca -cacccagctaatttttttgtattttcagtagagatgaggtttcactgtgttagccaggat -ggtctcgatttcctgacctcatgatccacccaccttggcctcccaaagtgctgggattac -aggtgtgagccactgcgcccggacacactttgctagttttttttttttgttttgtttttt -tagtagcagtgctgggattacaggtgtcagccaccatgcctggctcaaatactacactgt -cttgattactacagctttatactcaaatactacaccatcttgattactacagctttatac -tcaaataccacaccgtcttgattaccacagctg--------------------------- ------------tatactcaaataccacaccgtcttgattaccaaagctttatactcaaat -accacactgtcttgattaccacagctttatactcaaataacacaccgtcttgattaccac -agctttatactcaaata--------------------------------------ctaca -ccgtcttgattaccacagctttatactcaaataccacactgtcttgattaccacagcttt -atactcaaatactacactgtcttgattcctatagctttatactcaaataccacactgtct -tgattaccacagcttt---------------------------------atactcaaata -ctacactgtcttgattactatagctttatactcaaatactacactgtcttgattactata -gctttatactcaaatactacactgtctgattactacagctttatactcaaataccaccct -gtcttgattaccacagctttatactcaaataccacaccgtcttgattaccacagctgtat -actcaaatactactgtcctgattactacagctttatactcaaataccacaccgtcttgat -taccacagctgtatactcaaatactacaccgtcttgattaccacagctttatactcaaat -actacaccgtcttgattaccacagctttatactcaaataccacactgtcttgattactat -agctttatactcaaatactacactgtctgattactacagctttatactcaaataccacac -tgtcttgattaccacagctttatactcaaatactacactgtcttgattactatagcttta -tactcaaatactacactgtctgattactacagctttatactcaaataccacactatcttg -attactacagctttatactcaaatactacactgtctgattactacagctttatactcaaa -taccacaccgtcttgattaccacagctttatactcaaatactacactgtcttgattacta -cagctttatactcaaataccacaccgtcttgattaccacagctgtatactcaaatactac -accgtcttgattaccacagctttatactcaaatactacaccgtcttgattaccacagctt -tatactcaaataacacactgtcttgattactatagctttatactcaaatactacactgtc -tgattactacagctttatactcaaataccacactgtcttgattaccacagctttatactc -aaatactacactgtctgattactacagctttatactcaaataccacactgtcttgattac -cacagctttatactcaaatactacactgtcttgattaccacagctttatactcaaatacc -acaccgtcttgattaccacagctgtatactcaaataccacactgtcttgattaccacagc -tgtatactcaaataccacactgtcttgattaccacagctttatactcaaataccacactg -tcttgattactatagctttatactcaaataccacactgtcttgattaccacagctttata -cgcaaataccacactgtcttgattactatagctttatactcaaataccacactgtcttga -ttactacagctttatactcaaataccacactgtcttgattactacagctttatactcaaa -tactacactgtcttgattaacacagctttatactcaaatactacactgtcttgattacca -cagctttatactcaaatactacactgtcttgattactatagctttatactcaaataccac -actgtcttgattactatagctttatactcaaatactacactgtcttgattaccacagctt -tatactcaaatactacactgtcttgattact----------------------------- ----------atagctttatactcaaataccacactgtcttgattaccacagctttatact -caaataccacactgtcttgattaccacagctttatactcaaataccacactgtcttgatt -accacagctttatactcaaataccacactgtcttgattactatagctttatactcaaata -ccacactgtcttgattactacagctttatactcaaataccacactgtcttgattaacaca -gctttatactcaaatactacactgtcttgattaccacagctttatactcaaatactacac -tgtcttgattactatagctttatactcaaataccacactgtcttgattactatagcttta -tactcaaatactacactgtcttgattaccacagctttatactcaaatactacactgtctt -gattactatagctttgtactcaaataccacactgtcttgattaccacagctttatactca -aataccacactgtcttgattaccacagctttatactcaaataccacactgtcttgattac -tatagctttatactcaaataccacactgtcttgattactacagctttatactcaaatacc -acactgtcttgattactacagctttatactcaaatactacactgtcttgattaacacagc -tttatactcaaatactacactgtcttgattaccacagctttatactcaaatactacactg -tcttgattactatagctttatactcaaataccacactgtcttgattactatagctttata -ctctgttttgaggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggg -gattataggttctttgcaaatttctatgcaaattttggaatcagtttgttaatttccaga -aaaaagcctcttgcaattttaattgcattaaatctatagatgagtttgggtagaatcggc -atatggagttttctgatgcatgaacacagcataactcctatttacatctttaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_541535ac45889f61485b69c44137fd45.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_541535ac45889f61485b69c44137fd45.msa deleted file mode 100644 index a244f140..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_541535ac45889f61485b69c44137fd45.msa +++ /dev/null @@ -1,140 +0,0 @@ ->syndip_1_chr20:14861954-14862744 -gacattggaggttttatatataaatatatatatatatatttatatatatatttatatata -tatatttatatatatttatatatatttatatatatatttatatatatat--ttatatata -tatttatatatatatttatatatatatttatatatatatttatatatatatttatatata -tttatatatatttatatatatttttatatatttttatatatataaatatataaaaatata -tataaatatataaaaatatataaaaatatataaatatatataaatatataaatatatata -aatatatataaatatatatttatatataaatatatataaatatatatttatacataaata -tatataaatatatatttatacataaatatataaatatatataatatatataaatatatat -tatacatatatatataaatatatattatacataaatatataaatatatataaatatatat -aaatatatatttatacataaatatataaatatatatataaatatatataaatatatataa -atatatatataaatatatatataaatatatataaatatatatataaatatatatataaat -atatataaatatatataaatatatatataaatatatataaatatatataaatatatattt -atatattaatatataaatatatataa-atatatatttatatatta-------atatataa -atatat-----------atatattaatatatataaatatatataaatatatatttatata -ttaatatatatatattaatatatatatatttatatattaatatatatatttatatattaa -tatatataaatatattactatgtatatttatatatatttatataaatatatataaatata -tgtaaatatatatataaaaatatatattaatatataaaaatatatatataaatata---t -ataaatatatatataaatatatataaatatatatatataaatatatataaataaatatat -aaatatatataaatat--atatataaatatatataaatatatataaatatatataaaaat -atatataaatatatatataaatatatataaatatatatataaatatatatataaatatat -atataaatatatataa--atatatatataaatatatataaatatatatataattatatat -aaatatatataaatatatataaatatatatataaatatatataaatatatataaatatat -ataaatatatatataaatatatataaatatatatatataaatatatataaatatatatat -aaatatatataaatatatatataaatataaatatatataaatata----taaaaatatat -atataaatataaatatatataaatatatatgtataaatatatatataa----------at -ataaatatatatatataaatatatatataaatatatatatataaatatatatataaatat -atataaatatatatataaatatatataaatatatatatatatatttttttttaatagaga -ggatgaagacca ->syndip_2_chr20:14861954-14862744 -gacattggaggtttt--------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------atatataaatatatatatatatattt -atatatatatttatatatatatatttatatatatttatatatatttatatatatatttat -atatatatttatatatatttatatatttatatatatttatatatatttttatatatataa -atatataaaaatatataaatatatat----aaatatataaatatatataaatatatattt -atacataaatatataaatatatataatatatataaatatatattatacatatatatataa -atatatattatacataaatatataaatatatataaatatatataaatatatatttataca -taaatatataaat----atatatatatataaatatatataaatatatatttatatattaa -tatatataaatatattactatgtatatttatatatatttatataaatatatataaatata -tgtaaatatatatataaaaatatatattaatatataaaaatatatatataaatata---- ----------tatataaatatatataaataaatatatataaatatatatataaatatatat -aaatatatataaatat--atatataaatatatataaatatatataaatatatatataaat -atatatataaatatatataaatatatataaataaatatataaatatatatataaatatat -ataaatatatatataaatatatataaatatatatatataaatatatataaatatatatat -aaatatatataaatat------atatataaatatatataaatatatatatataaatatat -ataaatatatatataaatatatataaatatat--------atataaatataaatatatat -aaatatataaaaatatatatataaatataaatatatataaatatatatgtataaatatat -atataaatataaatatatataaatatatatatataaatatatatataa----------at -atatataaatatatataaaaatatatataa--atatatatataaatatatatataaatat -atataaatatatatataaatatatataaatatatatatatatatttttttttaatagaga -ggatgaagacca ->p:HG002_1_chr20:14861954-14862744 -gacattggaggtttt--------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------atatataaatatatatatatatattt -atatatatatttatatatatatatttatatatatttatatatatttatatatatatttat -atatatatttatatatatttatatatttatatatatttatatatatttttatatatataa -atatataaaaatatataaatatatat----aaatatataaatatatataaatatatattt -atacataaatatataaatatatataatatatataaatatatattatacatatatatataa -atatatattatacataaatatataaatatatataaatatatataaatatatatttataca -taaatatataaat----atatatatatataaatatatataaatatatatttatatattaa -tatatataaatatattactatgtatatttatatatatttatataaatatatataaatata -tgtaaatatatatataaaaatatatattaatatataaaaatatatatataaatata---- ----------tataaatatatatataaataaatatatataaatatatatataaatatatat -aaatatatataaatat--atatataaatatatataaatatatataaatatatatataaat -atatatataaatatatataaatatatataaataaatatataaatatatatataaatatat -ataaatatatatataa--atatataaatatatatatataaatatatataaatatatatat -aaatatatataaatat------atatataaatatatataaatatatatatataaatatat -ataaatatatatataaatatatataaatatat--------atataaatataaatatatat -aaatatataaaaatatatatataaatataaatatatataaatatatatgtataaatatat -atataaatataaatatatataaatatatatatataaatatatatataa----------at -atatataaatatatataaaaatatatataa--atatatatataaatatatatataaatat -atataaatatatatataaatatatataaatatatatatatatatttttttttaatagaga -ggatgaagacca ->p:HG002_2_chr20:14861954-14862744 -gacattggaggttttatatataaatatatatatatatatttatatatatatttatatata -tatatttatatatatttatatatatttatatatatatttatatatatataaatatatata -aatatataaatatatataaatatatatttatacataaatatataaatatatttatatata -tttatatatatttatatatatttttatatatttttatatatataaatatataaaaatata -tataaatatataaaaatatataaaaatatataaatatatataaatatataaatatatata -aatatatataaatatatatttatatataaatatatataaatatatatttatacataaata -tatataaatatatatttatacataaatatataaatatatataatatatataaatatatat -tatacataaatatataaatatatattatacataaatatataaatatatataaatatatat -aaatatatatttatacataaatatataaatatatatataaatatatataaatatatataa -atatatatataaatatatatataaatatatataaatatatatataaatatatatataaat -atatataaatatatataaatatatatataaatatatataaatatatataaatatatattt -atatattaatatataaatatatataa-atatatatttatatatta-------atatataa -atatat-----------atatattaatatatataaatatatataaatatatatttatata -ttaatatatatatattaatatatatatatttatatattaatatatatatttatatattaa -tatatataaatatattactatgtatatttatatatatttatataaatatatataaatata -tgtaaatatatatataaaaatatatattaatatataaa---atatatataaatatatatt -atacataaatatataaatatatataaatatatataaatatatatttatacataaatatat -aaatatatatatatataaatatatataaatatatatttatatattaatatatataaatat -attactatgtatatttatatatatttatataaatatatataaatatatgtaaatatatat -ataaaaatatatatta--atatataaaaatatatatataaatatatataaatatatatat -aaatatatataaatat------atatatataaatatatataaatatatatataaatatat -ataaatatatatataaatatatataaatatatatatataaatatatataaatatatatat -aaatatatataaatatatatataaatataaatatatataaatata----taaaaatatat -atataaatataaatatatataaatatatatgtataaatatatatataa----------at -ataaatatatatatataaatatatatataaatatatatatataaatatatatataaatat -atataaatatatatataaatatatataaatatatatatatatatttttttttaatagaga -ggatgaagacca ->ref_chr20:14861954-14862744 -gacattggaggttt---------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------tatatataaatatatatatatata -tt--tatatatatatttatatatatatatttatatatatttatatatatttatata---- -------------------tatatttatatatatataaatatatataaatatataaatata -tataaatatatatttatacataaatatataaatatata---atatatataaatatatatt -atacataaatatataaatatatataaatatatataaatatatatttatacataaatatat -aaatatatatatatataaatatatataaatatatatttatatattaatatatataaatat -attactatgtatatttatatatatttatataaatatatataaatatatgtaaatatatat -ataaaaatatatatta--atatataaaaatatatatataaatatatataaatatatatat -aaatatatataaatat------atatatataaatatatataaatatatatataaatatat -ataaatatatatataaatatatataaatatatatatataaatatatataaatatatatat -aaatatatataaatatatatataaatataaatatatataaatata----taaaaatatat -atataaatataaatatatataaatatatatgtataaatatatatataaatataaatatat -ataaatatatatatataaatatatatataaatatatatatataaatatatatataaatat -atataaatatatatataaatatatataaatatatatatatatatttttttttaatagaga -ggatgaagacca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_558c505e413a6398b429691dca26a4ea.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_558c505e413a6398b429691dca26a4ea.msa deleted file mode 100644 index 0e524eae..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_558c505e413a6398b429691dca26a4ea.msa +++ /dev/null @@ -1,50 +0,0 @@ ->syndip_1_chr20:62830550-62830797 -ccaggcccccagggcctccgaggtgacgtgggcgaccgggtaagtggccctctcagcagg -aagctcccctgcaccccctctacccatgtaccacagtcccccaccccccaccgtgctcca -ccccccaccacagtcccccaccccccaccccagtccccaaacccctaccacagtccccca -accccaccacagtcccccaccccctaccacagtcccccaccccctaccacagtcccccaa -cccccaccacagtcccccacccccaccacagtccgccaacccccatgacagtccctcaac -ccccaccacagtcccccaacccccatgacagtcccccaacccccaccacagtcccccaac -ccccaccacagt-ccccaccccctaccacagtcccccaacccccaccacagtcccccacc -ccctaccacaatcccccacccccca----------------------------------- --------------------------------------------- ->syndip_2_chr20:62830550-62830797 -ccaggcccccagggcctccgaggtgacgtgggcgaccgggtaagtggccctctcagcagg -aagctcccctgcaccccctctacccatgtaccacagtccccca----------------- -ccccccaccacagtcccccaccccccaccccagtccccaaacccctaccacagtccccca -accccaccacagtcccccaccccctaccacagtcccccaacccctaccacagtcccccaa -cccccaccacagtcccccacccccaccacagtccgccaacccccatgacagtcccccaac -ccccaccacagtccccc-acccccaccacagtccgccaacccccatgacagtcccccaac -ccccaccacagtcccccaacccccatgacagtcccccaacccccaccacagtcccccaac -ccctaccacagtcccccaacccccaccacagtccccaccccctaccacagtcccccaacc -cccaccacagtcccccaccccctaccacaatcccccacccccca ->p:HG002_1_chr20:62830550-62830797 -ccaggcccccagggcctccgaggtgacgtgggcgaccgggtaagtggccctctcagcagg -aagctcccctgcaccccctctacccatgtaccacagtccccca----------------- -ccccccaccacagtcccccaccccccaccccagtccccaaacccctaccacagtccccca -accccaccacagtcccccaccccctaccacagtcccccaacccctaccacagtcccccaa -cccccaccacagtcccccacccccaccacagtccgccaacccccatgacagtcccccaac -ccccaccacagtccccc-acccccaccacagtccgccaacccccatgacagtcccccaac -ccccaccacagtcccccaacccccatgacagtcccccaacccccaccacagtcccccaac -ccctaccacagtcccccaacccccaccacagtccccaccccctaccacagtcccccaacc -cccaccacagtcccccaccccctaccacaatcccccacccccca ->p:HG002_2_chr20:62830550-62830797 -ccaggcccccagggcctccgaggtgacgtgggcgaccgggtaagtggccctctcagcagg -aagctcccctgcaccccctctacccatgtaccacagtcccccaccccccaccgtgctcca -ccccccaccacagtcccccaccccccaccccagtccccaaacccctaccacagtccccca -accccaccacagtcccccaccccctaccacagtcccccaccccctaccacagtcccccaa -cccccaccacagtcccccacccccaccacagtccgccaacccccatgacagtcccccaac -ccccaccacagtcccccaacccccatgacagtcccccaacccctaccacagtcccccaac -ccccaccacagt-ccccaccccctaccacagtcccccaacccccaccacagtcccccacc -ccctaccacaatcccccacccccca----------------------------------- --------------------------------------------- ->ref_chr20:62830550-62830797 -ccaggcccccagggcctccgaggtgacgtgggcgaccgggtaagtggccctctcagcagg -aagctcccctgcaccccctctacccatgtaccacagtccccca----------------- --cccccatgacagtcccccaacccccaccacagtcccccaacccctaccacagtccccca -acccccaccacagtccccaccccctaccacagtcccccaacccccaccacagtcccccac -cccctaccacaatcccccacccccca---------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_55fd9b2e5e003be8141dfef04233afce.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_55fd9b2e5e003be8141dfef04233afce.msa deleted file mode 100644 index 5d5266fd..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_55fd9b2e5e003be8141dfef04233afce.msa +++ /dev/null @@ -1,135 +0,0 @@ ->syndip_1_chr20:64134883-64136386 -tctcctctttccggtccttgacagtgattccgtgcatcacaaacacacacgctccctcag -ttacacgaatcacaaacacacgctccctcagttttgtgcatcacaaacgcacacgctccc -tcagttttgtgcgtcacacacacgctccctcagttttgtgcgtc---------------- ----------------------acacacacgctccctcagttttgtgcg------------ ------------------------------------------------------------- ------------------------------------------------------------- -ccacaaacacgcgcactccctcagttatgtgcgtcacaaacacagacgctccctcagttt -tgcgcatcacaaacacacacgctccctcagttatggacatcacaaacacacacgctccct -cagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaacacacacg -ctccctcagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaaca -cacacgctccctcagttttgtgcgtcacaaacacagacgctccctcagttttgcgcatca -cacacacgctccctcagttttgtgtgtcacaaacacacacgctccttcagttttgtgctt -cacaaacacacacgctccctcagttttgtgcatcacacacacattccctcagttttgtgc -gccacaaacacgcgcgctccctcagttttgtgcatcacaaacgcacatgctccctcagtt -ttgggcatcacaaacacattccctcagttttgtgcatcacaaacgcacacgctccctcag -ttttgtgcgtcacaaacacacacgctacctcagttttgtgtgttacaaacacacacgctc -cctcagtttcgtgcatcccaaacatgctccctcagttatgtgcgtcacaaacacgctccc -tcagttttgtgtgtcacaaacacacacgctccctcagttttgtgcatcacaaacacacac -attccctcagttttgtgcgtcacaaacacgcgtgctctctcagttatgtgcgtcacaaac -acagacgctccctcagttttgcgcatcacacacacgctccctcagctttgtgcttcacaa -acacacacgctccctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgca -tcccaaagacgattcctcagttttgtgcatcacaaacacatatgctccctcagttttgtg -cgtcacaaacgcgcgctccctcagttatgtgcgtcacaaacacagacgctccctcagttt -tgcgcatcacacacacgctccctcagttttgtgtg------------------------- ---------tcacaaacacacacgctccctcagttgtcaggggactttgcactgtgccttt -gcat ->syndip_2_chr20:64134883-64136386 -tctcctctttccggtccttgacagtgattccgtgcatcacaaacacacacgctccctcag -ttacacgaatcacaaacacacgctccctcagttttgtgcatcacaaacgcacacgctccc -tcagttttgtgcgtcacacacacgctccctcagttttgtgcgccacaaacacgcgcactc -cctcagttatgtgcgtcacaaacacagacgctccctcagttttgcgca------------ ------------------------------------------------------------- ------------------------------------------------------------- -tcacaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagttt -tgtgcttcacaaacacacacgctccctcagttatggacatcacaaacacacacgctccct -cagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaacacacacg -ctccctcagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaaca -cacacgctccctcagttttgtgcgtcacaaacacagacgctccctcagttttgcgcatca -cacacacgctccctcagttttgtgtgtcacaaacacacacgctccttcagttttgtgctt -cacaaacacacacgctccctcagttttgtgcatcacacacacattccctcagttttgtgc -gccacaaacacgcgcgctccctcagttttgtgcatcacaaacgcacatgctccctcagtt -ttgggcatcacaaacacattccctcagttttgtgcatcacaaacgcacacgctccctcag -ttttgtgcgtcacaaacacacacgctacctcagttttgtgtgttacaaacacacacgctc -cctcagtttcgtgcatcccaaacatgctccctcagttatgtgcgtcacaaacacgctccc -tcagttttgtgtgtcacaaacacacacgctccctcagttttgtgcatcacaaacacacac -attccctcagttttgtgcgtcacaaacacgcgtgctctctcagttatgtgcgtcacaaac -acagacgctccctcagttttgcgcatcacacacacgctccctcagctttgtgcttcacaa -acacacacgctccctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgca -tcccaaagacgattcctcagttttgtgcatcacaaacacatatgctccctcagttttgtg -cgtcacaaacgcgcgctccctcagttatgtgcgtcacaaacacagacgctccctcagttt -tgcgcatcacacacacgctccctcagttttgtgtgtcacaaacacacacgctccctcagt -tttgcgcatcacaaacacacacgctccctcagttgtcaggggactttgcactgtgccttt -gcat ->p:HG002_1_chr20:64134883-64136386 -tctcctctttccggtccttgacagtgattccgtgcatcacaaacacacacgctccctcag -ttacacgaatcacaaacacacgctccctcagttttgtgcatcacaaacgcacacgctccc -tcagttttgtgcgtcacacacacgctccctcagttttgtgcgccacaaacacgcgcactc -cctcagttatgtgcgtcacaaacacagacgctccctcagttttgcgca------------ ------------------------------------------------------------- ------------------------------------------------------------- -tcacaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagttt -tgtgcttcacaaacacacacgctccctcagttatggacatcacaaacacacacgctccct -cagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaacacacacg -ctccctcagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaaca -cacacgctccctcagttttgtgcgtcacaaacacagacgctccctcagttttgcgcatca -cacacacgctccctcagttttgtgtgtcacaaacacacacgctccttcagttttgtgctt -cacaaacacacacgctccctcagttttgtgcatcacacacacattccctcagttttgtgc -gccacaaacacgcgcgctccctcagttttgtgcatcacaaacgcacatgctccctcagtt -ttgggcatcacaaacacattccctcagttttgtgcatcacaaacgcacacgctccctcag -ttttgtgcgtcacaaacacacacgctacctcagttttgtgtgttacaaacacacacgctc -cctcagtttcgtgcatcccaaacatgctccctcagttatgtgcgtcacaaacacgctccc -tcagttttgtgtgtcacaaacacacacgctccctcagttttgtgcatcacaaacacacac -attccctcagttttgtgcgtcacaaacacgcgtgctctctcagttatgtgcgtcacaaac -acagacgctccctcagttttgcgcatcacacacacgctccctcagctttgtgcttcacaa -acacacacgctccctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgca -tcccaaagacgattcctcagttttgtgcatcacaaacacatatgctccctcagttttgtg -cgtcacaaacgcgcgctccctcagttatgtgcgtcacaaacacagacgctccctcagttt -tgcgcatcacacacacgctccctcagttttgtgtgtcacaaacacacacgctccctcagt -tttgcgcatcacaaacacacacgctccctcagttgtcaggggactttgcactgtgccttt -gcat ->p:HG002_2_chr20:64134883-64136386 -tctcctctttccggtccttgacagtgattccgtgcatcacaaacacacacgctccctcag -ttacacgaatcacaaacacacgctccctcagttttgtgcatcacaaacgcacacgctccc -tcagttttgtgcgtcacacacacgctccctcagttttgtgcgtc---------------- ----------------------acacacacgctccctcagttttgtgcg------------ ------------------------------------------------------------- ------------------------------------------------------------- -ccacaaacacgcgcactccctcagttatgtgcgtcacaaacacagacgctccctcagttt -tgcgcatcacaaacacacacgctccctcagttatggacatcacaaacacacacgctccct -cagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaacacacacg -ctccctcagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaaca -cacacgctccctcagttttgtgcgtcacaaacacagacgctccctcagttttgcgcatca -cacacacgctccctcagttttgtgtgtcacaaacacacacgctccttcagttttgtgctt -cacaaacacacacgctccctcagttttgtgcatcacacacacattccctcagttttgtgc -gccacaaacacgcgcgctccctcagttttgtgcatcacaaacgcacatgctccctcagtt -ttgggcatcacaaacacattccctcagttttgtgcatcacaaacgcacacgctccctcag -ttttgtgcgtcacaaacacacacgctacctcagttttgtgtgttacaaacacacacgctc -cctcagtttcgtgcatcccaaacatgctccctcagttatgtgcgtcacaaacacgctccc -tcagttttgtgtgtcacaaacacacacgctccctcagttttgtgcatcacaaacacacac -attccctcagttttgtgcgtcacaaacacgcgtgctctctcagttatgtgcgtcacaaac -acagacgctccctcagttttgcgcatcacacacacgctccctcagctttgtgcttcacaa -acacacacgctccctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgca -tcccaaagacgattcctcagttttgtgcatcacaaacacatatgctccctcagttttgtg -cgtcacaaacgcgcgctccctcagttatgtgcgtcacaaacacagacgctccctcagttt -tgcgcatcacacacacgctccctcagttttgtgtg------------------------- ---------tcacaaacacacacgctccctcagttgtcaggggactttgcactgtgccttt -gcat ->ref_chr20:64134883-64136386 -tctcctctttccggtccttgacagtgattccgtgcatcacaaacacacacgctccctcag -ttacacgaatcacaaacacacgctccctcagttttgtgcatcacaaacgcacacgctccc -tcagttttgtgcgtcacacacacgctccctcagttttgtgcgccacaaacacgcgcactc -cctcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacaaacacac -acgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaa -acacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgct -tcacaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagttt -tgtgcttcacaaacacacacgctccctcagttatggacatcacaaacacacacgctccct -cagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaacacacacg -ctccctcagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaaca -cacacgctccctcagttttgtgcgtcacaaacacagacgctccctcagttttgcgcatca -cacacacgctccctcagttttgtgtgtcacaaacacacacgctccttcagttttgtgctt -cacaaacacacacgctccctcagttttgtgcatcacacacacattccctcagttttgtgc -gccacaaacacgcgcgctccctcagttttgtgcatcacaaacgcacatgctccctcagtt -ttgggcatcacaaacacattccctcagttttgtgcatcacaaacgcacacgctccctcag -ttttgtgcgtcacaaacacacacgctacctcagttttgtgtgttacaaacacacacgctc -cctcagtttcgtgcatcccaaacatgctccctcagttatgtgcgtcacaaacacgctccc -tcagttttgtgtgtcacaaacacacacgctccctcagttttgtgcatcacaaacacacac -attccctcagttttgtgcgtcacaaacacgcgtgctctctcagttatgtgcgtcacaaac -acagacgctccctcagttttgcgcatcacacacacgctccctcagctttgtgcttcacaa -acacacacgctccctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgca -tcccaaagacgattcctcagttttgtgcatcacaaacacatatgctccctcagttttgtg -cgtcacaaacgcgcgctccctcagttatgtgcgtcacaaacacagacgctccctcagttt -tgcgcatcacacacacgctccctcagttttgtgtgtcacaaacacacacgctccctcagt -tttgcgcatcacaaacacacacgctccctcagttgtcaggggactttgcactgtgccttt -gcat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_59d44cdfc1780250a34a80863967df95.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_59d44cdfc1780250a34a80863967df95.msa deleted file mode 100644 index bac9a791..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_59d44cdfc1780250a34a80863967df95.msa +++ /dev/null @@ -1,150 +0,0 @@ ->syndip_1_chr20:4032219-4033601 -tgccttggcctcccaaagagccgagattgcagcctctgcccggccgccaccccgtctggg -aagtgaggagcgtctctgcttggccacccatcgtctgggatatgaggagcccctctgcct -ggctgcccagtctggaaagt---------------------------------------- -gaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgcctcttcccggc -tgccatcccatctaggaagtgaggagcgtctctgcccggccgcccatcgtctgagatgtg -gggagcacctctgccccaccgccctgtctgggatgtgaggagcgcctctgctgggccgca -accctgtctgggaggtgaggagcgtctctgccccgccgctccgtctgagaagtgaggaaa -ccctctgcctggcaaccgccccgtctgagaagtgaggagcccctccgtccggcaaccacc -ccgtctgggaagtgaggagcgtctccgcccggcagccaccccgtccgggagggaggtggg -gggggtcagccccccgcccggccagccgccccgtccgggaggtgaggggctcctctgccc -ggccgcccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggagg -gaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagccc -cccgcccggccggccgccccgtccgggaggtgaggggcgcctctgcccggccgcccctac -tgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtgggggggt -cagtcccccgcccggccggctgccccgtccgggaggtgaggggcgcctctgcccggccgc -ccctactgggaagtgaggagcccctctgcccggccagctgccccgcccgggagggaggtg -ggggggtcagccccccgcctggccagccgccccatccgggagggaggtgggggggtcagc -cccccgcccggccagccgccccgtccgggaggggggagggggggtcagccccctgcccgg -ccagccgccccgtccgggagggaggtggg--ggggggtcagccccccgcccggccagccg -ccccgtccgggagggaggtggggggatcagccccccgcctggccagccgccccgtccggg -aggtgaggggcgcctctgcccggccacccctactgggaagtgaggagcccctctgcccgg -ccagccgccccgtccgggagggaggcgggggggggggtcggccagccgccccgtccggga -gggaggtgggggggtcagccccccttccggccggccgccctgtccgggaggtgaggggcg -cctctgcctggccgcccctactgggaagtgaggacccctctgcccggccagccgccccgt -ccgggagggaggtgggggggacagccccccgcccggccagccgccctatccaggaggtga -ggggcgcctctgcccggccgcccctactgggaagtgaggagcccctctgcccggccagcc -gccccgtccgggagggtagtgggggggtcagccccccgcccggccagccgccccatccgg -gaggtgaggggcgcttctgcccggccgcccctactgggaagtgaggagcccctctgcccg -gccacgaccccgtctgggaggtgtgcccagcggctcattggggatgggcca ->syndip_2_chr20:4032219-4033601 -tgccttggcctcccaaagagccgagattgcagcctctgcccggccgccaccccgtctggg -aagtgaggagcgtctctgcttggccacccatcgtctgggatatgaggagcccctctgcct -ggctgcccagtctggaaagtgaggagcgtctctgcccggccgccatcccatctaggaagc -gaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgcctcttcccggc -tgccatcccatctaggaactgaggagcgtctctgcccggccgcccatcgtctgagatgtg -gggagcacctctgccccaccgccctgtctgggatgtgaggagcgcctctgctgggccgca -accctgtctgggaggtgaggagcgtctctgccccgccgctccgtctgagaagtgaggaaa -ccctctgcctggcaaccgccccgtctgagaagtgaggagcccctccgtccggcaaccacc -ccgtctgggaagtgaggagcgtctccgcccggcagccaccccgtccgggagggaggt--- ------------------------------------------------------------- ------------------------------------------------------------- ------gggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagccc -cccgcccggccggccgccccgtccgggaggtgaggggcgcctctgcccggccgcccctac -tgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtgggggggt -cagccccccgcccggccggctgccccgtccgggaggtgaggggcgcctctgcccggccgc -ccctactgggaagtgaggagcccctctgcccggccagctgccccgcccgggagggaggtg -ggggggtcagccccccgcctggccagccgccccatccgggagggaggtgggggggtcagc -cccccgcccggccagccgccccgtccgggaggggggagggggggtcagccccctgcccgg -ccagccgccccgtccgggagggaggtgggggggggggtcagccccccgcccggccagccg -ccccgtccgggagggaggtggggggatcagccccccgcctggccagccgccccgtccggg -aggtgaggggcgcctctgcccggccacccctactgggaagtgaggagcccctctgcccgg -ccagccgccccgtccgggagggaggcgggggggggggtcggccagccgccccgtccggga -gggaggtgggggggtcagccccccttccggccggccgccctgtccgggaggtgaggggcg -cctctgcctggccgcccctactgggaagtgaggacccctctgcccggccagccgccccgt -ccgggagggaggtgggggggacagccccccgcccggccagccgccctatccaggaggtga -ggggcgcctctgcccggccgcccctactgggaagtgaggagcccctctgcctggccagcc -gccccgtccgggagggtagtgggggggtcagccccccgcccggccagccgccccatccgg -gaggtgaggggcgcttctgcccggccgcccctactgggaagtgaggagcccctctgcccg -gccacgaccccgtctgggaggtgtgcccagcggctcattggggatgggcca ->p:HG002_1_chr20:4032219-4033601 -tgccttggcctcccaaagagccgagattgcagcctctgcccggccgccaccccgtctggg -aagtgaggagcgtctctgcttggccacccatcgtctgggatatgaggagcccctctgcct -ggctgcccagtctggaaagtgaggagcgtctctgcccggccgccatcccatctaggaagc -gaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgcctcttcccggc -tgccatcccatctaggaactgaggagcgtctctgcccggccgcccatcgtctgagatgtg -gggagcacctctgccccaccgccctgtctgggatgtgaggagcgcctctgctgggccgca -accctgtctgggaggtgaggagcgtctctgccccgccgctccgtctgagaagtgaggaaa -ccctctgcctggcaaccgccccgtctgagaagtgaggagcccctccgtccggcaaccacc -ccgtctgggaagtgaggagcgtctccgcccggcagccaccccgtccgggagggaggt--- ------------------------------------------------------------- ------------------------------------------------------------- ------gggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagccc -cccgcccggccggccgccccgtccgggaggtgaggggcgcctctgcccggccgcccctac -tgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtgggggggt -cagccccccgcccggccggctgccccgtccgggaggtgaggggcgcctctgcccggccgc -ccctactgggaagtgaggagcccctctgcccggccagctgccccgcccgggagggaggtg -ggggggtcagccccccgcctggccagccgccccatccgggagggaggtgggggggtcagc -cccccgcccggccagccgccccgtccgggaggggggagggggggtcagccccctgcccgg -ccagccgccccgtccgggagggaggtgggggggggggtcagccccccgcccggccagccg -ccccgtccgggagggaggtggggggatcagccccccgcctggccagccgccccgtccggg -aggtgaggggcgcctctgcccggccacccctactgggaagtgaggagcccctctgcccgg -ccagccgccccgtccgggagggaggcgggggggggggtcggccagccgccccgtccggga -gggaggtgggggggtcagccccccttccggccggccgccctgtccgggaggtgaggggcg -cctctgcctggccgcccctactgggaagtgaggacccctctgcccggccagccgccccgt -ccgggagggaggtgggggggacagccccccgcccggccagccgccctatccaggaggtga -ggggcgcctctgcccggccgcccctactgggaagtgaggagcccctctgcctggccagcc -gccccgtccgggagggtagtgggggggtcagccccccgcccggccagccgccccatccgg -gaggtgaggggcgcttctgcccggccgcccctactgggaagtgaggagcccctctgcccg -gccacgaccccgtctgggaggtgtgcccagcggctcattggggatgggcca ->p:HG002_2_chr20:4032219-4033601 -tgccttggcctcccaaagagccgagattgcagcctctgcccggccgccaccccgtctggg -aagtgaggagcgtctctgcttggccacccatcgtctgggatatgaggagcccctctgcct -ggctgcccagtctggaaagt---------------------------------------- -gaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgcctcttcccggc -tgccatcccatctaggaagtgaggagcgtctctgcccggccgcccatcgtctgagatgtg -gggagcacctctgccccaccgccctgtctgggatgtgaggagcgcctctgctgggccgca -accctgtctgggaggtgaggagcgtctctgccccgccgctccgtctgagaagtgaggaaa -ccctctgcctggcaaccgccccgtctgagaagtgaggagcccctccgtccggcaaccacc -ccgtctgggaagtgaggagcgtctccgcccggcagccaccccgtccgggagggaggtggg -gggggtcagccccccgcccggccagccgccccgtccgggaggtgaggggctcctctgccc -ggccgcccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggagg -gaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagccc -cccgcccggccggccgccccgtccgggaggtgaggggcgcctctgcccggccgcccctac -tgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtgggggggt -cagtcccccgcccggccggctgccccgtccgggaggtgaggggcgcctctgcccggccgc -ccctactgggaagtgaggagcccctctgcccggccagctgccccgcccgggagggaggtg -ggggggtcagccccccgcctggccagccgccccatccgggagggaggtgggggggtcagc -cccccgcccggccagccgccccgtccgggaggggggagggggggtcagccccctgcccgg -ccagccgccccgtccgggagggaggtggg--ggggggtcagccccccgcccggccagccg -ccccgtccgggagggaggtggggggatcagccccccgcctggccagccgccccgtccggg -aggtgaggggcgcctctgcccggccacccctactgggaagtgaggagcccctctgcccgg -ccagccgccccgtccgggagggaggcgggggggggggtcggccagccgccccgtccggga -gggaggtgggggggtcagccccccttccggccggccgccctgtccgggaggtgaggggcg -cctctgcctggccgcccctactgggaagtgaggacccctctgcccggccagccgccccgt -ccgggagggaggtgggggggacagccccccgcccggccagccgccctatccaggaggtga -ggggcgcctctgcccggccgcccctactgggaagtgaggagcccctctgcccggccagcc -gccccgtccgggagggtagtgggggggtcagccccccgcccggccagccgccccatccgg -gaggtgaggggcgcttctgcccggccgcccctactgggaagtgaggagcccctctgcccg -gccacgaccccgtctgggaggtgtgcccagcggctcattggggatgggcca ->ref_chr20:4032219-4033601 -tgccttggcctcccaaagagccgagattgcagcctctgcccggccgccaccccgtctggg -aagtgaggagcgtctctgcttggccacccatcgtctgggatatgaggagcccctctgcct -ggctgcccagtctggaaagtgaggagcgtctctgcccggccgccatcccatctaggaagc -gaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgcctcttcccggc -tgccatcccatctaggaactgaggagcgtctctgcccggccgcccatcgtctgagatgtg -gggagcacctctgccccaccgccctgtctgggatgtgaggagcgcctctgctgggccgca -accctgtctgggaggtgaggagcgtctctgccccgccgctccgtctgagaagtgaggaaa -ccctctgcctggcaaccgccccgtctgagaagtgaggagcccctccgtccggcaaccacc -ccgtctgggaagtgaggagcgtctccgcccggcagccaccccgtccgggagggaggt--- ------------------------------------------------------------- ------------------------------------------------------------- ------gggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagccc -cccgcccggccggccgccccgtccgggaggtgaggggcgcctctgcccggccgcccctac -tgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtgggggggt -cagccccccgcccggccggctgccccgtccgggaggtgaggggcgcctctgcccggccgc -ccctactgggaagtgaggagcccctctgcccggccagctgccccgcccgggagggaggtg -ggggggtcagccccccgcctggccagccgccccatccgggagggaggtgggggggtcagc -cccccgcccggccagccgccccgtccgggaggggggagggggggtcagccccctgcccgg -ccagccgccccgtccgggagggaggtggg------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------gggggggtcagccccctttccggccg--ccgcctgtccgggaggtgaggggcg -cctctgcctggccgcccctactgggaagtgaggacccctctgcccggccagccgccccgt -ccgggagggaggtgggggggacagccccccgcccggccagccgccctatccaggaggtga -ggggcgcctctgcccggccgcccctactgggaagtgaggagcccctctgcctggccagcc -gccccgtccgggagggtagtgggggggtcagccccccgcccggccagccgccccatccgg -gaggtgaggggcgcttctgcccggccgcccctactgggaagtgaggagcccctctgcccg -gccacgaccccgtctgggaggtgtgcccagcggctcattggggatgggcca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_5d555b16b7cd6a89d52e14c12b1d7f92.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_5d555b16b7cd6a89d52e14c12b1d7f92.msa deleted file mode 100644 index 68f111c8..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_5d555b16b7cd6a89d52e14c12b1d7f92.msa +++ /dev/null @@ -1,75 +0,0 @@ ->syndip_1_chr20:32722424-32723212 -aataatgatttatcgttctggccgggtgtgatggctcatgcctgtaatcccagcgctgtg -ggaggcgtggccggcagatcacctgaggtcaggagttcaagaccagcctggccaacatgg -tgaaacttggtctctactaaaaatacaaaaattagccaggcatggtggtgggcgcctgca -atcccagctacccagaaggctgagtcagaagaatcacttgaacccgggaggtggaggttg -cagtgagccgagatcgtgccactgcactccagcctgggtgacagagtgagactcaggaaa -aaaaaaaaaaagacttggccgagcccagtggctcacacctgtaatcccagcactttggga -ggctgaggcgggtggatcacgaggtcaagagatcgagaccatcctggctaacacggtgaa -accccatctctactaaaaaatacaaaaaattagccgggcgtggtggtgggcacctgtagt -cccagctactcgggaggctgaggcagaatggcgtgaacctggtaggcagagcttgcagtg -agctgagatcacgccactgcactccagcctgggtgacagagcaagactccatctcaaaaa -taaataaataaataaataaata-------aataataataataataataaagacttgtgat -cctctccctctccctctccctctccgtctccctctccctctccctctccctccctctccg -tctccgtctccgtctccgtctccctctccctctccccacggtctccctctcatgcggagc -cgaagctggactgtac ->syndip_2_chr20:32722424-32723212 -aataatgatttatcgttctggccgggtgtgatggctcatgcctgtaatcccagcgctgtg -ggaggcgtggccggcagatcacctgaggtcaggagttcaagaccagcctggccaacatgg -tgaaacttggtctctactaaaaatacaaaaattagccaggcatggtggtgggcgcctgca -atcccagctacccagaaggctgagtcagaagaatcacttgaacccgggaggtggaggttg -cagtgagccgagatcgtgccactgcactccagcctgggtgacagagtgagactcaggaaa -aaaaaaaaaaagacttggccgagcccagtggctcacacctgtaatcccagcactttggga -ggctgaggcgggtggatcacgaggtcaagagatcgagaccatcctggctaacacggtgaa -accccatctctactaaaaaatacaaaaaattagccgggcgtggtggtgggcacctgtagt -cccagctactcgggaggctgaggcagaatggcgtgaacctggtaggcagagcttgcagtg -agctgagatcacaccactgcactccagcctgggtgacagagcaagactccatctcaaaaa -taaataaataaataaataaataaataaataataataataataataataaagacttgtgat -cctctccctctccctctccctctccgtctccctctccctctccctctccctccctctccg -tctccgtctccgtctccgtctccctctccctctccccacggtctccctctcatgcggagc -cgaagctggactgtac ->p:HG002_1_chr20:32722424-32723212 -aataatgatttatcgttctggccgggtgtgatggctcatgcctgtaatcccagcgctgtg -ggaggcgtggccggcagatcacctgaggtcaggagttcaagaccagcctggccaacatgg -tgaaacttggtctctactaaaaatacaaaaattagccaggcatggtggtgggcgcctgca -atcccagctacccagaaggctgagtcagaagaatcacttgaacccgggaggtggaggttg -cagtgagccgagatcgtgccactgcactccagcctgggtgacagagtgagactcaggaaa -aaaaaaaaaaagacttggccgagcccagtggctcacacctgtaatcccagcactttggga -ggctgaggcgggtggatcacgaggtcaagagatcgagaccatcctggctaacacggtgaa -accccatctctactaaaaaatacaaaaaattagccgggcgtggtggtgggcacctgtagt -cccagctactcgggaggctgaggcagaatggcgtgaacctggtaggcagagcttgcagtg -agctgagatcacaccactgcactccagcctgggtgacagagcaagactccatctcaaaaa -taaataaataaataaataaata-------aataataataataataataaagacttgtgat -cctctccctctccctctccctctccgtctccctctccctctccctctccctccctctccg -tctccgtctccgtctccgtctccctctccctctccccacggtctccctctcatgcggagc -cgaagctggactgtac ->p:HG002_2_chr20:32722424-32723212 -aataatgatttatcgttctggccgggtgtgatggctcatgcctgtaatcccagcgctgtg -ggaggcgtggccggcagatcacctgaggtcaggagttcaagaccagcctggccaacatgg -tgaaacttggtctctactaaaaatacaaaaattagccaggcatggtggtgggcgcctgca -atcccagctacccagaaggctgagtcagaagaatcacttgaacccgggaggtggaggttg -cagtgagccgagatcgtgccactgcactccagcctgggtgacagagtgagactcaggaaa -aaaaaaaaaaagacttggccgagcccagtggctcacacctgtaatcccagcactttggga -ggctgaggcgggtggatcacgaggtcaagagatcgagaccatcctggctaacacggtgaa -accccatctctactaaaaaatacaaaaaattagccgggcgtggtggtgggcacctgtagt -cccagctactcgggaggctgaggcagaatggcgtgaacctggtaggcagagcttgcagtg -agctgagatcacgccactgcactccagcctgggtgacagagcaagactccatctcaaaaa -taaataaataaataaataaata-------aataataataataataataaagacttgtgat -cctctccctctccctctccctctccgtctccctctccctctccctctccctccctctccg -tctccgtctccgtctccgtctccctctccctctccccacggtctccctctcatgcggagc -cgaagctggactgtac ->ref_chr20:32722424-32723212 -aataatgatttatcgttctggccgggtgtgatggctcatgcctgtaatcccagcgctgtg -ggaggcgtggccggcagatcacctgaggtcaggagttcaagaccagcctggccaacatgg -tgaaacttggtctctactaaaaatacaaaaattagccaggcatggtggtgggcgcctgca -atcccagctacccagaaggctgagtcagaagaatcacttgaacccgggaggtggaggttg -cagtgagccgagatcgtgccactgcactccagcctgggtgacagagtgagactcaggaaa -aaaaaaaaaaagacttggccgagcccagtggctcacacctgtaatcccagcactttggga -ggctgaggcgggtggatcacgaggtcaagagatcgagaccatcctggctaacacggtgaa -accccatctctactaaaaaatacaaaaaattagccgggcgtggtggtgggcacctgtagt -cccagctactcgggaggctgaggcagaatggcgtgaacctggtaggcagagcttgcagtg -agctgagatcacgccactgcactccagcctgggtgacagagcaagactccatctcaaaaa -taaataaataaataaataaata-------aataataataataataataaagacttgtgat -cctctccctctccctctccctctccgtctccctctccctctccctctccctccctctccg -tctccgtctccgtctccgtctccctctccctctccccacggtctccctctcatgcggagc -cgaagctggactgtac diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_5d5633150357392b3e03c84e6a8ef68e.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_5d5633150357392b3e03c84e6a8ef68e.msa deleted file mode 100644 index 8f5527bd..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_5d5633150357392b3e03c84e6a8ef68e.msa +++ /dev/null @@ -1,45 +0,0 @@ ->syndip_1_chr20:61744188-61744654 -cggagactgtgtggttggaaaggagccaaccagagagtggggaggcgatggagagaataa -cagagaggaaggcaggtgcagggagacagcaaaggagagggagaagagaatgagagaggg -atggggagaaagagagaagagaggtggagagagacaggaaaggagagggagggagaggaa -gagagggagagagagaaggagggagagagatggaaagaggtggagggagagagagaagga -aagggagggaga------------------------------------------------ ------------------------------------------------------------- ----------------------------------------------gagagagacagacag -acagcttcacacagacataaaacatctgctgttcaggatcccagctg ->syndip_2_chr20:61744188-61744654 -cggagactgtgtggttggaaaggagccaaccagagagtggggaggcgatggagagaataa -gagagaggaaggcaggtgcagggagacagcaaaggagagggagaagagaatgagagaggg -atggggagaaagagagaagagaggtggagagagacaggaaaggagagggagggagaggaa -gagagggagagagagaaggagggagagagatggaaagaggtggagggagagagagaagga -aagggagggagaggaagagagggagagagagaaggagggagagagatggagagaggtgga -gggagagagagaaggaaagggagg------------------------------------ ----------------------------------------------gagagagagagacag -acagcttcacacagacataaaacatctgctgttcaggatcccagctg ->p:HG002_1_chr20:61744188-61744654 -cggagactgtgtggttggaaaggagccaaccagagagtggggaggcgatggagagaataa -gagagaggaaggcaggtgcagggagacagcaaaggagagggagaagagaatgagagaggg -atggggagaaagagagaagagaggtggagagagacaggaaaggagagggagggagaggaa -gagagggagagagagaaggagggagagagatggaaagaggtggagggagagagagaagga -aagggagggagaggaagagagggagagagagaaggagggagagagatggagagaggtgga -gggagagagagaaggaaagggagg------------------------------------ ----------------------------------------------gagagagagagacag -acagcttcacacagacataaaacatctgctgttcaggatcccagctg ->p:HG002_2_chr20:61744188-61744654 -cggagactgtgtggttggaaaggagccaaccagagagtggggaggcgatggagagaataa -cagagaggaaggcaggtgcagggagacagcaaaggagagggagaagagaatgagagaggg -atggggagaaagagagaagagaggtggagagagacaggaaaggagagggagggagaggaa -gagagggagagagagaaggagggagagagatggaaagaggtggagggagagagagaagga -aagggagggaga------------------------------------------------ ------------------------------------------------------------- ----------------------------------------------gagagagacagacag -acagcttcacacagacataaaacatctgctgttcaggatcccagctg ->ref_chr20:61744188-61744654 -cggagactgtgtggttggaaaggagccaaccagagagtggggaggcgatggagagaataa -cagagaggaaggcaggtgcagggagacagcaaaggagagggagaagagaatgagagaggg -atggggagaaagagagaagagaggtggagagagacaggaaaggagagggagggagaggaa -gagagggagagagagaaggagggagagagatggaaagaggtggagggagagagagaagga -aagggagggagaggaagagagggagagagagaaggagggagagagatggagagaggtgga -gggagagagagaaggaaagggaggggagaggaagagagggagagagagaaggagggagag -agatggagagaggtggagggagagagagaaggaaagggagggagagagagagacagacag -acagcttcacacagacataaaacatctgctgttcaggatcccagctg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_5da6f8de8558383cf2418710d689c789.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_5da6f8de8558383cf2418710d689c789.msa deleted file mode 100644 index 2bb93277..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_5da6f8de8558383cf2418710d689c789.msa +++ /dev/null @@ -1,190 +0,0 @@ ->syndip_1_chr20:63948514-63948758 -aaacgaaggacgctcaccgccatgcgcctcggtgtgaggagggaggcgtgtgtgagaggg -agggg-cgtgtgtgagaggga-ggggcgtgtgtgagagggaggggcgtgtgtgagggagg -ggtgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagaggcagggg --gcgtgtgtgtgaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggg-gcgt -gtgtgagggggggcgtgtgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtga -gggagggggcgtgtgtgagaggg-----------------aggggcgtgtgtgtgaggga -ggggcgtgtgagag-ggagggggcgtgtgtgagaggcaggggcgtgtgtgtgagggaggg -gcgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagggggggcgtgtgtg -agaggtaggggcgtgtgt----gggagggggcgtgtgtgagagggagggggcgtgtgtga -gagggaggggcgtgtgtgagacggaggggcgtgtgtgagagggagggggcgtgtgtgaga -gggagaggcgtgtgtgagagggaggggcgtgtgtgagggagggg---gcgtgtgagaggg -aggggcgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggag -gggcgtgtgtgagggagggggcgtgtgtgagagggaggggcgtgtgagaggg-aggggcg -tgtgtgagagg----------gagggggcgtgtgtgagagggagggggcgtgtgtgagag -ggaggggcgtgtgtgaagggaggggcgtgtgtgagagggagggggcgtgagagggagggg -cgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcg -tgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgt -gtgagggaggggcgtgtgtgagag--------ggagggggcgtgtgagagggagggggcg -tgtgtgagagggagaggcgtgtgtgagaggga-ggggcgtgtgtgagaggcaggggcgtg -tgtgagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagggggcgtgt-- ------------gtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggaggg -ggcgtgtgtgagagggagaggcgtgtgtgagagggagggggcgtgtgtgagagggagagg -cgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagagggaggggcgtg -tgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtg -tgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggag------------ ---ggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggag -ggggcgtgtgtgagaggga-ggggcgtgtgtgagagggaggggcgtgtgtgaagggaggg -gcgtgtgtgagagtgggggcgtgtgtgagttaggggcgtgagaggtaggggcgtgtgtga -gagggaggggcgtgtgtgagagggagggggcgtg-----agagggaggggcgtgtgtgag -agggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagag -ggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagggagg -ggcgtgtgtgagagggagggg-gcgtgtgagagggaggggcgtgtgtgagagggaggggc ---gtgtgagagggaggggcgtgtgtgagaggga-ggggcgtgtgtgagagggaggggcgt -gtgtgagagggaggggcgtgagagggagggggcgtgtgtgagggaggggcgtgtgtgaga -ggg-aggggggcgtgtgtgagagggagggggcgtgtgtgagagggagggggtgtgtgtga -gaccgagggggcgtgtaagggagggggtgtgtgtgagagggaagcgtgtgcacacaccag -ccctaaccatga ->syndip_2_chr20:63948514-63948758 -aaacgaaggacgctcaccgccatgcgcctcggtgtgaggagggaggcgtgtgtgagaggg -agggg-cgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagggagg -ggtgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgaaagggagggg -cgtgtgtgagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgt -gtgagggagggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtga -gagtgggggcgtgtgtgagggggggcgtgtgtgagagggagggggcgtgtgtgagaggta -ggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggg -gcgtgtgtggggggggcgtgtgtgag-gggggggcgtgtgtgagagggagggggcgtgtg -agagggaggggcgtgtgtgagagggagggggcgtgtgtgtgaggga-ggggcgtgtgtga -gagggaggggcgtgtgtga---agggaggggtgtgtgtgagagtgggggcgtgtgtgaga -ggg--------gcgtgagaggtaggggcgtgtgtgagagggaggggtgtgtgtgagaggg -aggggcgtgtgtgagaggga-ggggcgtgtgtgag-ggagggggcgtgtgtgagagggag -gggcgtgtgtgagggagggggcgtgtgtgagagggaggggcgtgtgtgagagtgggggcg -tgtgtgggggggcgtgtgtgagggggggcgtgtgtgagaggta-ggggcgtgtgtgagag -ggaggggcgtgtgtg-agggaggggcgtgtgtgagaggcaggggcgtgtgtggggggggg -cgtgtgt--gaggggggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcg -tgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgt -gtggggggggcgtgtgtgaggggggcgtgtgagagggaggggcgtgtgtggggaggggcg -tgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtg -tgtgagagggaggggcgtgtgtgaagggaggggtgtgtgtgagagtgggggcgtgtgtga -gagttaggggcgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtgaggga-gg -ggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagggg -cgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgcgagagggaggggcgtg -tgtgagagggagggggcgtgtgtgag-ggagggggcgtgtgtgagagggaggggcgtgtg -agag-ggagggggcgtgtgtgagaggcaggggcgtgtgtgtgagggaggggcgtgagagg -gaggggcgtgtgtga---gggggggcgtgtgtgagaggtaggggcgtgtgtgagagggag -ggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagggagggg -gcgtgt-------------------------------gtgagagggaggggcgtgtgtga -gagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagggggcgtgtgtgag -agggaggggcgtgtgtga-agggaggggcgtgtgtgagagtgggggcgtgtgtgagaggg -----------gcgtgagaggtaggggcgtgtgtgagagggagggg-gcgtgagagggagg -ggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggc -gtgtgtgagaggcaggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgt -gt---------------gtgagagggaaggggcgtgtgagagggaggggcgtgtgtgaga -ggg-aggggcgtgtgtgaga---gggaggggcgtgtgtgagagggagggggtgtgtgtga -gaccgagggggcgtgtaagggagggggtgtgtgtgagagggaagcgtgtgcacacaccag -ccctaaccatga ->p:HG002_1_chr20:63948514-63948758 -aaacgaaggacgctcaccgccatgcgcctcggtgtgaggagggaggcgtgtgtgagaggg -agggg-cgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagggagg -ggtgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgaaagggagggg -cgtgtgtgagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgt -gtgagggagggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtga -gagtgggggcgtgtgtgagggggggcgtgtgtgagagggagggggcgtgtgtgagaggta -ggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggg -gcgtgtgtggggggggcgtgtgtgag-gggggggcgtgtgtgagagggagggggcgtgtg -agagggaggggcgtgtgtgagagggagggggcgtgtgtgtgaggga-ggggcgtgtgtga -gagggaggggcgtgtgtga---agggaggggtgtgtgtgagagtgggggcgtgtgtgaga -ggg--------gcgtgagaggtaggggcgtgtgtgagagggaggggtgtgtgtgagaggg -aggggcgtgtgtgagaggga-ggggcgtgtgtgag-ggagggggcgtgtgtgagagggag -gggcgtgtgtgagggagggggcgtgtgtgagagggaggggcgtgtgtgagagtgggggcg -tgtgtgggggggcgtgtgtgagggggggcgtgtgtgagaggta-ggggcgtgtgtgagag -ggaggggcgtgtgtg-agggaggggcgtgtgtgagaggcaggggcgtgtgtggggggggg -cgtgtgt--gaggggggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcg -tgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgt -gtggggggggcgtgtgtgaggggggcgtgtgagagggaggggcgtgtgtggggaggggcg -tgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtg -tgtgagagggaggggcgtgtgtgaagggaggggtgtgtgtgagagtgggggcgtgtgtga -gagttaggggcgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtgaggga-gg -ggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagggg -cgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgcgagagggaggggcgtg -tgtgagagggagggggcgtgtgtgag-ggagggggcgtgtgtgagagggaggggcgtgtg -agag-ggagggggcgtgtgtgagaggcaggggcgtgtgtgtgagggaggggcgtgagagg -gaggggcgtgtgtga---gggggggcgtgtgtgagaggtaggggcgtgtgtgagagggag -ggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagggagggg -gcgtgt-------------------------------gtgagagggaggggcgtgtgtga -gagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagggggcgtgtgtgag -agggaggggcgtgtgtga-agggaggggcgtgtgtgagagtgggggcgtgtgtgagaggg -----------gcgtgagaggtaggggcgtgtgtgagagggagggg-gcgtgagagggagg -ggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggc -gtgtgtgagaggcaggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgt -gt---------------gtgagagggaaggggcgtgtgagagggaggggcgtgtgtgaga -ggg-aggggcgtgtgtgaga---gggaggggcgtgtgtgagagggagggggtgtgtgtga -gaccgagggggcgtgtaagggagggggtgtgtgtgagagggaagcgtgtgcacacaccag -ccctaaccatga ->p:HG002_2_chr20:63948514-63948758 -aaacgaaggacgctcaccgccatgcgcctcggtgtgaggagggaggcgtgtgtgagaggg -agggg-cgtgtgtgagaggga-ggggcgtgtgtgagagggaggggcgtgtgtgagggagg -ggtgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagaggcagggg --gcgtgtgtgtgaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggg-gcgt -gtgtgagggggggcgtgtgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtga -gggagggggcgtgtgtgagaggg-----------------aggggcgtgtgtgtgaggga -ggggcgtgtgagag-ggagggggcgtgtgtgagaggcaggggcgtgtgtgtgagggaggg -gcgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagggggggcgtgtgtg -agaggtaggggcgtgtgt----gggagggggcgtgtgtgagagggagggggcgtgtgtga -gagggaggggcgtgtgtgagacggaggggcgtgtgtgagagggagggggcgtgtgtgaga -gggagaggcgtgtgtgagagggaggggcgtgtgtgagggagggg---gcgtgtgagaggg -aggggcgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggag -gggcgtgtgtgagggagggggcgtgtgtgagagggaggggcgtgtgagaggg-aggggcg -tgtgtgagagg----------gagggggcgtgtgtgagagggagggggcgtgtgtgagag -ggaggggcgtgtgtgaagggaggggcgtgtgtgagagggagggggcgtgagagggagggg -cgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcg -tgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgt -gtgagggaggggcgtgtgtgagag--------ggagggggcgtgtgagagggagggggcg -tgtgtgagagggagaggcgtgtgtgagaggga-ggggcgtgtgtgagaggcaggggcgtg -tgtgagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagggggcgtgt-- ------------gtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggaggg -ggcgtgtgtgagagggagaggcgtgtgtgagagggagggggcgtgtgtgagagggagagg -cgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagagggaggggcgtg -tgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtg -tgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggag------------ ---ggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggag -ggggcgtgtgtgagaggga-ggggcgtgtgtgagagggaggggcgtgtgtgaagggaggg -gcgtgtgtgagagtgggggcgtgtgtgagttaggggcgtgagaggtaggggcgtgtgtga -gagggaggggcgtgtgtgagagggagggggcgtg-----agagggaggggcgtgtgtgag -agggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagag -ggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagggagg -ggcgtgtgtgagagggagggg-gcgtgtgagagggaggggcgtgtgtgagagggaggggc ---gtgtgagagggaggggcgtgtgtgagaggga-ggggcgtgtgtgagagggaggggcgt -gtgtgagagggaggggcgtgagagggagggggcgtgtgtgagggaggggcgtgtgtgaga -ggg-aggggggcgtgtgtgagagggagggggcgtgtgtgagagggagggggtgtgtgtga -gaccgagggggcgtgtaagggagggggtgtgtgtgagagggaagcgtgtgcacacaccag -ccctaaccatga ->ref_chr20:63948514-63948758 -aaacgaaggacgctcaccgccatgcgcctcggtgtgaggagggaggcgtgtgtgagaggg -aggggatgtgtgtgagagggagggggcgtgtgtga------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------gagggaggggcgtgtgtgaga -gggaaggggcgtgtgtgaga---gggaggggcgtgtgtgagagggagggggtgtgtgtga -gaccgagggggcgtgtaagggagggggtgtgtgtgagagggaagcgtgtgcacacaccag -ccctaaccatga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_5ef7bf139cfea5c5f9a9bf2277bc98b2.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_5ef7bf139cfea5c5f9a9bf2277bc98b2.msa deleted file mode 100644 index 39ab79ea..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_5ef7bf139cfea5c5f9a9bf2277bc98b2.msa +++ /dev/null @@ -1,210 +0,0 @@ ->syndip_1_chr20:63027856-63029240 -cttattaatagggtaatttatgcgggtgcctgcgcaccgggacggaccagcatctatcat -ggctgttttgcgtttcttgatttcacgatgtctgttgtgtgctcaggcccctcctctcca -aggtcccagctgtccttgccctgttccctgtgaagagtgaagaaccaacgcgggcgggga -gtggaccggtggggagagggccggtggggagagggccggtggggagaggaccggtgggga -gggggccggtggagagggggccggtggggagggggccggtggggagaggaccggtgggga -ggggccggtggggagggggccggtggggagaggaccggtggggaggggccggtggggagg -gggccggtggggagaggaccggtggggaggggccggtggggagggggccggcggggaggg -ggccggcggggagggtgccggtggggagtggtctggtggggagggggccggtggggaggg -ggcccgcggggaggggccggtggggagggggcctgcggggagggggccggcggggaggga -ccggtggggaggggccggtggggtggggccggtggagagggggccggtggggagggggcc -ggcggggagtggtttggtggggaggaggctggtgaagtagcgtcaggtgcgggcctggcg -tcggcgagtcaagtcgagctgatccagggccttctttctgcagcttcatcaggttctcaa -ttagcggagggcgctggcggtggaggagggcattagccgtgcctgctctcgggctctgcc -tgccagagtgccctcatgtggcatgagattaaggctcagcctctttcctgacagcaggtt -ttccatttttcttctccttcctcctctcctggcaacaaagtcctttgctgggctgggggg -tctccactctgatccacttccctccttcctgcctccctcccacgccctggaaaccccggc -ccatgactctttccctgagggggccgcccgcagcctctcccccatgggggctttgctctg -ggcaccccctttcccccggggcgggtggggcagcggccgggactcaggaagatggtggcc -cagtggggctctctccttgggtgtgtgggagcggagtcccctcgctcttctgggatagaa -cgctccgttgagctccccaaactgctcccgtgccgagctctgggggagggagtctgttca -gagacggtgcagtcctaccttttagaaggtacgcctgcctttttaagcagctcagctctc -aacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctga -gcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactccaa -acgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc -ctccgtgtgcaggtcccccgggcctccgcctctccgtgtgcaggtcccccgggcctccgc -gcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctcc -gcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct -ccgcgtctgtgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggc -ctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgg -gcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtccccc -gggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtccc -ccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtc -ccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcagg -tcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgca -ggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtg -caggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtg -tgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccg -tgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctc -cgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcc -tccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg -cctccgtgtgcaggtcccccgggcctccgcgtctgtg ->syndip_2_chr20:63027856-63029240 -cttattaatagggtaatttatgcgggtgcctgcgcaccgggacggaccagcatctatcat -ggctgttttgcgtttcttgatttcacgatgtctgttgtgtgctcaggcccctcctctcca -aggtcccagctgtccttgccctgttccctgtgaagagtgaagaaccaacgcgggcgggga -gtggaccggtggggagagggccggtggggagaggaccggtggggag-gggccggtggaga -gggggccggtggggagggggccggcggggag----------------------------- -tggtttggtggggagggggccggtggggagggggcctgcggggaggggccggtggggag- -----------------------------ggggccggtggggagggggccggcggggaggg -ggccggcggggagggggccggcggggagtggtctggtggggagggggccggtggggaggg -ggccggcggggag----------------------------------------------- -----------ggggccggcggggaggggccggtggggagtggtctggtggggagggggcc ----------------ggtggggaggaggctggtgaagtagcgtcaggtgcgggcctggcg -tcggcgagtcaagtcgagctgatccagggccttctttctgcagcttcatcaggttctcaa -ttagcggagggcgctggcggtggaggagggcattagccgtgcctgctctcgggctctgcc -tgccagagtgccctcatgtggcatgagattaaggctcagcctctttcctgacagcaggtt -ttccatttttcttctccttcctcctctcctggcaacaaagtcctttgctgggctgggggg -tctccactctgatccacttccctccttcctgcctccctcccacgccctggaaaccccggc -ccatgactctttccctgagggggccgcccgcagcctctcccccatgggggctttgctctg -ggcaccccctttcccccggggcgggtggggcagcggccgggactcaggaagatggtggcc -cagtggggctctctccttgggtgtgtgggagcggagtcccctcgctcttctgggatagaa -cgctccgttgagctccccaaactgctcccgtgccgagctctgggggagggagtctgttca -gagacggtgcagtcctaccttttagaaggtacgcctgcctttttaagcagctcagctctc -aacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctga -gcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactccaa -acgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc -ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc -gcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctcc -gcgcctccgtgtgcaggtcccccgggcctccgcgtctgtg-------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------- ->p:HG002_1_chr20:63027856-63029240 -cttattaatagggtaatttatgcgggtgcctgcgcaccgggacggaccagcatctatcat -ggctgttttgcgtttcttgatttcacgatgtctgttgtgtgctcaggcccctcctctcca -aggtcccagctgtccttgccctgttccctgtgaagagtgaagaaccaacgcgggcgggga -gtggaccggtggggagagggccggtggggagaggaccggtggggag-gggccggtggaga -gggggccggtggggagggggccggcggggag----------------------------- -tggtttggtggggagggggccggtggggagggggcctgcggggaggggccggtggggag- -----------------------------ggggccggtggggagggggccggcggggaggg -ggccggcggggagggggccggcggggagtggtctggtggggagggggccggtggggaggg -ggccggcggggag----------------------------------------------- -----------ggggccggcggggaggggccggtggggagtggtctggtggggagggggcc ----------------ggtggggaggaggctggtgaagtagcgtcaggtgcgggcctggcg -tcggcgagtcaagtcgagctgatccagggccttctttctgcagcttcatcaggttctcaa -ttagcggagggcgctggcggtggaggagggcattagccgtgcctgctctcgggctctgcc -tgccagagtgccctcatgtggcatgagattaaggctcagcctctttcctgacagcaggtt -ttccatttttcttctccttcctcctctcctggcaacaaagtcctttgctgggctgggggg -tctccactctgatccacttccctccttcctgcctccctcccacgccctggaaaccccggc -ccatgactctttccctgagggggccgcccgcagcctctcccccatgggggctttgctctg -ggcaccccctttcccccggggcgggtggggcagcggccgggactcaggaagatggtggcc -cagtggggctctctccttgggtgtgtgggagcggagtcccctcgctcttctgggatagaa -cgctccgttgagctccccaaactgctcccgtgccgagctctgggggagggagtctgttca -gagacggtgcagtcctaccttttagaaggtacgcctgcctttttaagcagctcagctctc -aacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctga -gcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactccaa -acgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc -ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc -gcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctcc -gcgcctccgtgtgcaggtcccccgggcctccgcgtctgtg-------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------- ->p:HG002_2_chr20:63027856-63029240 -cttattaatagggtaatttatgcgggtgcctgcgcaccgggacggaccagcatctatcat -ggctgttttgcgtttcttgatttcacgatgtctgttgtgtgctcaggcccctcctctcca -aggtcccagctgtccttgccctgttccctgtgaagagtgaagaaccaacgcgggcgggga -gtggaccggtggggagagggccggtggggagaggaccggtggggag-gggccggtggaga -gggggccggtggggagggggccggtggggagggggccggtggggagaggaccggtgggga -ggggccggtggggagggggccggtggggagaggaccggtggggaggggccggtggggagg -gggccggtggggagaggaccggtggggaggggccggtggggagggggccggcggggaggg -ggccggcggggagggtgccggtggggagtggtctggtggggagggggccggtggggaggg -ggcccgcggggaggggccggtggggagggggcctgcggggagggggccggcggggagggg -ccggtggggaggggccggtggggtggggccggtggggagggggccggtgggg-gggggcc -tgcggggagtggtttggtggggaggaggctggtgaagtagcgtcaggtgcgggcctggcg -tcggcgagtcaagtcgagctgatccagggccttctttctgcagcttcatcaggttctcaa -ttagcggagggcgctggcggtggaggagggcattagccgtgcctgctctcgggctctgcc -tgccagagtgccctcatgtggcatgagattaaggctcagcctctttcctgacagcaggtt -ttccatttttcttctccttcctcctctcctggcaacaaagtcctttgctgggctgggggg -tctccactctgatccacttccctccttcctgcctccctcccacgccctggaaaccccggc -ccatgactctttccctgagggggccgcccgcagcctctcccccatgggggctttgctctg -ggcaccccctttcccccggggcgggtggggcagcggccgggactcaggaagatggtggcc -cagtggggctctctccttgggtgtgtgggagcggagtcccctcgctcttctgggatagaa -cgctccgttgagctccccaaactgctcccgtgccgagctctgggggagggagtctgttca -gagacggtgcagtcctaccttttagaaggtacgcctgcctttttaagcagctcagctctc -aacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctga -gcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactccaa -acgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc -ctccgtgtgcaggtcccccgggcctccgcctctccgtgtgcaggtcccccgggcctccgc -gcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctcc -gcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct -ccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggc -ctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgg -gcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtccccc -gggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtccc -ccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtc -ccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcagg -tcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgca -ggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtg -caggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtg -tgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccg -tgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctc -cgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcc -tccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg -cctccgtgtgcaggtcccccgggcctccgcgtctgtg ->ref_chr20:63027856-63029240 -cttattaatagggtaatttatgcgggtgcctgcgcaccgggacggaccagcatctatcat -ggctgttttgcgtttcttgatttcacgatgtctgttgtgtgctcaggcccctcctctcca -aggtcccagctgtccttgccctgttccctgtgaagagtgaagaaccaacgcgggcgggga -gtggaccggtggggagagggccggtggggagaggaccggtggggag-gggccggtggaga -gggggccggtggggagggggccggcggggag----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------tggtttggtggggaggaggctggtgaagtagcgtcaggtgcgggcctggcg -tcggcgagtcaagtcgagctgatccagggccttctttctgcagcttcatcaggttctcaa -ttagcggagggcgctggcggtggaggagggcattagccgtgcctgctctcgggctctgcc -tgccagagtgccctcatgtggcatgagattaaggctcagcctctttcctgacagcaggtt -ttccatttttcttctccttcctcctctcctggcaacaaagtcctttgctgggctgggggg -tctccactctgatccacttccctccttcctgcctccctcccacgccctggaaaccccggc -ccatgactctttccctgagggggccgcccgcagcctctcccccatgggggctttgctctg -ggcaccccctttcccccggggcgggtggggcagcggccgggactcaggaagatggtggcc -cagtggggctctctccttgggtgtgtgggagcggagtcccctcgctcttctgggatagaa -cgctccgttgagctccccaaactgctcccgtgccgagctctgggggagggagtctgttca -gagacggtgcagtcctaccttttagaaggtacgcctgcctttttaagcagctcagctctc -aacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctga -gcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactccaa -acgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc -ctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgc -gcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctcc -gcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct -ccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggc -ctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtg---------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_5fe415c2ed2e0f32531960dfdeaef1de.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_5fe415c2ed2e0f32531960dfdeaef1de.msa deleted file mode 100644 index 350d7480..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_5fe415c2ed2e0f32531960dfdeaef1de.msa +++ /dev/null @@ -1,125 +0,0 @@ ->syndip_1_chr20:61783403-61784839 -gtctccctcccttcctttcctccaatacgtgagagaaatgtaatcccagttccttgggac -agttctcgaggccctcagatgtcctgtgcccccgaaagaaatgtaatcccagttccttgg -gatagttctcaaggccctccgatatcctgtgcccctgggagaaatgtaagcccagttcct -caggacagttctcgaggccctcagatgtcctgtgctcccaggagaatataagcctagttc -ctcgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccag -ttccttgggacagttctccgggccctcagatgtcctgtgcccccgggagaaatgtaagcc -tagttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaa -tcccagttcctcgggacagttctcaaggccctcagatgtcctgtgcccccaagagaaatg -taatcccagttccttgggacagttctcaaggccctccgatatcctgtgcccccaggagaa -tgtaagcccagttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaggag -aatgtaagcccagttccttgggacagttctcgaggccctcaggtgtcttgtgcccccaag -agaaatgtaatcccagttcctcgggacagttctcaaggccctcagatgtcctgtgccccc -aagagaaatgtaatcccagttccttgggacagttctcaaggccctccgatatcctgtgcc -cccaggagaatgtaagcccagttcctcgggacagttctcgaggccctcaggtgtcttgtg -cccccaggagaatgtaagcccagttccttgggacagttctcgaggccctcaggtgtcttg -tgcccccaagagaaatgtaatcccagttcctcgggacagttctcaaggccctccgatatc -ctgtgcccccaggagaatgtaatcccagttcctcgggacagttctcgaggccctcaggtg -tcttgtgcccccaagagaaatgtaatcccagttcctcgggacagttctccaggccctccg -atatcctgtgcccccaggagaatgtaagcccagttcctcgggacagttctcgaggccctc -agatgtcctgtgcccccaagagaaatgtaatcccagttcctcgggacagttctcaaggcc -ctccgatatcctgtgcccccaggagaatgtaag--------------------------- -------------------------------------cccagttcctcgggacagttctcc -aggccctccgatatcctgtgcccccaggagaatgtaagcccagttcctcggaacagttct -ccaggccctcagatgtcctgtgcccccggggcctcatcagacattaagcatgcagtc ->syndip_2_chr20:61783403-61784839 -gtctccctcccttcctttcctccaatacgtgagagaaatgtaatcccagttccttgggac -agttctcgaggccctcagatgtcctgtgcccccgaaagaaatgtaatcccagttccttgg -gatagttctcaaggccctccgatatcctgtgcccctgggagaaatgtaagcccagttcct -caggacagttctcgaggccctcagatgtcctgtgctcccaggagaatataagcctagttc -ctcgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccag -ttccttgggacagttctccgggccctcagatgtcctgtgcccccgggagaaatgtaagcc -tagttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaa -tcccagttccttgggacagttctcgaggccctcagatgtcctgtgcccccgggagaaatg -taagcctagttcctcgggacagttctcaaggccctccgatatcctgtgcccccaggagaa -tgtaagcccagttcctc------------------------------------------- --------------------gggacagttctcgaggccctcaggtgtcttgtgcccccaag -agaaatgtaatcccagttcctcgggacagttctcaaggccctcagatgtcctgtgccccc -aagagaaatgtaatcccagttccttgggacagttctcaaggccctccgatatcctgtgcc -cccaggagaatgtaagcccagttcctcgggacagttctcgaggccctcaggtgtcttgtg -cccccaggagaatgtaagcccagttccttgggacagttctcgaggccctcaggtgtcttg -tgcccccaagagaaatgtaatcccagttcctcgggacagttctcaaggccctccgatatc -ctgtgcccccaggagaatgtaagcccagttcctcgggacagttctcgaggccttcaggtg -tcttgtgcccccaagagaaatgtaatcccagttcctcggaacagttctccaggccctcag -atgtcctgtgcccccaagaga--------------------------------------- ------------------------------------------------------------- --------------------------aatgtaat--------------------------- -------------------------------------cccagttcctcgggacagttctcc -aggccctccgatatcctgtgcccccaggagaatgtaagcccagttcctcggaacagttct -ccaggccctcagatgtcctgtgcccccggggcctcatcagacattaagcatgcagtc ->p:HG002_1_chr20:61783403-61784839 -gtctccctcccttcctttcctccaatacgtgagagaaatgtaatcccagttccttgggac -agttctcgaggccctcagatgtcctgtgcccccgaaagaaatgtaatcccagttccttgg -gatagttctcaaggccctccgatatcctgtgcccctgggagaaatgtaagcccagttcct -caggacagttctcgaggccctcagatgtcctgtgctcccaggagaatataagcctagttc -ctcgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccag -ttccttgggacagttctccgggccctcagatgtcctgtgcccccgggagaaatgtaagcc -tagttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaa -tcccagttccttgggacagttctcgaggccctcagatgtcctgtgcccccgggagaaatg -taagcctagttcctcgggacagttctcaaggccctccgatatcctgtgcccccaggagaa -tgtaagcccagttcctc------------------------------------------- --------------------gggacagttctcgaggccctcaggtgtcttgtgcccccaag -agaaatgtaatcccagttcctcgggacagttctcaaggccctcagatgtcctgtgccccc -aagagaaatgtaatcccagttccttgggacagttctcaaggccctccgatatcctgtgcc -cccaggagaatgtaagcccagttcctcgggacagttctcgaggccctcaggtgtcttgtg -cccccaggagaatgtaagcccagttccttgggacagttctcgaggccctcaggtgtcttg -tgcccccaagagaaatgtaatcccagttcctcgggacagttctcaaggccctccgatatc -ctgtgcccccaggagaatgtaagcccagttcctcgggacagttctcgaggccttcaggtg -tcttgtgcccccaagagaaatgtaatcccagttcctcggaacagttctccaggccctcag -atgtcctgtgcccccaagaga--------------------------------------- ------------------------------------------------------------- --------------------------aatgtaat--------------------------- -------------------------------------cccagttcctcgggacagttctcc -aggccctccgatatcctgtgcccccaggagaatgtaagcccagttcctcggaacagttct -ccaggccctcagatgtcctgtgcccccggggcctcatcagacattaagcatgcagtc ->p:HG002_2_chr20:61783403-61784839 -gtctccctcccttcctttcctccaatacgtgagagaaatgtaatcccagttccttgggac -agttctcgaggccctcagatgtcctgtgcccccgaaagaaatgtaatcccagttccttgg -gatagttctcaaggccctccgatatcctgtgcccctgggagaaatgtaagcccagttcct -caggacagttctcgaggccctcagatgtcctgtgctcccaggagaatataagcctagttc -ctcgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccag -ttccttgggacagttctccgggccctcagatgtcctgtgcccccgggagaaatgtaagcc -tagttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaa -tcccagttcctcgggacagttctcaaggccctcagatgtcctgtgcccccaagagaaatg -taatcccagttccttgggacagttctcaaggccctccgatatcctgtgcccccaggagaa -tgtaagcccagttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaggag -aatgtaagcccagttccttgggacagttctcgaggccctcaggtgtcttgtgcccccaag -agaaatgtaatcccagttcctcgggacagttctcaaggccctcagatgtcctgtgccccc -aagagaaatgtaatcccagttccttgggacagttctcaaggccctccgatatcctgtgcc -cccaggagaatgtaagcccagttcctcgggacagttctcgaggccctcaggtgtcttgtg -cccccaggagaatgtaagcccagttccttgggacagttctcgaggccctcaggtgtcttg -tgcccccaagagaaatgtaatcccagttcctcgggacagttctcaaggccctccgatatc -ctgtgcccccaggagaatgtaatcccagttcctcgggacagttctcgaggccctcaggtg -tcttgtgcccccaagagaaatgtaatcccagttcctcgggacagttctccaggccctccg -atatcctgtgcccccaggagaatgtaagcccagttcctcgggacagttctcgaggccctc -agatgtcctgtgcccccaagagaaatgtaatcccagttcctcgggacagttctcaaggcc -ctccgatatcctgtgcccccaggagaatgtaag--------------------------- -------------------------------------cccagttcctcgggacagttctcc -aggccctccgatatcctgtgcccccaggagaatgtaagcccagttcctcggaacagttct -ccaggccctcagatgtcctgtgcccccggggcctcatcagacattaagcatgcagtc ->ref_chr20:61783403-61784839 -gtctccctcccttcctttcctccaatacgtgagagaaatgtaatcccagttccttgggac -agttctcgaggccctcagatgtcctgtgcccccgaaagaaatgtaatcccagttccttgg -gatagttctcaaggccctccgatatcctgtgcccctgggagaaatgtaagcccagttcct -caggacagttctcgaggccctcagatgtcctgtgctcccaggagaatataagcctagttc -ctcgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccag -ttccttgggacagttctccgggccctcagatgtcctgtgcccccgggagaaatgtaagcc -tagttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaa -tcccagttcctcgggacagttctcaaggccctcagatgtcctgtgcccccaagagaaatg -taatcccagttccttgggacagttctcaaggccctccgatatcctgtgcccccaggagaa -tgtaagcccagttcctcgggacagttctcgaggccctcaggtgtcttgtgcccccaggag -aatgtaagcccagttccttgggacagttctcgaggccctcaggtgtcttgtgcccccaag -agaaatgtaatcccagttcctcgggacagttctcaaggccctcagatgtcctgtgccccc -aagagaaatgtaatcccagttccttgggacagttctcaaggccctccgatatcctgtgcc -cccaggagaatgtaagcccagttcctcgggacagttctcgaggccctcaggtgtcttgtg -cccccaggagaatgtaagcccagttccttgggacagttctcgaggccctcaggtgtcttg -tgcccccaagagaaatgtaatcccagttcctcgggacagttctcaaggccctccgatatc -ctgtgcccccaggagaatgtaatcccagttcctcgggacagttctcgaggccctcagatg -tcctgtgcccccaagagaaatgtaatcccagttcctcgggacagttctcaaggccctccg -atatcctgtgcccccaggagaatgtaagcccagttcctcgggacagttctcgaggccctc -aggtgtcttgtgcccccaagagaaatgtaatcccagttcctcgggacagttctccaggcc -ctccgatatcctgtgcccccaggagaatgtaagcccagttcctcgggacagttctcgagg -ccctcagatgtcctgtgcccccaagagaaatgtaatcccagttcctcgggacagttctca -aggccctccgatatcctgtgcccccaggagaatgtaagcccagttcctcggaacagttct -ccaggccctcagatgtcctgtgcccccggggcctcatcagacattaagcatgcagtc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_609908891cda9ec01ececd161f2b1453.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_609908891cda9ec01ececd161f2b1453.msa deleted file mode 100644 index 9dd55ccf..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_609908891cda9ec01ececd161f2b1453.msa +++ /dev/null @@ -1,80 +0,0 @@ ->syndip_1_chr20:62360200-62360812 -tcaggaaagtgggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcaga -caggtggacagatggatggaaacaaggaataaagggtgggtgctgcataggtaggggggt -gggtgggtggatggatgggtaggggtgggtgggtggatacgttgggggtgggtgggtggg -tgggtcagcaggcagagggatgggataggataggtgggtgggtgggtggatagggagggg -gtggggtgggtgcataggtaggggggtggatgggtcagcaggcagcgggatgggatagga -taggtgggtgggtggagggatagatgggtggtgggtgggtggagggatagatgggtgggt -gggtgggtagaaggataggtaggtgggtgggtgggtggatggataggtggatgggtgggt -ggaggaatagatgggtgggtgggtgggtgggtggatggataggtgggtgggtgggtggag -ggatagatgggtgggtgggtgggtggagggatagatgggtggtgggtgggtggagggata -gatgggtggatgggtgggtagaaggataggta---ggtgggtgggtgggtggatggatag -gtgggtgggtgggtggaggaata--------gatgggtgggtggatgggtgggtggaggg -atagatgggtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttc -ccaggtggagtggaaagggttcctcttccctccgtatcattttacagttggtgaaactga -ggctgtgagaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaa -aag ->syndip_2_chr20:62360200-62360812 -tcaggaaagtgggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcaga -caggtggacagatggatggaaacaaggaataaagggtgggtgctgcataggtaggggggt -gggtgggtggatggatgggtaggggtgggtgggtggatacgttgggggtgggtgggtggg -tgggtcagcaggcagagggatgggataggataggtgggtgggtggagggatagatgggt- ------------------------------------------------------------- ---ggtgggtgggtggagggataga-------tgggtgggtggagggatagatgggtggat -gggtgggtagaaggataggtaggtgggtgggtgggtggatggataggtggatgggtgggt -ggaggaatagatgggtg------------------------------------------- ------------------------------------------------------------- ------------------------------------ggtgggtgggtgggtggatggatag -gtgggtgggtgggtggaggaata--------gatgggtgggtggatgggtgggtggaggg -atagatgggtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttc -ccaggtggagtggaaagggttcctcttccctccgtatcattttacagttggtgaaactga -ggctgtgagaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaa -aag ->p:HG002_1_chr20:62360200-62360812 -tcaggaaagtgggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcaga -caggtggacagatggatggaaacaaggaataaagggtgggtgctgcataggtaggggggt -gggtgggtggatggatgggtaggggtgggtgggtggatacgttgggggtgggtgggtggg -tgggtcagcaggcagagggatgggataggataggtgggtgggtggagggatgggtg---- ------------------------------------------------------------- ---agtgggtgggtggagggatagatgggtggtgggtgggtggagggatagatgggtgg-t -gggtgggtggagggatagatgggtgggtgggtgggtggagggatagatgg---------- ---aggaa----------------------------------------------------- ------------------------------------------------------------- ----------------------------------gtggtgggtgggtggagggatagatgg -gtggatgggtgggtagaaggataggtaggtgggtgggtgggtggatgggtgggtggaggg -atagatgggtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttc -ccaggtggagtggaaagggttcctcttccctccgtatcattttacagttggtgaaactga -ggctgtgagaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaa -aag ->p:HG002_2_chr20:62360200-62360812 -tcaggaaagtgggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcaga -caggtggacagatggatggaaacaaggaataaagggtgggtgctgcataggtaggggggt -gggtgggtggatggatgggtaggggtgggtgggtggatacgttgggggtgggtgggtggg -tgggtcagcaggcagagggatgggataggataggtgggtgggtggagggatgggtgagtg -ggtgggtggagggatagatgggtgggtggatgggtcagcaggcagcgggatgggatagga -taggtgggtgggtggagggatagatgggtggtgggtgggtggagggatagatgggtgggt -gggtgggtagaaggataggtaggtgggtgggtgggtggatggataggtggatgggtgggt -ggaggaatagatgggtgggtgggtgggtgggtggatggataggtgggtgggtgggtggag -ggataga--------tgggtgggtggagggatagatgggtggtgggtgggtggagggata -gatgggtgggtgggtgggtggagggatagatgggtggtgggtgggtggagggatagatgg -gtggatgggtgggtagaaggataggtaggtgggtgggtgggtggatgggtgggtggaggg -atagatgggtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttc -ccaggtggagtggaaagggttcctcttccctccgtatcattttacagttggtgaaactga -ggctgtgagaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaa -aag ->ref_chr20:62360200-62360812 -tcaggaaagtgggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcaga -caggtggacagatggatggaaacaaggaataaagggtgggtgctgcataggtaggggggt -gggtgggtggatggatgggtaggggtgggtgggtggatacgttgggggtgggtgggtggg -tgggtcagcaggcagagggatgggataggataggtgggtgggtggagggatgggtg---- ------------------------------------------------------------- ---agtgggtgggtggagggatagatgggtggtgggtgggtggagggatagatgggtgg-t -gggtgggtggagggatagatgggtgggtgggtgggtggagggatagatgg---------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------gtggtgggtgggtggagggatagatgg -gtggatgggtgggtagaaggataggtaggtgggtgggtgggtggatgggtgggtggaggg -atagatgggtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttc -ccaggtggagtggaaagggttcctcttccctccgtatcattttacagttggtgaaactga -ggctgtgagaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaa -aag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_61682d6886e27e7851c5474cd512f7cb.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_61682d6886e27e7851c5474cd512f7cb.msa deleted file mode 100644 index 7eb10128..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_61682d6886e27e7851c5474cd512f7cb.msa +++ /dev/null @@ -1,70 +0,0 @@ ->syndip_1_chr20:61561920-61562503 -tgatggcagtaatgctgtgtctggaaatcctgaccccagggctcccagagagagagaggg -accttcgtgtggagaggtggaccccagggctcccggagagagagaggggccttcgtgtgg -agaggtggaccccagggctcccggagagagagaggggcctccgtgtggagaggtggaccc -cagggctcccggagagagggacttccgtgtggagaggtggaccccagggctcccggagag -agagagggacctccctgagagagagagggacctccctgtggagaggtggaccccagggct -cccggagagagagagggacctccctgtggagaggtggaccccagggctcccagagagaga -gagggaccttcgtgtggagaggtggaccccagggctcccggagagagagagggacctccg -tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg -gaccccagggctcccggagagagggacctccgtgtggagagctggaccccagggctcccg -gagagagagagggacctccgtgtggagaggtggaccccagggctcccggagagagagagg -gacctccgtgtggagaggtggaccccagggctcccggagagagagagggaccttcgtgtg -gagaggtggaccccaggactcccggagagagagaggggcctccgtgtgcagaggtggttt -gtcgcttctttcatcttcaggacagtc ->syndip_2_chr20:61561920-61562503 -tgatggcagtaatgctgtgtctggaaatcctgaccccagggctcccagagagagagaggg -accttcgtgtggagaggtggaccccagggctcccggagagagagaggggccttcgtgtgg -agaggtggaccccagggctcccggagagagagaggggcctccgtgtggagaggtggaccc -cagggctcccggagagagggacctccg--------------------------------- -------------------------------------tgtggagaggtggaccccagggct -cccggagagagagagggacctccctgtggagaggtggaccccagggctcccagagagaga -gagggaccttcgtgtggagaggtggaccccagggctcccgga------------------ ------------------------------------------------------------- -----------------gagagagggacctccgtgtggagaggtggaccccagggctcccg -gagagagagagggacctctgtgtggagaggtggaccccagggctcccggagagagagagg -gacctccgtgtggagaggtggaccccagggctcccggagagagagggggaccttcgtgtg -gagaggtggaccccaggactcccggagagagagaggggcctccgtgtgcagaggtggttt -gtcgcttctttcatcttcaggacagtc ->p:HG002_1_chr20:61561920-61562503 -tgatggcagtaatgctgtgtctggaaatcctgaccccagggctcccagagagagagaggg -accttcgtgtggagaggtggaccccagggctcccggagagagagaggggccttcgtgtgg -agaggtggaccccagggctcccggagagagagaggggcctccgtgtggagaggtggaccc -cagggctcccggagagagggacctccg--------------------------------- -------------------------------------tgtggagaggtggaccccagggct -cccggagagagagagggacctccctgtggagaggtggaccccagggctcccagagagaga -gagggaccttcgtgtggagaggtggaccccagggctcccgga------------------ ------------------------------------------------------------- -----------------gagagagggacctccgtgtggagaggtggaccccagggctcccg -gagagagagagggacctctgtgtggagaggtggaccccagggctcccggagagagagagg -gacctccgtgtggagaggtggaccccagggctcccggagagagagggggaccttcgtgtg -gagaggtggaccccaggactcccggagagagagaggggcctccgtgtgcagaggtggttt -gtcgcttctttcatcttcaggacagtc ->p:HG002_2_chr20:61561920-61562503 -tgatggcagtaatgctgtgtctggaaatcctgaccccagggctcccagagagagagaggg -accttcgtgtggagaggtggaccccagggctcccggagagagagaggggccttcgtgtgg -agaggtggaccccagggctcccggagagagagaggggcctccgtgtggagaggtggaccc -cagggctcccggagagagggacttccgtgtggagaggtggaccccagggctcccggagag -agagagggacctccctgagagagagagggacctccctgtggagaggtggaccccagggct -cccggagagagagagggacctccctgtggagaggtggaccccagggctcccagagagaga -gagggaccttcgtgtggagaggtggaccccagggctcccggagagagagagggacctccg -tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg -gaccccagggctcccggagagagggacctccgtgtggagagctggaccccagggctcccg -gagagagagagggacctccgtgtggagaggtggaccccagggctcccggagagagagagg -gacctccgtgtggagaggtggaccccagggctcccggagagagagagggaccttcgtgtg -gagaggtggaccccaggactcccggagagagagaggggcctccgtgtgcagaggtggttt -gtcgcttctttcatcttcaggacagtc ->ref_chr20:61561920-61562503 -tgatggcagtaatgctgtgtctggaaatcctgaccccagggctcccagagagagagaggg -accttcgtgtggagaggtggaccccagggctcccggagagagagaggggccttcgtgtgg -agaggtggaccccagggctcccggagagagagaggggcctccgtgtggagaggtggaccc -cagggctcccggagagagggacctccg--------------------------------- -------------------------------------tgtggagaggtggaccccagggct -cccggagagagagagggacctccctgtggagaggtggaccccagggctcccagagagaga -gagggaccttcgtgtggagaggtggaccccagggctcccgga------------------ ------------------------------------------------------------- -----------------gagagagggacctccgtgtggagaggtggaccccagggctcccg -gagagagagagggacctctgtgtggagaggtggaccccagggctcccggagagagagagg -gacctccgtgtggagaggtggaccccagggctcccggagagagagggggaccttcgtgtg -gagaggtggaccccaggactcccggagagagagaggggcctccgtgtgcagaggtggttt -gtcgcttctttcatcttcaggacagtc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_649eba2ef8750104fb27abd65692f3e5.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_649eba2ef8750104fb27abd65692f3e5.msa deleted file mode 100644 index f47c531d..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_649eba2ef8750104fb27abd65692f3e5.msa +++ /dev/null @@ -1,60 +0,0 @@ ->syndip_1_chr20:62360310-62360702 -gtaggggggtgggtgggtggatggatgggtaggggtgggtgggtggatacgttgggggtg -ggtgggtgggtgggtcagcaggcagagggatgggataggataggtgggtgggtgggtgga -tagggagggggtggggtgggtgcataggtaggggggtggatgggtcagcaggcagcggga -tgggataggataggtgggtgggtggagggatagatgggtggtgggtgggtggagggatag -atgggtgggtgggtgggtagaaggataggtaggtgggtgggtgggtggatggataggtgg ---------atgggtgggtggaggaatagatgggtgggtgggtgggtgggtggatggatag -gtgggtgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatgggtgg -tgggtgggtggagggatagatgggtggatgggtgggtagaaggataggta---ggtgggt -gggtgggtggatggataggtgggtgggtgggtggaggaata--------gatgggtgggt -ggatgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatgggtgggt -gggtggagggaccacttcccaggtggagtgg ->syndip_2_chr20:62360310-62360702 -gtaggggggtgggtgggtggatggatgggtaggggtgggtgggtggatacgttgggggtg -ggtgggtgggtgggtcagcaggcagagggatgggataggataggtgggtgggtggaggga -tagatgggt--------------------------------------------------- -------------ggtgggtgggtggagggataga-------tgggtgggtggagggatag -atgggtggatgggtgggtagaaggataggtaggtgggtgggtgggtggatggataggtgg ---------atgggtgggtggaggaatagatgggtgggtgggtgggtgggtggatggatag -gtgggtgggtgggtggaggaataga--------tgggtgggtgga--------------- -tgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatg---ggtgggt -gggtggaggga------------------------------------------------- ------------------------------------------------------------- ------------ccacttcccaggtggagtgg ->p:HG002_1_chr20:62360310-62360702 -gtaggggggtgggtgggtggatggatgggtaggggtgggtgggtggatacgttgggggtg -ggtgggtgggtgggtcagcaggcagagggatgggataggataggtgggtgggtggaggga -tgggtg------------------------------------------------------ -------------agtgggtgggtggagggatagatgggtggtgggtgggtggagggatag -atgggtgg-tgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatgg -aggaagtggtgggtgggtggagggatagatgggtggatgggtgggtagaaggataggtag -gtggg----------------------------tgggtgggtgga--------------- -tgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatg---ggtgggt -gggtggaggga------------------------------------------------- ------------------------------------------------------------- ------------ccacttcccaggtggagtgg ->p:HG002_2_chr20:62360310-62360702 -gtaggggggtgggtgggtggatggatgggtaggggtgggtgggtggatacgttgggggtg -ggtgggtgggtgggtcagcaggcagagggatgggataggataggtgggtgggtggaggga -tgggtgagtgggtgggtggagggatagatgggtgggtggatgggtcagcaggcagcggga -tgggataggataggtgggtgggtggagggatagatgggtggtgggtgggtggagggatag -atgggtgggtgggtgggtagaaggataggtaggtgggtgggtgggtggatggataggtgg ---------atgggtgggtggaggaatagatgggtgggtgggtgggtgggtggatggatag -gtgggtgggtgggtggagggataga--------tgggtgggtggagggatagatgggtgg -tgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatgggtggtgggt -gggtggagggatagatgggtggatgggtgggtagaaggataggtaggtgggtgggtgggt -ggatgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatgggtgggt -gggtggagggaccacttcccaggtggagtgg ->ref_chr20:62360310-62360702 -gtaggggggtgggtgggtggatggatgggtaggggtgggtgggtggatacgttgggggtg -ggtgggtgggtgggtcagcaggcagagggatgggataggataggtgggtgggtggaggga -tgggtg------------------------------------------------------ -------------agtgggtgggtggagggatagatgggtggtgggtgggtggagggatag -atgggtgg-tgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatgg ------gtggtgggtgggtggagggatagatgggtggatgggtgggtagaaggataggtag -gtggg----------------------------tgggtgggtgga--------------- -tgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatg---ggtgggt -gggtggaggga------------------------------------------------- ------------------------------------------------------------- ------------ccacttcccaggtggagtgg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_64bd5493de28d5b1d9fb1fbb35d289ef.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_64bd5493de28d5b1d9fb1fbb35d289ef.msa deleted file mode 100644 index 2974329a..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_64bd5493de28d5b1d9fb1fbb35d289ef.msa +++ /dev/null @@ -1,85 +0,0 @@ ->syndip_1_chr20:34235550-34236413 -accaggcaacagaagtatatctttcttagcacgataacaatcatggccaaaacaaaaagt -ttgtttgtgatgttgaaagaaaagtctggctgggcatggtagcgcatgcctgtggcccct -actactcaggaggcaggggtgggaggattgctagagcccaggaagtcgtggctgaagtgg -gctcatgataatgccactgcactccagcctgtgtgacagagtgagactctgagaaagaag -aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaggaaggaagg -aaggaaggaaggaaggaaggaaggaaggaagggaaggaaggaaggaaggaaggaagcggg -agggagggaagaaggaaggaaggaggagggagggaagaatgaaggaaggaaggaaggagg -gaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggaggga -gggaagaaggaaggaggagggagggagggaagcaggaaagaaggaaggaaggagaaagag -agaa--agagagagaagaagaaagagaaagaaacagaaaaggaaggaaggagagagagaa -agaaagagaaagagaaggaaggaaggagaaagaaaggaaaaggaaaggaaaggagtggaa -aggaaaggagaggaaaggagaaaggagggagggagggaaaagaaagaaagaaagaaaagg -ctaaacctgactatgatattgaatttactgctagctctaggtggtttaaatgattcaaga -atcatggccatggctgggcgcagtggctcacgcctataatcccagcactttgggaggccg -aagcgggcagatcacctgaggtcaggagtttgagaccagcctggccaacatggtgaaacc -ctgtctctactaaaaatacacaaaaaaattagccaggcatggtggtg ->syndip_2_chr20:34235550-34236413 -accaggcaacagaagtatatctttcttagcacgataacaatcatggccaaaacaaaaagt -ttgtttgtgatgttgaaagaaaagtctggctgggcatggtagcgcatgcctgtggcccct -actactcaggaggcaggggtgggaggattgctagagcccaggaagtcgtggctgaagtgg -gctcatgataatgccactgcactccagcctgtgtgacagagtgagactctgagaaagaag -aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaggaaggaagg -aaggaaggaaggaaggaaggaaggaaggaagggaaggaaggaaggaaggaaggaagcggg -agggagggaagaaggaaggaaggaggagggagggaagaatgaaggaaggaaggaaggagg -gaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggaggga -gggaagaaggaaggaggagggagggagggaagcaggaaagaaggaaggaaggagaaagag -agaa--agagagagaagaagaaagagaaagaaacagaaaaggaaggaaggagagagagaa -agaaagagaaagagaaggaaggaaggagaaagaaaggaaaaggaaaggaaaggagtggaa -aggaaaggagaggaaaggagaaaggagggagggagggaaaagaaagaaagaaagaaaagg -ctaaacctgactatgatattgaatttactgctagctctaggtggtttaaatgattcaaga -atcatggccatggctgggcgcagtggctcacgcctataatcccagcactttgggaggccg -aagcgggcagatcacctgaggtcaggagtttgagaccagcctggccaacatggtgaaacc -ctgtctctactaaaaatacacaaaaaaattagccaggcatggtggtg ->p:HG002_1_chr20:34235550-34236413 -accaggcaacagaagtatatctttcttagcacgataacaatcatggccaaaacaaaaagt -ttgtttgtgatgttgaaagaaaagtctggctgggcatggtagcgcatgcctgtggcccct -actactcaggaggcaggggtgggaggattgctagagcccaggaagtcgtggctgaagtgg -gctcatgataatgccactgcactccagcctgtgtgacagagtgagactctgagaaagaag -aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaggaaggaagg -aaggaaggaaggaaggaaggaaggaaggaagggaaggaaggaaggaaggaaggaagcggg -agggagggaagaaggaaggaaggaggagggagggaagaatgaaggaaggaaggaaggagg -gaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggaggga -gggaagaaggaaggaggagggagggagggaagcaggaaagaaggaaggaaggagaaagag -agaa--agagagagaagaagaaagagaaagaaacagaaaaggaaggaaggagagagagaa -agaaagagaaagagaaggaaggaaggagaaagaaaggaaaaggaaaggaaaggagtggaa -aggaaaggagaggaaaggagaaaggagggagggagggaaaagaaagaaagaaagaaaagg -ctaaacctgactatgatattgaatttactgctagctctaggtggtttaaatgattcaaga -atcatggccatggctgggcgcagtggctcacgcctataatcccagcactttgggaggccg -aagcaggcagatcacctgaggtcaggagtttgagaccagcctggccaacatggtgaaacc -ctgtctctactaaaaatacacaaaaaaattagccaggcatggtggtg ->p:HG002_2_chr20:34235550-34236413 -accaggcaacagaagtatatctttcttagcacgataacaatcatggccaaaacaaaaagt -ttgtttgtgatgttgaaagaaaagtctggctgggcatggtagcgcatgcctgtggcccct -actactcaggaggcaggggtgggaggattgctagagcccaggaagtcgtggctgaagtgg -gctcatgataatgccactgcactccagcctgtgtgacagagtgagactctgagaaagaag -aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaggaaggaagg -aaggaaggaaggaaggaaggaaggaaggaagggaaggaaggaaggaaggaaggaagcggg -agggagggaagaaggaaggaaggaggagggagggaagaatgaaggaaggaaggaaggagg -gaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggaggga -gggaagaaggaaggaggagggagggagggaagcaggaaagaaggaaggaaggagaaagag -agaa--agagagagaagaagaaagagaaagaaacagaaaaggaaggaaggagagagagaa -agaaagagaaagagaaggaaggaaggagaaagaaaggaaaaggaaaggaaaggagtggaa -aggaaaggagaggaaaggagaaaggagggagggagggaaaagaaagaaagaaagaaaagg -ctaaacctgactatgatattgaatttactgctagctctaggtggtttaaatgattcaaga -atcatggccatggctgggcgcagtggctcacgcctataatcccagcactttgggaggccg -aagcaggcagatcacctgaggtcaggagtttgagaccagcctggccaacatggtgaaacc -ctgtctctactaaaaatacacaaaaaaattagccaggcatggtggtg ->ref_chr20:34235550-34236413 -accaggcaacagaagtatatctttcttagcacgataacaatcatggccaaaacaaaaagt -ttgtttgtgatgttgaaagaaaagtctggctgggcatggtagcgcatgcctgtggcccct -actactcaggaggcaggggtgggaggattgctagagcccaggaagtcgtggctgaagtgg -gctcatgataatgccactgcactccagcctgtgtgacagagtgagactctgagaaagaag -aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaggaagg -aaggaaggaaggaaggaaaggaaggaaggaaggaaggaaggaaggaagga---------- ----------------------------------------------aaggaaggaaggaag -gaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggaggga -gggaaga--------------------------aggaaagaaggaaggaaggagaaagag -agaaagagagagagaagaagaaagagaaagaaacagaaaaggaaggaaggagagagagaa -agaaagagaaagagaaggaaggaaggaaggagaaag--aaaggaaaggaaaggagtggaa -aggaaaggagaggaaaggagaaaggagggagggagggaaaagaaagaaagaaagaaaagg -ctaaacctgactatgatattgaatttactgctagctctaggtggtttaaatgattcaaga -atcatggccatggctgggcgcagtggctcacgcctataatcccagcactttgggaggccg -aagcgggcagatcacctgaggtcaggagtttgagaccagcctggccaacatggtgaaacc -ctgtctctactaaaaatacacaaaaaaattagccaggcatggtggtg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_655ba1ce8cc5f4582bf8ee89955a3142.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_655ba1ce8cc5f4582bf8ee89955a3142.msa deleted file mode 100644 index e1b878ec..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_655ba1ce8cc5f4582bf8ee89955a3142.msa +++ /dev/null @@ -1,80 +0,0 @@ ->syndip_1_chr20:57090672-57091411 -gaaacgaacgcactcaggtgctcctgccacacacactcacagttgcacaagctggtgcag -ctccagacccacacacctccaccaccacacactccaccatgcacacacacctccacgcac -acacacctccacccgcacacacacacaccttcaccaccacacactccacccacacacacc -tccacccacacacctcca----------------cccacacacacctccgcccacacaca -cctccgcccacacacacctccacccacacacacctccacccacacacctccgcccacaca -cacctccgccctcacacacctccacccacacacacctccacccacacacgcctccacccg -cacacacctccaccaccacacacacctccacccacacacaccacccatgcacacacctcc -acccacacacacacacctccacccacacacacctccacccacacgccacccatgcacaca -cctccacccacacacacacacaccacccacccacacacacctccacccgcacacacctcc -accaccacacacacctccacccacacacaccacccatgcacacacctccacccacacaca -cacacacctccacccacacacacctccacccacacacacctccacccacacacacacacc -tccacccacccacacacacctccacccgcacacacctccaccaccacacacatctccacc -cacacacaccacccatgtgcacacctccactggcacacaccacccatgcacacacctcca -ctggcacgcactactccacctgcgtgcgcctcccacctgcgttcaccctccacctgtgtt -cgctcccacccactcatgcctctccacccgcaaaagtgtgagtgctgaggctgggac ->syndip_2_chr20:57090672-57091411 -gaaacgaacgcactcaggtgctcctgccacacacactcacagttgcacaagctggtgcag -ctccagacccacacacctccaccaccacacactccgccatgcacacacacctccacgcac -acacacctccacccgcacacacacacaccttcaccaccacacactccacccacacacacc -tccacccacacacctccacccacacacacctccgcccacacacacctccgcccacacaca -cctccgcccacacacacctccacccacacacacctccgcccacacacctccgcccacaca -cacctccgccctcacacacctccacccacacacacctccacccacacacgcctccacccg -cacacacctccaccaccacacacacctccacccacacacaccacccatgcacacacctcc -acccacacacacacacctccacccacacaca-----------------------cacaca -cctccacccacacaca-------------------------------------------- -----------------ccacccacacacaccacccatgcacacacctccacccaca---- ------------------------------------------------------------- -----------cacacacacctccacccgcacacacctccaccaccacacacatctccacc -cacacacaccacccatgtgcacacctccactggcacacaccacccatgcacacacctcca -ctggcacgcactactccacctgcgtgcgcctcccacctgcgttcaccctccacctgtgtt -cgctcccacccactcatgcctctccacccgcaaaagtgtgagtgctgaggctgggac ->p:HG002_1_chr20:57090672-57091411 -gaaacgaacgcactcaggtgctcctgccacacacactcacagttgcacaagctggtgcag -ctccagacccacacacctccaccaccacacactccgccatgcacacacacctccacgcac -acacacctccacccgcacacacacacaccttcaccaccacacactccacccacacacacc -tccacccacacacctccacccacacacacctccgcccacacacacctccgcccacacaca -cctccgcccacacacacctccacccacacacacctccgcccacacacctccgcccacaca -cacctccgccctcacacacctccacccacacacacctccacccacacacgcctccacccg -cacacacctccaccaccacacacacctccacccacacacaccacccatgcacacacctcc -acccacacacacacacctccacccacacaca-----------------------cacaca -cctccacccacacaca-------------------------------------------- -----------------ccacccacacacaccacccatgcacacacctccacccaca---- ------------------------------------------------------------- -----------cacacacacctccacccgcacacacctccaccaccacacacatctccacc -cacacacaccacccatgtgcacacctccactggcacacaccacccatgcacacacctcca -ctggcacgcactactccacctgcgtgcgcctcccacctgcgttcaccctccacctgtgtt -cgctcccacccactcatgcctctccacccgcaaaagtgtgagtgctgaggctgggac ->p:HG002_2_chr20:57090672-57091411 -gaaacgaacgcactcaggtgctcctgccacacacactcacagttgcacaagctggtgcag -ctccagacccacacacctccaccaccacacactccaccatgcacacacacctccacgcac -acacacctccacccgcacacacacacaccttcaccaccacacactccacccacacacacc -tccacccacacacctcca----------------cccacacacacctccgcccacacaca -cctccgcccacacacacctccacccacacacacctccacccacacacctccgcccacaca -cacctccgccctcacacacctccacccacacacacctccacccacacacgcctccacccg -cacacacctccaccaccacacacacctccacccacacacaccacccatgcacacacctcc -acccacacacacacacctccacccacacacacctccacccacacgccacccatgcacaca -cctccacccacacacacacacaccacccacccacacacacctccacccgcacacacctcc -accaccacacacacctccacccacacacaccacccatgcacacacctccacccacacaca -cacacacctccacccacacacacctccacccacacacacctccacccacacacacacacc -tccacccacccacacacacctccacccgcacacacctccaccaccacacacatctccacc -cacacacaccacccatgtgcacacctccactggcacacaccacccatgcacacacctcca -ctggcacgcactactccacctgcgtgcgcctcccacctgcgttcaccctccacctgtgtt -cgctcccacccactcatgcctctccacccgcaaaagtgtgagtgctgaggctgggac ->ref_chr20:57090672-57091411 -gaaacgaacgcactcaggtgctcctgccacacacactcacagttgcacaagctggtgcag -ctccagacccacacacctccaccaccacacactccgccatgcacacacacctccacgcac -acacacctccacccgcacacacacacaccttcaccaccacacactccacccacacacacc -tccacccacacacctccacccacacacacctccgcccacacacacctccgcccacacaca -cctccgcccacacacacctccacccacacacacctccgcccacacacctccgcccacaca -cacctccgccctcacacacctccacccacacacacctccacccacacacgcctccacccg -cacacacctccaccaccacacacacctccacccacacacaccacccatgcacacacctcc -acccacacacacacacctccacccacacaca-----------------------cacaca -cctccacccacacaca-------------------------------------------- -----------------ccacccacacacaccacccatgcacacacctccacccaca---- ------------------------------------------------------------- -----------cacacacacctccacccgcacacacctccaccaccacacacatctccacc -cacacacaccacccatgtgcacacctccactggcacacaccacccatgcacacacctcca -ctggcacgcactactccacctgcgtgcgcctcccacctgcgttcaccctccacctgtgtt -cgctcccacccactcatgcctctccacccgcaaaagtgtgagtgctgaggctgggac diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_663a3106c58f22627d09337763c8c49f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_663a3106c58f22627d09337763c8c49f.msa deleted file mode 100644 index 54aec1f1..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_663a3106c58f22627d09337763c8c49f.msa +++ /dev/null @@ -1,170 +0,0 @@ ->syndip_1_chr20:14861737-14862941 -gccatcttggcattgagctgggcacttttaggtggaatgacctcccgaagggctaacccc -atctggcacctcttgacaacgttccttcttaatatcagtggctctcctgctgctggccaa -gcaggaccccaaggtccactgggatgtacatacttatggtattatgctctgcaatacttg -tgggggctgtggaatgcacacttccaaagtgaaataggacattggaggttttatatataa -atatatatatatatttatatatatatttatatatatatatatttatatatatttatatat -atatttatatatatatttatatatatatttatatatatatttatatatatatttatatat -atatttatatatatatttatatatatatttatatatatttatatatatttatatatattt -ttatatatttttatatatataaatatataaaaatatatataaatatataaaaatatataa -aaatatataaatatatataaatatataaatatatataaatatatataaatatatatttat -atataaatatatataaatatatatttatacataaatatatataaatatatatttatacat -aaatatataaatatatataatatatataaatatatattatacataaatatataaatatat -attatacataaatatataaatatatataaatatatataaatatatatttatacataaata -tataaatatatatataaatatatataaatatatataaatatatatataaatatatatata -aatatatataaatatatatataaatatatatataaatatatataaatatatataaatata -tatataaatatatataaatatatataaatatatatttatatattaatatataaatatata -taaatatatatttatatattaatatataaatatatatatattaatatatataaatatata -taaatatatatttatatattaatatatatatattaatatatatatatttatatattaata -tatatatttatatattaatatatataaatatattactatgtatatttatatatatttata -taaatatatataaatatatgtaaatatatatataaaaatatatattaatatataaaatat -atatataaatataaataaatatatatataaatatatataaataaatatatatataaatat -atataaataaatatataaatatatataaatatatatataaatatatataaatatatataa -atatatataaaaatatatataaatatatatataaatatatataaatatatatataaatat -atatataaatatatatataaatatatataaatatatatataaatatatataaatatatat -ataattatatataaatatatataaatatatataaatatatatataaatatatataaatat -atataaatatatataaatatatatataaatatatataaatatatatatataaatatatat -aaatatatatataaatatatataaatatatatatataaatatatataaatatatatataa -atatatataaatatatatataaatataaatatatatgtataaatatatatataaatataa -atatatatgtataaatatatatataaatatatatatataaatatatatatacatatataa -atatatatataaatatatataaaaatatatatatatatatttttttaatagagaggatga -agaccaaagcagtgagttccacctaagctggcccttgccttttgtctaacaggaaaccca -gtccttcctaatgggcacagaattttcagagaagagagcagaagttgagttggcatacct -actgtagtgagggattttgaacaatgagctgtacattcctatatgggagccaaactttta -gttaaatagtaatacaaaaatgc ->syndip_2_chr20:14861737-14862941 -gccatcttggcattgagctgggcacttttaggtggaatgacctcccgaagggctaacccc -atctggcacctcttgacaacgttccttcttaatatcagtggctctcctgctgctggccaa -gcaggaccccaaggtccactgggatgtacatacttatggtattatgctctgcaatacttg -tgggggctgtggaatgcacacttccaaagtgaaataggacattggaggttttatatataa -atatatatatatatatttatatatatatttatatatatatatttatatatatt------- --------------------------------------------------------tatat -atatttatatatatatttttatatatatttatatatatt--tatatatttatatatattt -atatatatttttatatatataaatatataaaa---------------------------- ------------------------------------------------------------- ---------atatataaatatatataaatatataaatatatataaatatatatttatacat -aaatatataaatatatataatatatataaatatatattatacataaatatataaatatat -attatacataaatatataaatatatataaatatatataaatatatatttatacataaata -tataaatatat------atatatataaatatatataa----------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------a -tatatatttatatattaatatatataaatatattactatgtatatttatatatatttata -taa--atatataaatatatgtaaatatatatataaaaatatatattaatatataaaa--- -------atatatatataaatatatatataaatatatataaataaatatatataaatatat -atataaat--atatataaatatatataaatatatatataaatatatataaatatatataa -atatatatataaatatatatataaatatatataaatatatataaataaatatataaatat -atatataaatatatataaatatatatataaatatatataaatatatatataaatatatat -aaatatatatataaatatatataaat--------atatatataaatatatatataaatat -atataaatatatataaatatatatatataaatatatataaatatatatataaatataaat -atatataaatatataaaaatatatatataaatataaatatatataaatatatatgtataa -atatatatataaatataaatatatataaatatatatatataaatatatatataaatatat -ataaatatatataaaaatatatataaatatatatataaatatatatataaatatatataa -atatatatataaatatatataaaaatatatatatatttttttttttaatagagaggatga -agaccaaagcagtgagttccacctaagctggcccttgccttttgtctaacaggaaaccca -gtccttcctaatgggcacagaattttcagagaagagagcagaagttgagttggcatacct -actgtagtgagggattttgaacaatgagctgtacattcctatatgggagccaaactttta -gttaaatagtaatacaaaaatgc ->p:HG002_1_chr20:14861737-14862941 -gccgtcttggcattgagctgggcacttttaggtggaatgacctcccgaagggctaacccc -atctggcacctcttgacaacgttccttcttaatatcagtggctctcctgctgctggccaa -gcaggaccccaaggtccactgggatgtacatacttatggtattatgctctgcaatacttg -tgggggctgtggaatgcacacttccaaagtgaaataggacattggaggttttatatataa -atatatatatatatatttatatatatatttatatatatatatttatatatatt------- --------------------------------------------------------tatat -atatttatatatatatttttatatatatttatatatatt--tatatatttatatatattt -atatatatttttatatatataaatatataaaa---------------------------- ------------------------------------------------------------- ---------atatataaatatatataaatatataaatatatataaatatatatttatacat -aaatatataaatatatataatatatataaatatatattatacataaatatataaatatat -attatacataaatatataaatatatataaatatatataaatatatatttatacataaata -tataaatatat------atatatataaatatatataa----------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------a -tatatatttatatattaatatatataaatatattactatgtatatttatatatatttata -taa--atatataaatatatgtaaatatatatataaaaatatatattaatatataaaa--- -------atatatatataaatatatatataaatatatataaataaatatatataaatatat -atataaat--atatataaatatatataaatatatatataaatatatataaatatatataa -atatatatataaatatatatataaatatatataaatatatataaataaatatataaatat -atatataaatatatataaatatatatataaatatatataaatatatatataaatatatat -aaatatatatataaatatatataaat--------atatatataaatatatatataaatat -atataaatatatataaatatatatatataaatatatataaatatatatataaatataaat -atatataaatatataaaaatatatatataaatataaatatatataaatatatatgtataa -atatatatataaatataaatatatataaatatatatatataaatatatatataaatatat -ataaatatatataaaaatatatataaatatatatataaatatatatataaatatatataa -atatatatataaatatatataaaaatatatatatatttttttttttaatagagaggatga -agaccaaagcagtgagttccacctaagctggcccttgccttttgtctaacaggaaaccca -gtccttcctaatgggcacagaattttcagagaagagagcagaagttgagttggcatacct -actgtagtgagggattttgaacaatgagctgtacattcctatatgggagccaaactttta -gttaaatagtaatacaaaaatgc ->p:HG002_2_chr20:14861737-14862941 -gccgtcttggcattgagctgggcacttttaggtggaatgacctcccgaagggctaacccc -atctggcacctcttgacaacgttccttcttaatatcagtggctctcctgctgctggccaa -gcaggaccccaaggtccactgggatgtacatacttatggtattatgctctgcaatacttg -tgggggctgtggaatgcacacttccaaagtgaaataggacattggaggttttatatataa -atatatatatatatttatatatatatttatatatatatatatttatatatatttatatat -atatttatatatatatttatatatatatttatatatatatttatatatatatttatatat -atatttatatatatatttatatatatatttatatatatttatatatatttatatatattt -ttatatatttttatatatataaatatataaaaatatatataaatatataaaaatatataa -aaatatataaatatatataaatatataaatatatataaatatatataaatatatatttat -atataaatatatataaatatatatttatacataaatatatataaatatatatttatacat -aaatatataaatatatataatatatataaatatatattatacataaatatataaatatat -attatacataaatatataaatatatataaatatatataaatatatatttatacataaata -tataaatatatatataaatatatataaatatatataaatatatatataaatatatatata -aatatatataaatatatatataaatatatatataaatatatataaatatatataaatata -tatataaatatatataaatatatataaatatatatttatatattaatatataaatatata -taaatatatatttatatattaatatataaatatatatatattaatatatataaatatata -taaatatatatttatatattaatatatatatattaatatatatatatttatatattaata -tatatatttatatattaatatatataaatatattactatgtatatttatatatatttata -taaatatatataaatatatgtaaatatatatataaaaatatatattaatatataaaatat -atatataaatataaataaatatatatataaatatatataaataaatatatatataaatat -atataaataaatatataaatatatataaatatatatataaatatatataaatatatataa -atatatataaaaatatatataaatatatatataaatatatataaatatatatataaatat -atatataaatatatatataaatatatataaatatatatataaatatatataaatatatat -ataattatatataaatatatataaatatatataaatatatatataaatatatataaatat -atataaatatatataaatatatatataaatatatataaatatatatatataaatatatat -aaatatatatataaatatatataaatatatatatataaatatatataaatatatatataa -atatatataaatatatatataaatataaatatatatgtataaatatatatataaatataa -atatatatgtataaatatatatataaatatatatatataaatatatatatacatatataa -atatatatataaatatatataaaaatatatatatatatatttttttaatagagaggatga -agaccaaagcagtgagttccacctaagctggcccttgccttttgtctaacaggaaaccca -gtccttcctaatgggcacagaattttcagagaagagagcagaagttgagttggcatacct -actgtagtgagggattttgaacaatgagctgtacattcctatatgggagccaaactttta -gttaaatagtaatacaaaaatgc ->ref_chr20:14861737-14862941 -gccatcttggcattgagctgggcacttttaggtggaatgacctcccgaagggctaacccc -atctggcacctcttgacaacgttccttcttaatatcagtggctctcctgctgctggccaa -gcaggaccccaaggtccactgggatgtacatacttatggtattatgctctgcaatacttg -tgggggctgtggaatgcacacttccaaagtgaaataggacattggaggttttatatataa -atatatatatatatatttatatatatatttatatatatatatttatatatatt------- --------------------------------------------------------tatat -atatttatatatatatttatat-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------atatataaatatatataaatatataaatatatataaatatatatttatacat -aaatatataaatatata---------------------------atatatataaatatat -attatacataaatatataaatatatataaatatatataaatatatatttatacataaata -tataaatatat------atatatataaatatatataa----------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------a -tatatatttatatattaatatatataaatatattactatgtatatttatatatatttata -taaatatatataaatatatgtaaatatatatataaaaatatatattaatatataaaa--- -------atatatat--------------------------ataaatatatataaatatat -atataaat--atatataaat---------------------------------------- ------------------------------------------------------------- -------------------atatatatataaatatatataaatatatatataaatatatat -aaatatatatataaatatatataaat--------atatatatataaatatatataa---- -------------------atatatatataaatatatataaatatatatataaatataaat -atatataaatatataaaaatatatatataaatataaatatatataaatatatatgtataa -atatatatataaatataaatatatataaatatatatatataaatatatatataaat---- ---------------------------atatatatataaatatatatataaatatatataa -atatatatataaatatatataaatatatatatatatatttttttttaatagagaggatga -agaccaaagcagtgagttccacctaagctggcccttgccttttgtctaacaggaaaccca -gtccttcctaatgggcacagaattttcagagaagagagcagaagttgagttggcatacct -actgtagtgagggattttgaacaatgagctgtacattcctatatgggagccaaactttta -gttaaatagtaatacaaaaatgc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_665d55ccf51ea1943f3e8bb50e41c014.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_665d55ccf51ea1943f3e8bb50e41c014.msa deleted file mode 100644 index 26edb0db..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_665d55ccf51ea1943f3e8bb50e41c014.msa +++ /dev/null @@ -1,140 +0,0 @@ ->syndip_1_chr20:8661734-8662329 -tgtttaaagcaggccaaatagtactagaggaagcacacagtctctggtgttctagtctta -caaactcaaacttacaagccaacctacgttaagtaattcataacttcagtatttaataaa -tcttcagtgaaaggcaagaggctacacacagtgacagacccagagataaaccctgtgccc -ctagagatttgcactcctcttaaaagtgtatatatatataattatataattatttattat -ataattatatataattatataattatttattatataattatatataattatataattatt -tattatataattatatataa-tatacaattatttattatataattatatataattatata -tttattatatttat-----tatacagttatataataaataattatataattatatataat -tatat-atatataattatata---------ta-attatatataattatataattatatat -aattg-tatataattatttattatataattatatat-----tatttattatataattata -taattata------tattatttattatatattatataattata------taattatatat -tatttattatataatatataattatatattatttattatataattatatattatttatta -t----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----atatattatttattatata----------------------attatatattatgta -ttatataattatataattatatattatgtattatataat----------------tatat -attatgtattatataattatataattatatattatgtattatataattatatattattta -ttatataattatataattatatattatttattatataattatataattatatattattta -ttatataat---------------------tatataattatatattatttattatataat -tatataattatatattattt--------attatataattatatattatttattatataat -tatatattatttattacataaatatatattatttattacataagtatatatcacttatta -tataattgcatataattatttattatataattgcatataa----ttattatataattgta -tatagttatttattatataattg-------------------------tatatagttatt -tattatataattctatata-------attatttattatctaattctatattaaatataat -tatttattatctaattctatattatatataattatttattatataattctatattatata -taattattatataattctatatataattatttattatataattctatacataagtattta -ttatataattatgtatataattatttattatataattatgtataatatgtaattat ->syndip_2_chr20:8661734-8662329 -tgtttaaagcaggccaaatagtactagaggaagcacacagtctctggtgttctagtctta -caaactcaaacttacaagccaacctacgttaagtaattcataacttcagtatttaataaa -tcttcagtgaaaggcaagaggctacacacagtgacagacccagagataaaccctgtgccc -ctagagatttgcactcctcttaaaagtgtatatatatataattatataattatttattat -ataattatatataattatataa---------------------------------ttatt -tattatataatgatatataattatataattatttattatataattatatataattatata -attatttattatataattatatataattatataattatttattatataattatatataat -tatataattatttattatataattatatataattatataattatttattatataattata -tataattatataattatttattatataattatatataattatataatt--atttattata -taattatatataattat--ataattatttattatataattatatataattatataattat -ttattatataattatatataatatacaattatttattatataattatatataatatacaa -ttatttattatataattatatataattatatatttattatatttattatacagttatata -ataaataattatataattatatataattatataattatatataattatatatatataatt -atatgtaattatatataattatataattattatataattgtatataatatataattatat -aattatatattatttattatataatatataattatataattatatattatttattatata -atatataattatataattatatattatttattatataattatatattatttattatatat -attatttattatataattatataattatatattatttattatataattatatattattta -ttatataa-tatataattatatattatttattatataa-tatataattatatattattta -ttatataattatatattatgtattatataatatataattatatattatgtattatataat -tatataattatatattatttattatataattatataattatatattatttattacataat -tatatattatttattacataagtatatattatttattacataagtatatatcacttatta -tataattgtatataattatttattatataattgcatataattatttattatataattgta -tatagttatttattatataattctatatagttatttattatataattctatataattatt -tattatctaattctatattatatataattatttattatctaattctatattaaatataat -tatttattatctaattctatattatatataattatttattatataattctatattatata -taattattatataattctatatataattatttattatataattctatacataagtattta -ttatataattatgtatataattatttattatataattatgtataatatgtaattat ->p:HG002_1_chr20:8661734-8662329 -tgtttaaagcaggccaaatagtactagaggaagcacacagtctctggtgttctagtctta -caaactcaaacttacaagccaacctacgttaagtaattcataacttcagtatttaataaa -tcttcagtgaaaggcaagaggctacacacagtgacagacccagagataaaccctgtgccc -ctagagatttgcactcctcttaaaagtgtatatatatataattatataattatttattat -ataattatatataattatataa---------------------------------ttatt -tattatataattatatataa-tatacaattatttattatataattatatataattatata -tttatttattatataattatatataattatataattatttattatataattatatataat -tatataattatttattatataattatatataattatataattatttattatataattata -tataattatataattatttattatataattatatataattatataatt--atttattata -taattatatataattat--ataattatttattatataattatatataattatataattat -ttattatataattatatataatatacaattatttattatataattatatataatatacaa -ttatttattatataattatatataattatatatttattatatttattatacagttatata -ataaa----tatataattatatataaatatataattatatataattatatatatataatt -atatgtaattatatataattatataattattatataattgtatataatatataattatat -aattatatattatttattatataatatataattatataattatatattatttattatata -atatataattatataattatatattatttattatataattatatattatttattatatat -attatttattatataattatataattatatattatttattatataattatatattattta -ttatataa-tatataattatatattatttattatataa-tatataattatatattattta -ttatataattatatattatgtattatataatatataattatatattatgtattatataat -tatataattatatattatttattatataattatataattatatattatttattacataat -tatatattatttattacataagtatatattatttattacataagtatatatcacttatta -tataattgtatataattatttattatataattgcatataattatttattatataattgta -tatagttatttattatataattctatatagttatatttattatacagttatataataaat -aattatataattatatataattatatattatttattatctaattctatattaaatataat -tatttattatctaattctatattatatataattatttattatataattctatattatata -taattattatataattctatatataattatttattatataattctatacataagtattta -ttatataattatgtatataattatttattatataattatgtataatatgtaattat ->p:HG002_2_chr20:8661734-8662329 -tgtttaaagcaggccaaatagtactagaggaagcacacagtctctggtgttctagtctta -caaactcaaacttacaagccaacctacgttaagtaattcataacttcagtatttaataaa -tcttcagtgaaaggcaagaggctacacacagtgacagacccagagataaaccctgtgccc -ctagagatttgcactcctcttaaaagtgtatatatatataattatataattatttattat -ataattatatataattatataattatttattatataattatatataa-tatacaattatt -tattatataattatatataa-tatacaattatttattatataattatatataattatata -tttattatatttat-----tatacagttatataataaataattatataattatatataat -tatat-atatataattatata---------ta-attatatataattatataattatatat -aattg-tatataattatttattatataattatatat-----tatttattatataattata -taattata------tattatttattatatattatataattata------taattatatat -tatttattatataatatataattatatattatttattatataattatatattatttatta -t----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----atatattatttattatata----------------------attatatattatgta -ttatataattatataattatatattatgtattatataat----------------tatat -attatgtattatataattatataattatatattatgtattatataattatatattattta -ttatataattatataattatatattatttattatataattatataattatatattattta -ttatataat---------------------tatataattatatattatttattatataat -tatataattatatattattt--------attatataattatatattatttattatataat -tatatattatttattacataaatatatattatttattacataagtatatatcacttatta -tataattgcatataattatttattatataattgcatataa----ttattatatatttat- -----tatatttattatacagt---------------------------tatataataaat -aattatataattatatataattatatattatttattatctaattctatattaaatataat -tatttattatctaattctatattatatataattatttattatataattctatattatata -taattattatataattctatatataattatttattatataattctatacataagtattta -ttatataattatgtatataattatttattatataattatgtataatatgtaattat ->ref_chr20:8661734-8662329 -tgtttaaagcaggccaaatagtactagaggaagcacacagtctctggtgttctagtctta -caaactcaaacttacaagccaacctacgttaagtaattcataacttcagtatttaataaa -tcttcagtgaaaggcaagaggctacacacagtgacagacccagagataaaccctgtgccc -ctagagatttgcactcctcttaaaagtgtatatatatataattatataattatttattat -ataattatatataattatataa---------------------------------ttatt -tattatataattatatataa-tatacaattatttattatataattatatataattatata -tttattatatttat-----tatacagttatataataaataattatataattatatataat -tatat-attatttattatctaattctatatta-aatataattatttattatctaattcta -tatta-tatataattatttattatataattctatat-----tatatat--aattattata -taattcta------tat--ataattatttattatataattcta------tacataagtat -ttattatataattatgtata-----taattatttattatataattatgtataatatgtaa -ttat-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_667044cd3ee0f44ef9fdce05209a8ea9.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_667044cd3ee0f44ef9fdce05209a8ea9.msa deleted file mode 100644 index 8077a9d4..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_667044cd3ee0f44ef9fdce05209a8ea9.msa +++ /dev/null @@ -1,110 +0,0 @@ ->syndip_1_chr20:63221280-63222076 -tagccccggtcctgctggtctgcaggcctcagctccctccctgcttttccaggagttgaa -acagggcctctcctaactccactttgccaagagcctcttctcccactgcagagaactgtc -atctgcctgtaagtaccagtgccaggtgctctggggccgatgtctccgttagccccaagg -tggaggctcagggagcagatgtgagcgtgccttgctcatcgcagtagcttcggac----- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------tgcagggactgcagggattgcagggactgcagggattg -cagggactgcagggattgcagggattgcagggattgcagggattgcagggactgcaggga -ctgcattgctcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgca -ggctctgctacaagaggtgcttactgggctctgctctggtgaggagaggcctcgcctggc -agccagacagagtcccagcagggcaagatgaaaattcggggccctcgttcaaacagcaag -agaaggctctttccttccttccagcgcccctccctgcacctgtgatggtgtttttatttg -ttatttaacgtcatgtgctcttgggcaaggggaggggaaactctcacaggcacctgaacc -tgtccctgtggctccatgca ->syndip_2_chr20:63221280-63222076 -tagccccggtcctgctggtctgcaggcctcagctccctccctgcttttccaggagttgaa -acagggcctctcctaactccactttgccaagagcctcttctcccactgcagagaactgtc -atctgcctgtaagtaccagtgccaggtgctctggggccgatgtctccgttagccccaagg -tggaggctcagggagcagatgtgagcgtgccttgctcatcgcagtagcttcggactgcag -ggattgcagggactgcagggattgcagggattgcagggagtgcagggactgcagggactg -cagggattgcagggactgcagggactgcagggactgcagggactgcagggactgcaggga -ctgcagggattgcagggactgcagggactgcagggattgcagggattgcagggactgcag -ggactgcagggattgcagggactgcagggactgcagggactgcagggactgcagggactg -cagggactgcagggattgcagggattgcagggattgcagggattgcagggactgcaggga -ctgcagggactgcagggactgcagggactgcagggactgcagggattgcagggattgcag -ggattgcagggattgcagggattgcagggactgcagggactgcagggactgcagggactg -cagggattgcagggattgcagggattgcagggattgcagggactgcagggactgcaggga -ttgcagggattgcagggattgcagggattgcagggattgcagggattgcagggactgcag -ggactgcagggactgcagggattgcagggattgcagggattgcagggattgcagggactg -cagggactgcagggattgcagggattgcagggattgcagggattgcagggactgcagggc -ctgcattgctcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgca -ggctctgctacaagaggtgcttactgggctctgctctggtgaggagaggcctcgcctggc -agccagacagagtcccagcagggcaagatgaaaattcggggccctcgttcaaacagcaag -agaaggctctttccttccttccagcgcccctccctgcacctgtgatggtgtttttatttg -ttatttaacgtcatgtgctcttgggcaaggggaggggaaactctcacaggcacctgaacc -tgtccctgtggctccatgca ->p:HG002_1_chr20:63221280-63222076 -tagccccggtcctgctggtctgcaggcctcagctccctccctgcttttccaggagttgaa -acagggcctctcctaactccactttgccaagagcctcttctcccactgcagagaactgtc -atctgcctgtaagtaccagtgccaggtgctctggggccgatgtctccgttagccccaagg -tggaggctcagggagcagatgtgagcgtgccttgctcatcgcagtagcttcggactgcag -ggattgcagggactgcagggattgcagggattgcagggagtgcagggactgcagggactg -cagggattgcagggactgcagggactgcagggactgcagggactgcagggactgcaggga -ctgcagggattgcagggactgcagggactgcagggattgcagggattgcagggactgcag -ggactgcagggattgcagggactgcagggactgcagggactgcagggactgcagggactg -cagggactgcagggattgcagggattgcagggattgcagggattgcagggactgcaggga -ctgcagggactgcagggactgcagggactgcagggactgcagggattgcagggattgcag -ggattgcagggattgcagggattgcagggactgcagggactgcagggactgcagggactg -cagggattgcagggattgcagggattgcagggattgcagggactgcagggactgcaggga -ttgcagggattgcagggattgcagggattgcagggattgcagggattgcagggactgcag -ggactgcagggactgcagggattgcagggattgcagggattgcagggattgcagggactg -cagggactgcagggattgcagggattgcagggattgcagggattgcagggactgcagggc -ctgcattgctcttgcagcaccacccgcctccgtggccaccttcagcagtgagacaatgca -ggctctgctacaagaggtgcttactgggctctgctctggtgaggagaggcctcgcctggc -agccagacagagtcccagcagggcaagatgaaaattcggggccctcgttcaaacagcaag -agaaggctctttccttccttccagcgcccctccctgcacctgtgatggtgtttttatttg -ttatttaacgtcatgtgctcttgggcaaggggaggggaaactctcacaggcacctgaacc -tgtccctgtggctccatgca ->p:HG002_2_chr20:63221280-63222076 -tagccccggtcctgctggtctgcaggcctcagctccctccctgcttttccaggagttgaa -acagggcctctcctaactccactttgccaagagcctcttctcccactgcagagaactgtc -atctgcctgtaagtaccagtgccaggtgctctggggccgatgtctccgttagccccaagg -tggaggctcagggagcagatgtgagcgtgccttgctcatcgcagtagcttcggac----- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------tgcagggactgcagggattgcagggactgcagggattg -cagggactgcagggattgcagggattgcagggattgcagggattgcagggactgcaggga -ctgcattgctcttgcagcaccacccgcctccgtggccaccttcagcagtgagacaatgca -ggctctgctacaagaggtgcttactgggctctgctctggtgaggagaggcctcgcctggc -agccagacagagtcccagcagggcaagatgaaaattcggggccctcgttcaaacagcaag -agaaggctctttccttccttccagcgcccctccctgcacctgtgatggtgtttttatttg -ttatttaacgtcatgtgctcttgggcaaggggaggggaaactctcacaggcacctgaacc -tgtccctgtggctccatgca ->ref_chr20:63221280-63222076 -tagccccggtcctgctggtctgcaggcctcagctccctccctgcttttccaggagttgaa -acagggcctctcctaactccactttgccaagagcctcttctcccactgcagagaactgtc -atctgcctgtaagtaccagtgccaggtgctctggggccgatgtctccgttagccccaagg -tggaggctcagggagcagatgtgagcgtgccttgctcatcgcagtagcttcggactgcag -ggat-------------------------------------------------------- ------------------------------------------------------------- --------------------tgcagggactgcagggattgcagggattgcagggattgcag -ggactgcagggattgcagggactgcagggactgcagggactgcagggactgcagggactg -cagggattgcagggattgcagggattgcagggac-------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------tgcagggattgcagggactgcagggactgcagggattg -cagggactgcagggactgcagggactgcagggattgcagggattgcagggactgcaggga -ctgcattgctcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgca -ggctctgctacaagaggtgcttactgggctctgctctggtgaggagaggcctcgcctggc -agccagacagagtcccagcagggcaagatgaaaattcggggccctcgttcaaacagcaag -agaaggctctttccttccttccagcgcccctccctgcacctgtgatggtgtttttatttg -ttatttaacgtcatgtgctcttgggcaaggggaggggaaactctcacaggcacctgaacc -tgtccctgtggctccatgca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_68fc62a5b88f54811eb9157c4bf9278e.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_68fc62a5b88f54811eb9157c4bf9278e.msa deleted file mode 100644 index f3feedbc..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_68fc62a5b88f54811eb9157c4bf9278e.msa +++ /dev/null @@ -1,85 +0,0 @@ ->syndip_1_chr20:23155368-23156067 -ctagtttagattgtgtggtccaaccccagtcaatgggggaaagacacagaggtagaatct -gcgttaggaataaaaaccgctactctccgttgttctgtgtgcttttgcagtcatgattga -tgcaggcagcacccttctgcagaagtaaattttgccctgcagcacaaaagaggaaggaaa -gcaagggaagggaaggggaggggaggaagggaaggggaggggaggaagggaaggggaggg -gaggaaggcgaggtgaggggaggagaggtgaggggagggggggaggggaggggagggaga -gtgaggaagagagagagaaagggagagaggaaggaaagaagaaaggaaggaaggaaagaa -ggaaggaagggagggagggagggaggaaagaaggaaggaaaggagggaggaagggaggga -aagagagagagaggaaaagagagagaaagagaaagagagaaagagaggaaggaaggaagg -aaggagagagagaaagaaagaaggaaagaggaaggaaggaagaaagaaaagaaagaaaga -aaaaagaaagaaaggaaggagagaaagaaatgaaagagaaagaaagaaagaaagaaagaa -agaaagaaaggagagaaaaaggaaaaacaaagaaagagaaaagaaggagagaaggaaagg -aaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaagaaagaagaaagaaagaaag -aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacaccttggtaatttttg -tgctcttccctggactttggactttgcagccttagggagacagagctctttaatgtacac -tttcccatcaggcactgcatggccaagaacctgcctgca ->syndip_2_chr20:23155368-23156067 -ctagtttagattgtgtggtccaaccccagtcaatgggggaaagacacagaggtagaatct -gcgttaggaataaaaaccgctactctccgttgttctgtgtgcttttgcagtcatgattga -tgcaggcagcacccttctgcagaagtaaattttgccctgcagcacaaaagaggaaggaaa -gcaag-------------------ggaagggaaggggaggggaggaagggaaggggaggg -gaggaaggcgaggtgaggggaggagaggtgaggggagggggggaggggaggggagggaga -gtgaggaagagagagagaaagggagagaggaaggaaagaagaaaggaaggaaggaaagaa -ggaaggaagggagggagggagggaggaaagaaggaaggaaaggagggaggaagggaggga -aagagagagagaggaaaagagagagaaagagaaagagagaaagagaggaaggaaggaagg -aaggagagagagaaagaaagaaggaaagaggaaggaaggaagaaagaaaagaaagaaaga -aaaaagaaagaaaggaaggagagaaagaaatgaaag--------agaaagaaagaaagaa -agaaagaaaggagagaaaaaggaaaaacaaagaaagagaaaagaaggagagaaggaaagg -aaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaagaaag--------------- ----------aagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacaccttggtaatttttg -tgctcttccctggactttggactttgcagccttagggagacagagctctttaatgtacac -tttcccatcaggcactgcatggccaagaacctgcctgca ->p:HG002_1_chr20:23155368-23156067 -ctagtttagattgtgtggtccaaccccagtcaatgggggaaagacacagaggtagaatct -gcgttaggaataaaaaccgctactctccgttgttctgtgtgcttttgcagtcatgattga -tgcaggcagcacccttctgcagaagtaaattttgccctgcagcacaaaagaggaaggaaa -gcaag-------------------ggaagggaaggggaggggaggaagggaaggggaggg -gaggaaggcgaggtgaggggaggagaggtgaggggagggggggaggggaggggagggaga -gtgaggaagagagagagaaagggagagaggaaggaaagaagaaaggaaggaaggaaagaa -ggaaggaagggagggagggagggaggaaagaaggaaggaaaggagggaggaagggaggga -aagagagagagaggaaaagagagagaaagagaaagagagaaagagaggaaggaaggaagg -aaggagagagagaaagaaagaaggaaagaggaaggaaggaagaaagaaaagaaagaaaga -aaaaagaaagaaaggaaggagagaaagaaatgaaag--------agaaagaaagaaagaa -agaaagaaaggagagaaaaaggaaaaacaaagaaagagaaaagaaggagagaaggaaagg -aaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaagaaag--------------- ------aagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacaccttggtaatttttg -tgctcttccctggactttggactttgcagccttagggagacagagctctttaatgtacac -tttcccatcaggcactgcatggccaagaacctgcctgca ->p:HG002_2_chr20:23155368-23156067 -ctagtttagattgtgtggtccaaccccagtcaatgggggaaagacacagaggtagaatct -gcgttaggaataaaaaccgctactctccgttgttctgtgtgcttttgcagtcatgattga -tgcaggcagcacccttctgcagaagtaaattttgccctgcagcacaaaagaggaaggaaa -gcaagggaagggaaggggaggggaggaagggaaggggaggggaggaagggaaggggaggg -gaggaaggcgaggtgaggggaggagaggtgaggggagggggggaggggaggggagggaga -gtgaggaagagagagagaaagggagagaggaaggaaagaagaaaggaaggaaggaaagaa -ggaaggaagggagggagggagggaggaaagaaggaaggaaaggagggaggaagggaggga -aagagagagagaggaaaagagagagaaagagaaagagagaaagagaggaaggaaggaagg -aaggagagagagaaagaaagaaggaaagaggaaggaaggaagaaagaaaagaaagaaaga -aaaaagaaagaaaggaaggagagaaagaaatgaaagagaaagaaagaaagaaagaaagaa -agaaagaaaggagagaaaaaggaaaaacaaagaaagagaaaagaaggagagaaggaaagg -aaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaagaaagaagaaagaaagaaag -aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacaccttggtaatttttg -tgctcttccctggactttggactttgcagccttagggagacagagctctttaatgtacac -tttcccatcaggcactgcatggccaagaacctgcctgca ->ref_chr20:23155368-23156067 -ctagtttagattgtgtggtccaaccccagtcaatgggggaaagacacagaggtagaatct -gcgttaggaataaaaaccgctactctccgttgttctgtgtgcttttgcagtcatgattga -tgcaggcagcacccttctgcagaagtaaattttgccctgcagcacaaaagaggaaggaaa -gcaag-------------------ggaagggaaggggaggggaggaaggga--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------aggaaaagagagagaaagagaaagagagaaagagaggaaggaaggaagg -aaggagagagagaaagaaagaaggaaagaggaaggaaggaagaaagaaaagaaagaaaga -aaaaagaaagaaaggaaggagagaaagaaatgaaag--------agaaagaaagaaagaa -agaaagaaaggagagaaaaaggaaaaacaaagaaagagaaaagaaggagagaaggaaagg -aaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaagaaag------------aag -aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacaccttggtaatttttg -tgctcttccctggactttggactttgcagccttagggagacagagctctttaatgtacac -tttcccatcaggcactgcatggccaagaacctgcctgca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_6ab622358b0189242a15e470f601cb6b.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6ab622358b0189242a15e470f601cb6b.msa deleted file mode 100644 index d87897ff..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_6ab622358b0189242a15e470f601cb6b.msa +++ /dev/null @@ -1,75 +0,0 @@ ->syndip_1_chr20:63221409-63221821 -taagtaccagtgccaggtgctctggggccgatgtctccgttagccccaaggtggaggctc -agggagcagatgtgagcgtgccttgctcatcgcagtagcttcggactgcagggattgcag -ggactgcagggactgcagggattgcagggactgcagggactgcagggactgcagggattg -cagggattgcagggactgcagggactgca------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------ttgc -tcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgcaggctc ->syndip_2_chr20:63221409-63221821 -taagtaccagtgccaggtgctctggggccgatgtctccgttagccccaaggtggaggctc -agggagcagatgtgagcgtgccttgctcatcgcagtagcttcggactgcagggattgcag -ggactgcagggattgcagggattgcagggagtgcagggactgcagggactgcagggattg -cagggactgcagggactgcagggactgcagggactgcagggactgcagggactgcaggga -ttgcagggactgcagggactgcagggattgcagggattgcagggattgcagggactgcag -ggattgcagggactgcagggactgcagggactgcagggactgcagggactgcagggattg -cagggattgcagggattgcagggactgcagggattgcagggactgcagggactgcaggga -ttgcagggactgcagggactgcagggactgcagggattgcagggattgcagggattgcag -ggattgcagggattgcagggactgcagggactgcagggactgcagggactgcagggattg -cagggattgcagggattgcagggattgcagggactgcagggactgcagggattgcaggga -ttgcagggattgcagggattgcagggattgcagggattgcagggactgcagggactgcag -ggactgcagggattgcagggattgcagggattgcagggattgcagggactgcagggactg -cagggattgcagggattgcagggattgcagggattgcagggactgcagggactgcattgc -tcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgcaggctc ->p:HG002_1_chr20:63221409-63221821 -taagtaccagtgccaggtgctctggggccgatgtctccgttagccccaaggtggaggctc -agggagcagatgtgagcgtgccttgctcatcgcagtagcttcggactgcagggattgcag -ggactgcagggattgcagggattgcagggattgcagggactgcagggattgcagggactg -cagggactgcagggactgcagggactgcagggactgcagggattgcagggattgcaggga -ttgcagggactgcagggactgcagggattgcagggattgcagggactgcagggactgcag -ggattgcagggactgcagggactgcagggactgcagggactgcagggactgcagggactg -cagggattgcagggattgcagggattgcagggattgcagggactgcagggactgcaggga -ctgcagggactgcagggactgcagggactgcagggattgcagggattgcagggattgcag -ggattgcagggattgcagggactgcagggactgcagggactgcagggactgcagggattg -cagggattgcagggattgcagggattgcagggactgcagggactgcagggattgcaggga -ttgcagggattgcagggattgcagggattgcagggattgcagggactgcagggactgcag -ggactgcagggattgcagggattgcagggactgcagggactgcagggattgcagggactg -cagggactgcagggactgcagggattgcagggattgcagggactgcagggactgcattgc -tcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgcaggctc ->p:HG002_2_chr20:63221409-63221821 -taagtaccagtgccaggtgctctggggccgatgtctccgttagccccaaggtggaggctc -agggagcagatgtgagcgtgccttgctcatcgcagtagcttcggactgcagggattgcag -ggactgcagggactgcagggattgcagggactgcagggactgcagggactgcagggattg -cagggattgcagggactgcagggactgca------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------ttgc -tcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgcaggctc ->ref_chr20:63221409-63221821 -taagtaccagtgccaggtgctctggggccgatgtctccgttagccccaaggtggaggctc -agggagcagatgtgagcgtgccttgctcatcgcagtagcttcggactgcagggattgcag -ggactgcagggattgcagggattgcagggattgcagggactgcagggattgcagggactg -cagggactgcagggactgcagggactgcagggactgcagggattgcagggattgcaggga -ttgcagggactgcagggattgcagggactgcagggactgcagggattgcagggactgcag -ggactgcagggactgcagggattgcagggattgcagggactgcagggactgca------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------ttgc -tcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgcaggctc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_6c3ae6985541ddd1146ec32d22021912.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6c3ae6985541ddd1146ec32d22021912.msa deleted file mode 100644 index 662f3074..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_6c3ae6985541ddd1146ec32d22021912.msa +++ /dev/null @@ -1,65 +0,0 @@ ->syndip_1_chr20:23155478-23155957 -tcatgattgatgcaggcagcacccttctgcagaagtaaattttgccctgcagcacaaaag -aggaaggaaagcaagggaagggaaggggaggggaggaagggaaggggaggggaggaaggg -aaggggaggggaggaaggcgaggtgaggggaggagaggtgaggggagggggggaggggag -gggagggagagtgaggaagagagagagaaagggagagaggaaggaaagaagaaaggaagg -aaggaaagaaggaaggaagggagggagggagggaggaaagaaggaaggaaaggagggagg -aagggagggaaagagagagagaggaaaagagagagaaagagaaagagagaaagagaggaa -ggaaggaaggaaggagagagagaaagaaagaaggaaagaggaaggaaggaagaaagaaaa -gaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaagagaaagaaagaaag -aaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaagagaaaagaaggaga -gaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaagaaagaagaa -agaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaa -agaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacacctt ->syndip_2_chr20:23155478-23155957 -tcatgattgatgcaggcagcacccttctgcagaagtaaattttgccctgcagcacaaaag -aggaaggaaagcaag-------------------ggaagggaaggggaggggaggaaggg -aaggggaggggaggaaggcgaggtgaggggaggagaggtgaggggagggggggaggggag -gggagggagagtgaggaagagagagagaaagggagagaggaaggaaagaagaaaggaagg -aaggaaagaaggaaggaagggagggagggagggaggaaagaaggaaggaaaggagggagg -aagggagggaaagagagagagaggaaaagagagagaaagagaaagagagaaagagaggaa -ggaaggaaggaaggagagagagaaagaaagaaggaaagaggaaggaaggaagaaagaaaa -gaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag--------agaaag -aaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaagagaaaagaaggaga -gaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaagaaag----- --------------------aagaaagaaagaaagaaagaaagaaagaaagaaagaaagaa -agaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacacctt ->p:HG002_1_chr20:23155478-23155957 -tcatgattgatgcaggcagcacccttctgcagaagtaaattttgccctgcagcacaaaag -aggaaggaaagcaag-------------------ggaagggaaggggaggggaggaaggg -aaggggaggggaggaaggcgaggtgaggggaggagaggtgaggggagggggggaggggag -gggagggagagtgaggaagagagagagaaagggagagaggaaggaaagaagaaaggaagg -aaggaaagaaggaaggaagggagggagggagggaggaaagaaggaaggaaaggagggagg -aagggagggaaagagagagagaggaaaagagagagaaagagaaagagagaaagagaggaa -ggaaggaaggaaggagagagagaaagaaagaaggaaagaggaaggaaggaagaaagaaaa -gaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag--------agaaag -aaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaagagaaaagaaggaga -gaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaagaaag----- ----------------aagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaa -agaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacacctt ->p:HG002_2_chr20:23155478-23155957 -tcatgattgatgcaggcagcacccttctgcagaagtaaattttgccctgcagcacaaaag -aggaaggaaagcaagggaagggaaggggaggggaggaagggaaggggaggggaggaaggg -aaggggaggggaggaaggcgaggtgaggggaggagaggtgaggggagggggggaggggag -gggagggagagtgaggaagagagagagaaagggagagaggaaggaaagaagaaaggaagg -aaggaaagaaggaaggaagggagggagggagggaggaaagaaggaaggaaaggagggagg -aagggagggaaagagagagagaggaaaagagagagaaagagaaagagagaaagagaggaa -ggaaggaaggaaggagagagagaaagaaagaaggaaagaggaaggaaggaagaaagaaaa -gaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaagagaaagaaagaaag -aaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaagagaaaagaaggaga -gaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaagaaagaagaa -agaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaa -agaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacacctt ->ref_chr20:23155478-23155957 -tcatgattgatgcaggcagcacccttctgcagaagtaaattttgccctgcagcacaaaag -aggaaggaaagcaag-------------------ggaagggaaggggaggggaggaaggg -a----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------aggaaaagagagagaaagagaaagagagaaagagaggaa -ggaaggaaggaaggagagagagaaagaaagaaggaaagaggaaggaaggaagaaagaaaa -gaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag--------agaaag -aaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaagagaaaagaaggaga -gaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaagaaag----- --------aagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaa -agaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacacctt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_6c66998f8bd2f037c15b01da2bb40668.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6c66998f8bd2f037c15b01da2bb40668.msa deleted file mode 100644 index 0645149b..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_6c66998f8bd2f037c15b01da2bb40668.msa +++ /dev/null @@ -1,160 +0,0 @@ ->syndip_1_chr20:63964768-63966617 -ttacccccaggccgtggccgaggag----------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------caccctgacctggaacgagcccccataccttttctcaccactgttccctg -acctgggacgagcccccataccttttctcaccactgttcctccccgacctgggacgagcc -cccataccttttctcaccactgt---tccctgacctgggacgagcccccataccttttct -taccactgttcctccctgtggcacgaggtgctttgttctccgacctggtcagcagcacca -ttttgcagggcggtgtgtgtctgctgatagcaatgggcctgctgactgtcaccggcttgc -tgaccacaatgggcctgctgactgtcactggcttggtgaccggcacgggtttcgtaactg -tcacaagctttgttaccgtaatgggtttggtgacaggtacgggtttggtgaccggcacag -acttggtgactgtgatgggtttggtgaccggcatggccttggtgacgggcatgggcctgc -tgactgtgacaggtttggtgactggcacgggcctagtgaccgggatggccttggtgactg -gcatgggtctgccgaccgagactggcttgctgatgccaatgggtttgctgacacccacag -gtttgccaatagtgacaggtttgctcactccgatgggcttgctgacccca ->syndip_2_chr20:63964768-63966617 -ttacccccaggccgtggccgaggagcaccctgacctggaacgagcccccataccttttct -caccactgttccccgacctgggacaagcccccataccttttcttaccactgttccctgac -ctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagcccccat -accttttctcaccactgttccccgacctgggacgagcccccataccttttctcaccactg -ttccctgacctgggacgagcccccataccttttctcaccactgttcctccccgacctggg -acgagcccccataccttttctcaccactgttccccgacctgggacgagcccccatacctt -ttctcaccactgttccctgacctggaacgagcccccataccttttctcaccactgttccc -cgacctgggacgagcccccataccttttctcaccactgttccccgacctgggacgagccc -ccataccttttctcaccactgttccccgacctgggacgagcccccataccttttctcacc -actgttccccgacctgggacgagcccccataccttttctcaccactgttccccgacctgg -gacgagcccccataccttttctcaccactgttccctgacctgggacgagcccccatacct -tttctcaccactgttccccgacctgggacgagcccccataccttttcttaccactgttcc -ccgacctgggacgagcccccataccttttcttaccactgttcctccccgacctgggacga -gcccccataccttttcttaccactgttcctccccaacctgggacgagcccccataccttt -tctcaccactgttcctccccgacctgggacgagcccccataccttttctcaccactgttc -cctgacctgggacgagcccccataccttttcttaccactgttcctccccgacctgggacg -agcccccataccttttcttaccactgttcctccccgacctgggacgagcccccatacctt -ttcttaccactgttcctccccgacctgggacgagcccccataccttttcttaccactgtt -ccccgacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgag -cccccataccttttcttaccactgttccctgacctgggacgagcccccataccttttctc -accactgttcctccccgacctgggacgagcccccataccttttctcaccactgttccccg -acctgggacgagcccccataccttttcttaccactgttcctccctgacctgggacgagcc -cccataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttct -taccactgttcctccctgtggcacgaggtgctttgttctccgacctggtcagcagcacca -ttttgcagggcggtgtgtgtctgctgatagcaatgggcctgctgactgtcaccggcttgc -tgaccacaatgggcctgctgactgtcactggcttggtgaccggcacgggtttcgtaactg -tcacaagctttgttaccgtaatgggtttggtgacaggtacgggtttggtgaccggcacag -acttggtgactgtgatgggtttggtgaccggcatggccttggtgacgggcatgggcctgc -tgactgtgacaggtttggtgactggcacgggcctagtgaccgggatggccttggtgactg -gcatgggtctgccgaccgagactggcttgctgatgccaatgggtttgctgacacccacag -gtttgccaatagtgacaggtttgctcactccgatgggcttgctgacccca ->p:HG002_1_chr20:63964768-63966617 -ttacccccaggccgtggccgaggagcaccctgacctggaacgagcccccataccttttct -caccactgttccccgacctgggacaagcccccataccttttcttaccactgttccctgac -ctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagcccccat -accttttctcaccactgttccccgacctgggacgagcccccataccttttctcaccactg -ttccctgacctgggacgagcccccataccttttctcaccactgttcctccccgacctggg -acgagcccccataccttttctcaccactgttccccgacctgggacgagcccccatacctt -ttctcaccactgttccctgacctggaacgagcccccataccttttctcaccactgttccc -cgacctgggacgagcccccataccttttctcaccactgttccccgacctgggacgagccc -ccataccttttctcaccactgttccccgacctgggacgagcccccataccttttctcacc -actgttccccgacctgggacgagcccccataccttttctcaccactgttccccgacctgg -gacgagcccccataccttttctcaccactgttccctgacctgggacgagcccccatacct -tttctcaccactgttccccgacctgggacgagcccccataccttttcttaccactgttcc -ccgacctgggacgagcccccataccttttcttaccactgttcctccccgacctgggacga -gcccccataccttttcttaccactgttcctccccaacctgggacgagcccccataccttt -tctcaccactgttcctccccgacctgggacgagcccccataccttttctcaccactgttc -cctgacctgggacgagcccccataccttttcttaccactgttcctccccgacctgggacg -agcccccataccttttcttaccactgttcctccccgacctgggacgagcccccatacctt -ttcttaccactgttcctccccgacctgggacgagcccccataccttttcttaccactgtt -ccccgacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgag -cccccataccttttcttaccactgttccctgacctgggacgagcccccataccttttctc -accactgttcctccccgacctgggacgagcccccataccttttctcaccactgttccccg -acctgggacgagcccccataccttttcttaccactgttcctccctgacctgggacgagcc -cccataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttct -taccactgttcctccctgtggcacgaggtgctttgttctccgacctggtcagcagcacca -ttttgcagggcggtgtgtgtctgctgatagcaatgggcctgctgactgtcaccggcttgc -tgaccacaatgggcctgctgactgtcactggcttggtgaccggcacgggtttcgtaactg -tcacaagctttgttaccgtaatgggtttggtgacaggtacgggtttggtgaccggcacag -acttggtgactgtgatgggtttggtgaccggcatggccttggtgacgggcatgggcctgc -tgactgtgacaggtttggtgactggcacgggcctagtgaccgggatggccttggtgactg -gcatgggtctgccgaccgagactggcttgctgatgccaatgggtttgctgacacccacag -gtttgccaatagtgacaggtttgctcactccgatgggcttgctgacccca ->p:HG002_2_chr20:63964768-63966617 -ttacccccaggccgtggccgaggag----------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------caccctgacctggaacgagcccccataccttttctcaccactgttccctg -acctgggacgagcccccataccttttctcaccactgttcctccccgacctgggacgagcc -cccataccttttctcaccactgt---tccctgacctgggacgagcccccataccttttct -taccactgttcctccctgtggcacgaggtgctttgttctccgacctggtcagcagcacca -ttttgcagggcggtgtgtgtctgctgatagcaatgggcctgctgactgtcaccggcttgc -tgaccacaatgggcctgctgactgtcactggcttggtgaccggcacgggtttcgtaactg -tcacaagctttgtgaccgtaatgggtttggtgacaggtacgggtttggtgaccggcacag -acttggtgactgtgatgggtttggtgaccggcatggccttggtgacgggcatgggcctgc -tgactgtgacaggtttggtgactggcacgggcctagtgaccgggatggccttggtgactg -gcatgggtctgccgaccgagactggcttgctgatgccaatgggtttgctgacacccacag -gtttgccaatagtgacaggtttgctcactccgatgggcttgctgacccca ->ref_chr20:63964768-63966617 -ttacccccaggccgtggccgaggagcaccctgacctggaacgagcccccataccttttct -caccactgttccccgacctgggacaagcccccataccttttcttaccactgttccctgac -ctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagcccccat -accttttctcaccactgttccccgacctgggacgagcccccataccttttctcaccactg -ttccctgacctgggacgagcccccataccttttctcaccactgttcctccccgacctggg -acgagcccccataccttttctcaccactgttccccgacctgggacgagcccccatacctt -ttctcaccactgttccctgacctggaacgagcccccataccttttctcaccactgttccc -cgacctgggacgagcccccataccttttctcaccactgttccccgacctgggacgagccc -ccataccttttctcaccactgttccccgacctgggacgagcccccataccttttctcacc -actgttccccgacctgggacgagcccccataccttttctcaccactgttccccgacctgg -gacgagcccccataccttttctcaccactgttccctgacctgggacgagcccccatacct -tttctcaccactgttccccgacctgggacgagcccccataccttttcttaccactgttcc -ccgacctgggacgagcccccataccttttcttaccactgttcctccccgacctgggacga -gcccccataccttttctcaccactgttcctccccaacctgggacgagcccccataccttt -tctcaccactgttcctccccgacctgggacgagcccccataccttttctcaccactgttc -cctgacctgggacgagcccccataccttttcttaccactgttcctccccgacctgggacg -agcccccataccttttcttaccactgttcctccccgacctgggacgagcccccatacctt -ttcttaccactgttcctccccgacctgggacgagcccccataccttttcttaccactgtt -ccccgacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgag -cccccataccttttcttaccactgttccctgacctgggacgagcccccataccttttctc -accactgttcctccccgacctgggacgagcccccataccttttctcaccactgttccccg -acctgggacgagcccccataccttttcttaccactgttcctccctgacctgggacgagcc -cccataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttct -taccactgttcctccctgtggcacgaggtgctttgttctccgacctggtcagcagcacca -ttttgcagggcggtgtgtgtctgctgatagcaatgggcctgctgactgtcaccggcttgc -tgaccacaatgggcctgctgactgtcactggcttggtgaccggcacgggtttcgtaactg -tcacaagctttgttaccgtaatgggtttggtgacaggtacgggtttggtgaccggcacag -acttggtgactgtgatgggtttggtgaccggcatggccttggtgacgggcatgggcctgc -tgactgtgacaggtttggtgactggcacgggcctagtgaccgggatggccttggtgactg -gcatgggtctgccgaccgagactggcttgctgatgccaatgggtttgctgacacccacag -gtttgccaatagtgacaggtttgctcactccgatgggcttgctgacccca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_6cd0a80412f89ca6c32c00ac5ea5731a.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6cd0a80412f89ca6c32c00ac5ea5731a.msa deleted file mode 100644 index 20a96e35..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_6cd0a80412f89ca6c32c00ac5ea5731a.msa +++ /dev/null @@ -1,155 +0,0 @@ ->syndip_1_chr20:53203787-53204673 -aaaccaaacccacctaaaaactgaaactgggttataaactctgccttgggaacttgatcc -caagctctctagacctgcaatgttcaagcggtatgtcccacataccacatggggctacta -agcccttcaaatgtgactggtccaaattaaaatatactgtaagtataaaacacactgaac -ttgaaaggcttagtccaaaaaccgtagtgcacaatatctccttcatttttataatatgat -actattatatcataattttataatatactattatatcatattatatgatactatttatat -catcatatgatgatatactattatatcatcatatgatgatatactattatatcatcatat -gatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgat-- --atactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactat -atcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcat -atgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgat -atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc -atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg -atatgatactatatcatcatatgatgatatgatactatatcatcacatgatgatatgata -ctatatcatcacatgatgatatgatactatatcatcacatgatgatatgatactatatca -tcacatgatgatatgatactatatcatcacatgatgatatgatactatatcatcacatga -tgatatgatactatatcatcacatgatgatatgatactatatcatc-------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------acatgatgatatgatactatatcatcatataacatgatgata -tgatactatatcatcatataacatgatgatatgatactatatcatcatataacatgatga -tatgatactatatcatcatataacatgatgatatgatactatatcatcatataacatgat -gatatgatactatatcatcatataacatgatgatatgatactattatatcataatatgat -ataatattttggacatactaggttaaataagatatagttatataaatcaatttcacttat -ttctttctcattctttaatgtgactactgaagcatatgaaattccatgcatagctgacat -tctacttctattgggcagcgctgcttgaagccttcagtatctgatcacttgcaacaaaaa -cagagacataataataatcacagacaccatttaccgggttcctaccatgcat ->syndip_2_chr20:53203787-53204673 -aaaccaaacccacctaaaaactgaaactgggttataaactctgccttgggaacttgatcc -caagctctctagacctgcaatgttcaagcggtatgtcccacataccacatggggctacta -agcccttcaaatgtgactggtccaaattaaaatatactgtaagtataaaacacactgaac -ttgaaaggcttagtccaaaaaccgtagtgcacaatatctccttcatttttataatatgat -actattatatcataattttataatatactattatatcatattatatgatactatttatat -catcatatgatgatatactattatatcatcatatgatgatatgatactatatcatcatat -gatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatat -gatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactat -atcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcat -atgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgat -atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc -atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg -atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata -ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca -tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga -tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatat -gatgatatgatactatatcatcatatgatgatatgatactatatcataacatgatgatat -gatactatatcataacatgatgatatgatactatatcatcatataacatgatgatatgat -actatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatg -atactatatcatcatataacatgatgatatgatactatatcatcatataacatgatgata -tgatactatatcatcatataacatgatgatatgatactatatcatcatataacatgatga -tatgatactatatcatcatataacatgatgatatgatactatatcatcatataacatgat -gatatgatactatatcatcatataacatgatgatatgatactattatatcataatatgat -ataatattttggacatactaggttaaataagatatagttatataaatcaatttcacttat -ttctttctcattctttaatgtgactactgaagcatatgaaattccatgcatagctgacat -tctacttctattgggcagcgctgcttgaagccttcagtatctgatcacttgcaacaaaaa -cagagacataataataatcacagacaccatttaccgggttcctaccatgcat ->p:HG002_1_chr20:53203787-53204673 -aaaccaaacccacctaaaaactgaaactgggttataaactctgccttgggaacttgatcc -caagctctctagacctgcaatgttcaagcggtatgtcccacataccacatggggctacta -agcccttcaaatgtgactggtccaaattaaaatatactgtaagtataaaacacactgaac -ttgaaaggcttagtccaaaaaccgtagtgcacaatatctccttcatttttataatatgat -actattatatcataattttataatatactattatatcatattatatgatactatttatat -catcatatgatgatatactattatatcatcatatgatgatatgatactatatcatcatat -gatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatat -gatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactat -atcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcat -atgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgat -atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc -atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg -atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata -ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca -tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga -tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatat -gatgatatgatactatatcatcatatgatgatatgatactatatcataacatgatgatat -gatactatatcataacatgatgatatgatactatatcatcatataacatgatgatatgat -actatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatg -atactatatcatcatataacatgatgatatgatactatatcatcatataacatgatgata -tgatactatatcatcatataacatgatgatatgatactatatcatcatataacatgatga -tatgatactatatcatcatataacatgatgatatgatactatatcatcatataacatgat -gatatgatactatatcatcatataacatgatgatatgatactattatatcataatatgat -ataatattttggacatactaggttaaataagatatagttatataaatcaatttcacttat -ttctttctcattctttaatgtgactactgaagcatatgaaattccatgcatagctgacat -tctacttctattgggcagcgctgcttgaagccttcagtatctgatcacttgcaacaaaaa -cagagacataataataatcacagacaccatttaccgggttcctaccatgcat ->p:HG002_2_chr20:53203787-53204673 -aaaccaaacccacctaaaaactgaaactgggttataaactctgccttgggaacttgatcc -caagctctctagacctgcaatgttcaagcggtatgtcccacataccacatggggctacta -agcccttcaaatgtgactggtccaaattaaaatatactgtaagtataaaacacactgaac -ttgaaaggcttagtccaaaaaccgtagtgcacaatatctccttcatttttataatatgat -actattatatcataattttataatatactattatatcatattatatgatactatttatat -catcatatgatgatatactattatatcatcatatgatgatatactattatatcatcatat -gatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgat-- --atactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactat -atcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcat -atgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgat -atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc -atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg -atatgatactatatcatcatatgatgatatgatactatatcatcacatgatgatatgata -ctatatcatcacatgatgatatgatactatatcatcacatgatgatatgatactatatca -tcacatgatgatatgatactatatcatcacatgatgatatgatactatatcatcacatga -tgatatgatactatatcatcacatgatgatatgatactatatcatc-------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------acatgatgatatgatactatatcatcatataacatgatgata -tgatactatatcatcatataacatgatgatatgatactatatcatcatataacatgatga -tatgatactatatcatcatataacatgatgatatgatactatatcatcatataacatgat -gatatgatactatatcatcatataacatgatgatatgatactattatatcataatatgat -ataatattttggacatactaggttaaataagatatagttatataaatcaatttcacttat -ttctttctcattctttaatgtgactactgaagcatatgaaattccatgcatagctgacat -tctacttctattgggcagcgctgcttgaagccttcagtatctgatcacttgcaacaaaaa -cagagacataataataatcacagacaccatttaccgggttcctaccatgcat ->ref_chr20:53203787-53204673 -aaaccaaacccacctaaaaactgaaactgggttataaactctgccttgggaacttgatcc -caagctctctagacctgcaatgttcaagcggtatgtcccacataccacatggggctacta -agcccttcaaatgtgactggtccaaattaaaatatactgtaagtataaaacacactgaac -ttgaaaggcttagtccaaaaaccgtagtgcacaatatctccttcatttttataatatgat -actattatatcataattttataatatactattatatcatattatatgatactatttatat -catcatatgatgat---------------------------------------------- ------------------------------------------------------atgat-- --atactatatcatcatatgatgatatgat------------------------atactat -atcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcat -atgatgatatgatactatatcatcatatgatgatatgatactatatcatcat-------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------atgatgata -tgatactatatcatcatataacatgatgatatgatactatatcatcatataacatgatga -tatgatactatatcatcatataacatgatgatatgatactatatcatcatataacatgat -gatatgatactatatcatcatataacatgatgatatgatactattatatcataatatgat -ataatattttggacatactaggttaaataagatatagttatataaatcaatttcacttat -ttctttctcattctttaatgtgactactgaagcatatgaaattccatgcatagctgacat -tctacttctattgggcagcgctgcttgaagccttcagtatctgatcacttgcaacaaaaa -cagagacataataataatcacagacaccatttaccgggttcctaccatgcat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_6e65d89ed629815fdf096d2b24431eda.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6e65d89ed629815fdf096d2b24431eda.msa deleted file mode 100644 index 65f27d73..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_6e65d89ed629815fdf096d2b24431eda.msa +++ /dev/null @@ -1,130 +0,0 @@ ->syndip_1_chr20:61282506-61283669 -tctgaacaaaccacttttaatctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtg -tgtgtgtatgtctatctgtacttgtacctgcacacacaactggatgagcatggtgtgtgt -gtacacatgtattgtgttcatatgtacatatgtgggtgccttgtgcacacgtgtgtggct -gtgggatgttcagatgtgcatgtgagttggtgtgtgtgcatgcccacaagcatgcatgta -aatgtgatgtgctgtgtatgcacacggataagcatgtgtgaaggagtgcatgagagtggt -gcatggctgtggtgtgcacgtgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctg -tggtgtgtgtgatgtacgtgcatttgcacgcatgtgctgtggcgtgtgtgatgtacgtgc -atttgcacgcgtgtgctgtgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgt -gtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgc -acgcgt-------------------------------------gtgctgtggcgtgtgtg -atgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcg -tgtgctgtg----------------gtgtgtgatgtacgtgcgtttgcacgcgtgtgctg -tggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgc -gtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtgg -cgtgtgtgatgtacgtgcgtttgcacgcgtgttctgtggcgtgtgtgatgtacgtgcgtt -tgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgt -gtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgc -acgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtg -tgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacg -cgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgc-------------- ------------------------------------------------------------- ----------tgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggt -gcatttacacgcgtgtgctgtggtgtgtgatgtaggtgcatttgcacgcgtgtgctgtgg -tgtgtgtgatgtgtgtgcgtttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatg -ggaggatatttccagtgct ->syndip_2_chr20:61282506-61283669 -tctgaacaaaccacttttaatctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtg -tgtgtgtatgtctatctgtacttgtacctgcacacacaactggatgagcatggtgtgtgt -gtacacatgtaatgtgttcatatgtacatatgtgggtgccttgtgcacacgtgtgtggct -gtgggatgttcagatgtgcatgtgagttggtgtgtgtgcatgcccacaagcatgcatgta -aatgtgatgtgctgtgtatgcacacggataagcatgtgtgaaggagtgcatgagagtggt -gcatggctgtggtgtgcacgtgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctg -tggtgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgc -atttgcacgcgtgtgctgtgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgt -gtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgc -acgcgtgtgctgtggcgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtg -atgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcg -cgtgctgtggcgtgtgtgatgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctg -tggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgc -gtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtgg -cgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtt -tgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgt -gtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgc -acgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtg -tgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacg -cgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtga -tgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgt -gtgctgtggtgtgtgatgtaggtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggt -gcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtgg -tgtgtgtgatgtgtgtgcatttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatg -ggaggatatttccagtgct ->p:HG002_1_chr20:61282506-61283669 -tctgaacaaaccacttttaatctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtg -tgtgtgtatgtctatctgtacttgtacctgcacacacaactggatgagcatggtgtgtgt -gtacacatgtaatgtgttcatatgtacatatgtgggtgccttgtgcacacgtgtgtggct -gtgggatgtttagatgtgcatgtgagttggtgtgtgtgcatgcccacaagcatgcatgta -aatgtgatgtgctgtgtatgcacacggataagcatgtgtgaaggagtgcatgagagtggt -gcatggctgtggtgtgcacgtgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctg -tggtgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgc -atttgcacgcgtgtgctgtgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgt -gtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgc -acgcgtgtgctgtggcgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtg -atgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcg -cgtgctgtggcgtgtgtgatgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctg -tggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgc -gtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtgg -cgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtt -tgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgt -gtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgc -acgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtg -tgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacg -cgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtga -tgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgt -gtgctgtggtgtgtgatgtaggtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggt -gcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtgg -tgtgtgtgatgtgtgtgcatttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatg -ggaggatatttccagtgct ->p:HG002_2_chr20:61282506-61283669 -tctgaacaaaccacttttaatctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtg -tgtgtgtatgtctatctgtacttgtacctgcacacacaactggatgagcatggtgtgtgt -gtacacatgtattgtgttcatatgtacatatgtgggtgccttgtgcacacgtgtgtggct -gtgggatgttcggatgtgcatgtgagttggtgtgtgtgcatgcccacaagcatgcatgta -aatgtgatgtgctgtgtatgcacacggataagcatgtgtgaaggagtgcatgagagtggt -gcatggctgtggtgtgcacgtgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctg -tggtgtgtgtgatgtacgtgcatttgcacgcatgtgctgtggcgtgtgtgatgtacgtgc -atttgcacgcgtgtgctgtgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgt -gtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgc -acgcgt-------------------------------------gtgctgtggcgtgtgtg -atgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcg -tgtgctgtg----------------gtgtgtgatgtacgtgcgtttgcacgcgtgtgctg -tggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgc -gtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtgg -cgtgtgtgatgtacgtgcgtttgcacgcgtgttctgtggcgtgtgtgatgtacgtgcgtt -tgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgt -gtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgc -acgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtg -tgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacg -cgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgc-------------- ------------------------------------------------------------- ----------tgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggt -gcatttacacgcgtgtgctgtggtgtgtgatgtaggtgcatttgcacgcgtgtgctgtgg -tgtgtgtgatgtgtgtgcgtttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatg -ggaggatatttccagtgct ->ref_chr20:61282506-61283669 -tctgaacaaaccacttttaatctttggcatggtgtgtgtgcatgtgtgtgtgtgtgtgtg -tgtgtgtatgtctatctgtacttgtacctgcacacacaactggatgagcatggtgtgtgt -gtacacatgtaatgtgttcatatgtacatatgtgggtgccttgtgcacacgtgtgtggct -gtgggatgttcagatgtgcatgtgagttggtgtgtgtgcatgcccacaagcatgcatgta -aatgtgatgtgctgtgtatgcacacggataagcatgtgtgaaggagtgcatgagagtggt -gcatggctgtggtgtgcacgtgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctg -tggtgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgc -atttgcacgcgtgtgctgtg---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------gcgtgtgatgtacgtgcgtttgcacgcg -cgtgctgtg----------------gcgtgtgatgtacgtgcgtttgcacgcgcgtgctg -tggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgc -gtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtgg -cgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtt -tgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgt -gtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgc -acgcgcgtgctgtggc---------gtgtgtgcgtttgcacgcgcgtgctgtggcgtgtg -tgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacg -cgtgtgctgtggtgtgtgtgatgtgtgtgcgtttgcacgcgtgtgc-------------- ------------------------------------------------------------- -----tgtggtgtgtgatgtaggtgcatttgcacgcgtgtgctgtggtgtgtgatgtaggt -gcatttacacgcgtgtgctgtggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtgg -tgtgtgtgatgtgtgtgcatttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatg -ggaggatatttccagtgct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_6fb85211643593e3d988c41116b83239.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6fb85211643593e3d988c41116b83239.msa deleted file mode 100644 index 567a3a8b..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_6fb85211643593e3d988c41116b83239.msa +++ /dev/null @@ -1,180 +0,0 @@ ->syndip_1_chr20:61100711-61102615 -tgcaagacaataggacaccagacagatccccgggctccacagcagaagtctggttactgg -gcaggcaggccccaaacactgtatttaaaacaaaaccccactgacaagtcctgtgactgg -agagaccccgagtgaaggcagacctccatgtcctctacatcctgtgccacatctggagag -acccctgtgagggcagagagctacctcctcttcttcctgtgtcacacctggagagacccc -gagtgagggcggatggccacgtcttctacttcctgtgtcacacctggagagaccccgagt -gagggcagatggccacatcctctacttcctgtgtcacacctggggagaccctgagtgagg -gcagacagccatgtcctctacgtcctgtgccacatccggagagaccccaagagagggcag -acagccacctcctctacttcctgtgtcacacctggagagaccccgagtgagggcggatgg -ccacgtcttctacttcctgtgtcacacctggagagaccccgagtgagggcagatggccac -atcctctacttcctgtgtcacacctggggagaccctgagtgagggcaga----------- ----------------------------------------------cagccatgtcctcta -cgtcctgtgccacatccggagagaccccaagagagggcagacagccacctcctctacttc -ctgtgtcacacctggagagactccaagtgaggagagacggccacatcttctacttcctgt -gtcac------------------------------------------------------- --acctggagagacctcgagtgagggcagatggccacatcctctaattcctgtgtcatacc -tggagagaccccgagtgagggcagatggccacctcctctacttcctgtgtcacacctgga -gagaccccaagtgagggcagactgccacctcctctacttcctgtgtcacacctagagaga -ccccgagtgaggacagccagccatgtcctctacttcctgtgccacatccggagagatccc -gagtgagggcagacagccatgtcctctacttcctgtgtcacacctggagagaccccgagt -gagggcagacggccacatcctctaattcctgtgtcacacctggagagaccccgagtgagg -gcagacggccacctcctctacttcctgtgtcacacctggagagaccccgagtgagggcag -acggccacatcctctaattcctgtgtcatgcctggagagaccccgagtgagggcatatgg -ccacatcctctaattcctatgtcacacctggagagaccccgagtgagggtggatggccac -atcctctaattcctgtgtcatacctggagagaccccgagtgagggcagatggccacctcc -tctacttcctgtgtcacacctggagagaccccgagtgagggcagatggccacctcctcta -cttcctgtgtcacacctggagagaccccaagtgagggcagacagccatgtcctctacgtc -ctgtgccacatccggagagaccccga-tgagggcagacagctaccccctctacttcctgt -gtcacacctgcagagaccccaagtgagggcagatggccacctcttctacttcctgtgtca -cacctggagaggccccgagtgagggcagacggccacctcctctacttcctgtgtcacacc -tggagagaccccgagtgagggcagacggccacatcctctatttcctgtgtcacacctgga -gagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacatggagaga -ccccgagtgagggcagaaggccacatcctctacttcctgtgtcacacctagagagacccc -gagtgagggcggatggccacatcctctaattcctgtgtcacacctggggagaccccgagt -gagggcagatggccacatcctctaattcctgtgtcacacctggagacacacagagtaaag -gtggacagccacctcctctacgtcctgtgccaca ->syndip_2_chr20:61100711-61102615 -tgcaagacaataggacaccagacagatccccgggctccacagcagaagtctggttactgg -gcaggcaggccccaaacactgtatttaaaacaaaaccccactgacaagtcctgtgactgg -agagaccccgagtgaaggcagacctccatgtcctctacatcctgtgccacatctggagag -acccctgtgagggcagagagctacctcctcttcttcctgtgtcacacctggagagacccc -gagtgagggcggatggccacgtcttctacttcctgtgtcacacctggagagaccccgagt -gagggcagatggccacatcctctacttcctgtgtcacacctggggagaccctgagtgagg -gcagacagccatgtcctctacgtcctgtgccacatccggagagaccccaagagagggcag -acagccacctcctctacttcctgtgtcacacctggagagactccaagtgaggagagacgg -ccacatcttctacttcctgtgtcacacctggagagacctcgagtgagggcagatggccac -atcctctaattcctgtgtcacacctggagagaccccaagtgagggcagactgccacctcc -tctacttcctgtgtcacacctagagagaccccgagtgaggacagccagccatgtcctcta -cttcctgtgccacatccggagagatcccgagtgagggcagacagccatgtcctctacttc -ctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattcctgt -gtcacacctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtca -tgcctggagagaccccgagtgagggcatatggccacatcctctaattcctatgtcacacc -tggagagaccccgagtgagggtggatggccacatcctctaattcctgtgtcatacctgga -gagaccccgagtgagggcagatggccacctcctctacttcctgtgtcacacctggagaga -ccccaagtgagggcagacagccatgtcctctacgtcctgtgccacatccggagagacccc -ga-tgagggcagacagctaccccctctacttcctgtgtcacacctgcagagaccccaagt -gagggcagatggccacctcttctacttcctgtgtcacacctggagaggccccgagtgagg -gcagacggccacctcctctacttcctgtgtcacacctggagagaccccgagtgagggcag -acggccacatcctctatttcctgtgtcacacctggagagaccccgagtgagggcagacgg -ccacatcctctaattcctgtgtcacacatggagagaccccgagtgaaggcagaaggccac -atcctctacttcctgtgtcacacctagagagaccccgagtgagggcggatggccacatcc -tctaattcctatgtcacacctggagagaccccgagtgagggtggatggccacatcctcta -attcctgtgtcatacctggagagaccccgagtgagggcagatggccacctcctctacttc -ctgtgtcacacctggagagaccccaagtgagggcagacagccatgtcctctacgtcctgt -gccacatccggagagaccccga-tgagggcagacagctaccccctctacttcctgtgtca -cacctgcagagaccccaagtgagggcagatggccacctcttctacttcctgtgtcacacc -tggagaggccccgagtgagggcagacggccacctcctctacttcctgtgtcacacctgga -gagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacatggagaga -ccctgagtgagggcagaaggccacatcctctacttcctgtgtcacacctagagagacccc -gagtgagggcggatggccacatcctctaattcctgtgtcacacctggggagaccccgagt -gagggcagatggccacatcctctaattcctgtgtcacacctggagacacacagagtaaag -gtggacagccacctcctctacgtcctgtgccaca ->p:HG002_1_chr20:61100711-61102615 -tgcaagacaataggacaccagacagatccccgggctccacagcagaagtctggttactgg -gcaggcaggccccaaacactgtatttaaaacaaaaccccactgacaagtcctgtgactgg -agagaccccgagtgaaggcagacctccatgtcctctacatcctgtgccacatctggagag -acccctgtgagggcagagagctacctcctcttcttcctgtgtcacacctggagagacccc -gagtgagggcggatggccacgtcttctacttcctgtgtcacacctggagagaccccgagt -gagggcagatggccacatcctctacttcctgtgtcacacctggggagaccctgagtgagg -gcagacagccatgtcctctacgtcctgtgccacatccggagagaccccaagagagggcag -acagccacctcctctacttcctgtgtcacacctggagagaccccgagtgagggcggatgg -ccacgtcttctacttcctgtgtcacacctggagagaccccgagtgagggcagatggccac -atcctctaattcctgtgtcacacctggagaaaccccaagtgagggcagactgccacctcc -tctacttcctgtgtcacacctagagagaccccgagtgaggacagccagccatgtcctcta -cttcctgtgccacatccggagagatcccgagtgagggcagacagccatgtcctctacttc -ctgtgtcacacctggggagaccctgagtgagggcagacagccatgtcctctacgtcctgt -gccacatccggagagaccccaagagagggcagacagccacctcctctacttcctgtgtca -cacctggagagactccaagtgaggagagacggccacatcttctacttcctgtgtcacacc -tggagagacctcgagtgagggcagatggccacatcctctaattcctgtgtcacacctgga -gagaccccaagtgagggcagactgccacctcctctacttcctgtgtcacacctagagaga -ccccgagtgaggacagccagccatgtcctctacttcctgtgccacatccggagagatccc -gagtgagggcagacagccatgtcctctacttcctgtgtcacacctggagagaccccgagt -gagggcagacggccacatcctctaattcctgtgtcacacctggagagaccccgagtgagg -gcagacggccacctcctctacttcctgtgtcacacctggagagaccccgagtgagggcag -acggccacatcctctaattcctgtgtcatgcctggagagaccccgagtgagggcatatgg -ccacatcctctaattcctatgtcacacctggagagaccccgagtgagggtggatggccac -atcctctaattcctgtgtcatacctggagagaccccgagtgagggcagatggccacctcc -tctacttcctgtgtcacacctggagagaccccgagtgagggcagatggccacctcctcta -cttcctgtgtcacacctggagagaccccaagtgagggcagacagccatgtcctctacgtc -ctgtgccacatccggagagaccccga-tgagggcagacagctaccccctctacttcctgt -gtcacacctgcagagaccccaagtgagggcagatggccacctcttctacttcctgtgtca -cacctggagaggccccgagtgagggcagacggccacctcctctacttcctgtgtcacacc -tggagagaccccgagtgagggcagacggccacatcctctatttcctgtgtcacacctgga -gagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacatggagaga -ccccgagtgagggcagaaggccacatcctctacttcctgtgtcacacctagagagacccc -gagtgagggcggatggccacatcctctaattcctgtgtcacacctggggagaccccgagt -gagggcagatggccacatcctctaattcctgtgtcacacctggagacacacagagtaaag -gtggacagccacctcctctacgtcctgtgccaca ->p:HG002_2_chr20:61100711-61102615 -tgcaagacaataggacaccagacagatccccgggctccacagcagaagtctggttactgg -gcaggcaggccccaaacactgtatttaaaacaaaaccccactgacaagtcctgtgactgg -agagaccccgagtgaaggcagacctccatgtcctctacatcctgtgccacatctggagag -acccctgtgagggcagagagctacctcctcttcttcctgtgtcacacctggagagacccc -gagtgagggcggatggccacgtcttctacttcctgtgtcacacctggagagaccccgagt -gagggcagatggccacatcctctacttcctgtgtcacacctggggagaccctgagtgagg -gcagacagccatgtcctctacgtcctgtgccacatccggagagaccccaagagagggcag -acagccacctcctctacttcctgtgtcacacctggagagaccccgagtgagggcggatgg -ccacgtcttctacttcctgtgtcacacctggagagaccccgagtgagggcagatggccac -atcctctacttcctgtgtcacacctggggagaccctgagtgagggcaga----------- ----------------------------------------------cagccatgtcctcta -cgtcctgtgccacatccggagagaccccaagagagggcagacagccacctcctctacttc -ctgtgtcacacctggagagactccaagtgaggagagacggccacatcttctacttcctgt -gtcac------------------------------------------------------- --acctggagagaccccgagtgagggtggatggccacatcctctaattcctgtgtcatacc -tggagagacctcgagtgagggcagatggccacatcctctaattcctgtgtcacacctgga -gagaccccaagtgagggcagactgccacctcctctacttcctgtgtcacacctagagaga -ccccgagtgaggacagccagccatgtcctctacttcctgtgccacatccggagagatccc -gagtgagggcagacagccatgtcctctacttcctgtgtcacacctggagagaccccgagt -gagggcagacggccacatcctctaattcctgtgtcacacctggagagaccccgagtgagg -gcagacggccacctcctctacttcctgtgtcacacctggagagaccccgagtgagggcag -acggccacatcctctaattcctgtgtcatgcctggagagaccccgagtgagggcatatgg -ccacatcctctaattcctatgtcacacctggagagaccccgagtgagggtggatggccac -atcctctaattcctgtgtcatacctggagagaccccgagtgagggcagatggccacctcc -tctacttcctgtgtcacacctggagagaccccgagtgagggcagatggccacctcctcta -cttcctgtgtcacacctggagagaccccaagtgagggcagacagccatgtcctctacgtc -ctgtgccacatccggagagaccccga-tgagggcagacagctaccccctctacttcctgt -gtcacacctgcagagaccccaagtgagggcagatggccacctcttctacttcctgtgtca -cacctggagaggccccgagtgagggcagacggccacctcctctacttcctgtgtcacacc -tggagagaccccgagtgagggcagacggccacatcctctatttcctgtgtcacacctgga -gagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacatggagaga -ccccgagtgagggcagaaggccacatcctctacttcctgtgtcacacctagagagacccc -gagtgagggcggatggccacatcctctaattcctgtgtcacacctggggagaccccgagt -gagggcagatggccacatcctctaattcctgtgtcacacctggagacacacagagtaaag -gtggacagccacctcctctacgtcctgtgccaca ->ref_chr20:61100711-61102615 -tgcaagacaataggacaccagacagatccccgggctccacagcagaagtctggttactgg -gcaggcaggccccaaacactgtatttaaaacaaaaccccactgacaagtcctgtgactgg -agagaccccgagtgaaggcagacctccatgtcctctacatcctgtgccacatctggagag -acccctgtgagggcagagagctacctcctcttcttcctgtgtcacacctggagagacccc -gagtgagggcggatggccacgtcttctacttcctgtgtcacacctggagagaccccgagt -gagggcagatggccacatcctctacttcctgtgtcacacctggggagaccctgagtgagg -gcagacagccatgtcctctacgtcctgtgccacatccggagagaccccaagagagggcag -acagccacctcctctacttcctgtgtcacacctggagagaccccgagtgagggcggatgg -ccacgtcttctacttcctgtgtcacacctggagagaccccgagtgagggcagatggccac -atcctctacttcctgtgtcacacctggggagaccctgagtgagggcaga----------- ----------------------------------------------cagccatgtcctcta -cgtcctgtgccacatccggagagaccccaagagagggcagacagccacctcctctacttc -ctgtgtcacacctggagagactccaagtgaggagagacggccacatcttctacttcctgt -gtcac------------------------------------------------------- ----------------------------------------------------------acc -tggagagacctcgagtgagggcagatggccacatcctctaattcctgtgtcacacctgga -gagaccccaagtgagggcagactgccacctcctctacttcctgtgtcacacctagagaga -ccccgagtgaggacagccagccatgtcctctacttcctgtgccacatccggagagatccc -gagtgagggcagacagccatgtcctctacttcctgtgtcacacctggagagaccccgagt -gagggcagacggccacatcctctaattcctgtgtcacacctggagagaccccgagtgagg -gcagacggccacctcctctacttcctgtgtcacacctggagagaccccgagtgagggcag -acggccacatcctctaattcctgtgtcatgcctggagagaccccgagtgagggcatatgg -ccacatcctctaattcctatgtcacacctggagagaccccgagtgagggtggatggccac -atcctctaattcctgtgtcatacctggagagaccccgagtgagggcagatggccacctcc -tctacttcctgtgtcacacctggagagaccccgagtgagggcagatggccacctcctcta -cttcctgtgtcacacctggagagaccccaagtgagggcagacagccatgtcctctacgtc -ctgtgccacatccggagagaccccga-tgagggcagacagctaccccctctacttcctgt -gtcacacctgcagagaccccaagtgagggcagatggccacctcttctacttcctgtgtca -cacctggagaggccccgagtgagggcagacggccacctcctctacttcctgtgtcacacc -tggagagaccccgagtgagggcagacggccacatcctctatttcctgtgtcacacctgga -gagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacatggagaga -ccccgagtgagggcagaaggccacatcctctacttcctgtgtcacacctagagagacccc -gagtgagggcggatggccacatcctctaattcctgtgtcacacctggggagaccccgagt -gagggcagatggccacatcctctaattcctgtgtcacacctggagacacacagagtaaag -gtggacagccacctcctctacgtcctgtgccaca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_6fd67fa2ef9fa6b196ea7300c51ad82c.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6fd67fa2ef9fa6b196ea7300c51ad82c.msa deleted file mode 100644 index 0cb649c4..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_6fd67fa2ef9fa6b196ea7300c51ad82c.msa +++ /dev/null @@ -1,75 +0,0 @@ ->syndip_1_chr20:62270279-62271094 -tccctgttgccactagcacctcctcctccactccctcctggcctctctgggtcctctcct -tgtccctcctggcctctctgggtcctctccttgtccctccctgacctctctgggtcctct -ccttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtc -ctctccttgtccctctctgggtcctctccttgtccctc-ctggcctctctgggtcctctc -cttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctct---g -acctctctgagtcctctccttgtc-----------------------------cctctct -gggtcctctccttgtccctctctgggtcctctccttgtccctctctgggtcctctccttg -tccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctctc -cttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgt -ccctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctc -tctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtc -cctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctct -ctggcctctctgggtcctttccttgtccctttctggtctctctggtcctctccttctctc -cttgtccctctccctctgcctctgctttgcccacccc ->syndip_2_chr20:62270279-62271094 -tccctgttgccactagcacctcctcctccactccctcctggcctctctgggtcctctcct -tgtccctcctggcctctctgggtcctctccttgtccctccctgacctctctgggtcctct -ccttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtc -ctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctc -cttgtccctctctgggtcctctccttgtccctc-ct-----------------------g -gcctctctgggtcctctccttgtc------------------------------------ ------------------------------------------------------------- ------------cctctctgggtcctctccttgtccctctctgacctctctgggtcctctc -cttgtccctctctgggtcctctccttgtc------------------------------- -----------cctctctgggtcctctccttgtccctctctgggtcctctccttgtccctc -tctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtc -cctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctct -ctggcctctctgggtcctttccttgtccctttctggtctctctggtcctctccttctctc -cttgtccctctccctctgcctctgctttgcccacccc ->p:HG002_1_chr20:62270279-62271094 -tccctgttgccactagcacctcctcctccactccctcctggcctctctgggtcctctcct -tgtccctcctggcctctctgggtcctctccttgtccctccctgacctctctgggtcctct -ccttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtc -ctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctc -cttgtccctctctgggtcctctccttgtccctc-ct-----------------------g -gcctctctgggtcctctccttgtc------------------------------------ ------------------------------------------------------------- ------------cctctctgggtcctctccttgtccctctctgacctctctgggtcctctc -cttgtccctctctgggtcctctccttgtc------------------------------- -----------cctctctgggtcctctccttgtccctctctgggtcctctccttgtccctc -tctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtc -cctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctct -ctggcctctctgggtcctttccttgtccctttctggtctctctggtcctctccttctctc -cttgtccctctccctctgcctctgctttgcccacccc ->p:HG002_2_chr20:62270279-62271094 -tccctgttgccactagcacctcctcctccactccctcctggcctctctgggtcctctcct -tgtccctcctggcctctctgggtcctctccttgtccctccctgacctctctgggtcctct -ccttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtc -ctctccttgtccctctctgggtcctctccttgtccctc-ctggcctctctgggtcctctc -cttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctct---g -acctctctgagtcctctccttgtc-----------------------------cctctct -gggtcctctccttgtccctctctgggtcctctccttgtccctctctgggtcctctccttg -tccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctctc -cttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgt -ccctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctc -tctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtc -cctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctct -ctggcctctctgggtcctttccttgtccctttctggtctctctggtcctctccttctctc -cttgtccctctccctctgcctctgctttgcccacccc ->ref_chr20:62270279-62271094 -tccctgttgccactagcacctcctcctccactccctcctggcctctctgggtcctctcct -tgtccctcctggcctctctgggtcctctccttgtccctccctgacctctctgggtcctct -ccttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtc -ctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctc -cttgtccctctctgggtcctctccttgtccctc-ctggcctctctgggtcctctccttgt -ccctctctgggtcctctccttgtccctctctggcctctctgggtcctctctgacctctct -gggtcctctccttgtccctctctgggtcctctccttgtccctctctgggtcctctccttg -tccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctctc -cttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgt -ccctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctc -tctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtc -cctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctct -ctggcctctctgggtcctttccttgtccctttctggtctctctggtcctctccttctctc -cttgtccctctccctctgcctctgctttgcccacccc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_71a4fc69c43e60ca0e23760b42947280.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_71a4fc69c43e60ca0e23760b42947280.msa deleted file mode 100644 index 3d2a2ffd..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_71a4fc69c43e60ca0e23760b42947280.msa +++ /dev/null @@ -1,70 +0,0 @@ ->syndip_1_chr20:62360190-62360712 -atccacgtggtcaggaaagtgggtgagaaggaaggaagacggtgcaggtgtggagggagg -aatgagcagacaggtggacagatggatggaaacaaggaataaagggtgggtgctgcatag -gtaggggggtgggtgggtggatggatgggtagggggtgggtgggtggatacgttgggggt -gggtgggtgggtgggtcagcaggcagagggatgggataggataggtgggtgggtgggtgg -atagggagggggtggggtgggtgcataggtaggggggtggatgggtcagcaggcagcggg -atgggataggataggtgggtgggtggagggatagatgggtggtgggtgggtggagggata -gatgggtgggtgggtgggtagaaggataggtaggtgggtgggtgggtggatggataggtg -gatgggtgggtggaggaatagatgggtgggtgggtgggtgggtggatggataggtgggtg -ggtgggtggagggatagatgggtgggtggatgggtgggtggagggatagatgggtggtgg -gtgggtggagggatagatgggtgggtgggtgggtagaaggataggtaggtgggtgggtgg -gtggatggataggtgggtgggtgggtggaggaatagatgggtgggtggatgggtgggtgg -agggatagatgggtgggtgggtgggtggagggatagatgggtgggtgggtggagggacca -cttcccaggtggagtggaaagggttcc ->syndip_2_chr20:62360190-62360712 -atccacgtggtcaggaaagtgggtgagaaggaaggaagacggtgcaggtgtggagggagg -aatgagcagacaggtggacagatggatggaaacaaggaataaagggtgggtgctgcatag -gtaggggggtgggtgggtggatggatgggtagggggtgggtgggtggatacgttgggggt -gggtgggtgggtgggtcagcaggcagagggatgggataggataggtgggtgggtggaggg -atagatggg--------------------------------------------------- -------------tggtgggtgggtggagggatagatgggtgg-------gtggagggata -ga----tgggtgggtgggtagaaggataggtaggtgggtgggtgggtggatggataggtg -gatgggtgggtggaggaatagatgggtg-------------------------------- --------------------------------------------------------ggtgg -gtgggtgggtggatggataggtgggtgggtgggtggaggaataga--------------- --------------------------------------tgggtgggtggatgggtgggtgg -agggatagatgggtgggtgggtgggtggagggatagatgggtgggtgggtggagggacca -cttcccaggtggagtggaaagggttcc ->p:HG002_1_chr20:62360190-62360712 -atccacgtggtcaggaaagtgggtgagaaggaaggaagacggtgcaggtgtggagggagg -aatgagcagacaggtggacagatggatggaaacaaggaataaagggtgggtgctgcatag -gtaggggggtgggtgggtggatggatgggtagggggtgggtgggtggatacgttgggggt -gggtgggtgggtgggtcagcaggcagagggatgggataggataggtgggtgggtggaggg -atagatggg--------------------------------------------------- -------------tggtgggtgggtggagggatagatgggtgg-------gtggagggata -ga----tgggtgggtgggtagaaggataggtaggtgggtgggtgggtggatggataggtg -gatgggtgggtggaggaatagatgggtg-------------------------------- --------------------------------------------------------ggtgg -gtgggtgggtggatggataggtgggtgggtgggtggaggaataga--------------- --------------------------------------tgggtgggtggatgggtgggtgg -agggatagatgggtgggtgggtgggtggagggatagatgggtgggtgggtggagggacca -cttcccaggtggagtggaaagggttcc ->p:HG002_2_chr20:62360190-62360712 -atccacgtggtcaggaaagtgggtgagaaggaaggaagacggtgcaggtgtggagggagg -aatgagcagacaggtggacagatggatggaaacaaggaataaagggtgggtgctgcatag -gtaggggggtgggtgggtggatggatgggtagggggtgggtgggtggatacgttgggggt -gggtgggtgggtgggtcagcaggcagagggatgggataggataggtgggtgggtgggtgg -atagggagggggtggggtgggtgcataggtaggggggtggatgggtcagcaggcagcggg -atgggataggataggtgggtgggtggagggatagatgggtggtgggtgggtggagggata -gatgggtgggtgggtgggtagaaggataggtaggtgggtgggtgggtggatggataggtg -gatgggtgggtggaggaatagatgggtgggtgggtgggtgggtggatggataggtgggtg -ggtgggtggagggatagatgggtgggtggatgggtgggtggagggatagatgggtggtgg -gtgggtggagggatagatgggtgggtgggtgggtagaaggataggtaggtgggtgggtgg -gtggatggataggtgggtgggtgggtggaggaatagatgggtgggtggatgggtgggtgg -agggatagatgggtgggtgggtgggtggagggatagatgggtgggtgggtggagggacca -cttcccaggtggagtggaaagggttcc ->ref_chr20:62360190-62360712 -atccacgtggtcaggaaagtgggtgagaaggaaggaagacggtgcaggtgtggagggagg -aatgagcagacaggtggacagatggatggaaacaaggaataaagggtgggtgctgcatag -gtaggggggtgggtgggtggatggatgggta-ggggtgggtgggtggatacgttgggggt -gggtgggtgggtgggtcagcaggcagagggatgggataggataggtgggtgggtggaggg -atgggtg----------------------------------------------------- --------------agtgggtgggtggagggatagatgggtgg------------------ -------tgggtgggtggagggatagatgggt-ggtgggtgggtggagggatagatgggtg -ggtgggtgggtggagggatagatgggt--------------------------------- --------------------------------------------------------ggtgg -gtgggtggagggatagatgggtggatgggtgggtagaaggataggtaggtggg------- --------------------------------------tgggtgggtggatgggtgggtgg -agggatagatgggtgggtgggtgggtggagggatagatgggtgggtgggtggagggacca -cttcccaggtggagtggaaagggttcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_7253cbbea437a5ec4d1dc4d570629ba6.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7253cbbea437a5ec4d1dc4d570629ba6.msa deleted file mode 100644 index 5d9682a7..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_7253cbbea437a5ec4d1dc4d570629ba6.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:35580586-35580856 -gcagtgagccgagatcgcgccactgcagcctaggcagcagagtgagactctgtcttaaaa -tatatattatggtttattttattttatggttaaaggccatatatatatatatat-atata -tatataatatatatatatataaaatatatatatataaaatatatatatatataaaatata -tatatataaaatatatatatatatataaaatatatatatataaaatatatatatataaaa -tatatatatatataaaatatatatatatataaaatatatatatataaaatatatatatat -ataaaatatatatatataaaatatatatatataaaatatatatatatataaaatatatat -atataaaatatatatatataaaatatatatatatataatatatatatataaaatatatat -atat--aaaatatatataaaatatatatatataaaatatatatataatatatatatataa -aatatatatatataatatatatatataaaatatatatatataaaatatatatatatataa -aatatatatatatataaaatatatatat ->syndip_2_chr20:35580586-35580856 -gcagtgagccgagatcgcgccactgcagcctaggcagcagagtgagactctgtcttaaaa -tatatattatggtttattttattttatggttaaaggccatatatatat---------ata -tatatatataaaatatatataaaatatatatatata---------------------ata -tatatataaaatatatatatat------aatatatatatataaaatatatatatataaaa -tatatatatatataaaatatatatatatataaaatatatatat----------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------- ->p:HG002_1_chr20:35580586-35580856 -gcagtgagccgagatcgcgccactgcagcctaggcagcagagtgagactctgtcttaaaa -tatatattatggtttattttattttatggttaaaggccatatatat-------------- -------------atatatataaaatatatatatataaaatatatatat------aatata -tatatataaaatatatatatat------aatatatatatataaaatatatatatataaaa -tatatatatatataaaatatatatatatataaaatatatatat----------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------- ->p:HG002_2_chr20:35580586-35580856 -gcagtgagccgagatcgcgccactgcagcctaggcagcagagtgagactctgtcttaaaa -tatatattatggtttattttattttatggttaaaggccatatatatatatatataaaata -tatatatataatatatatataaaatatatatatataaaatatatatatatataaaatata -tatatataaaatatatatatatatataaaatatatatatataaaatatatatatataaaa -tatatatatatataaaatatatatatatataaaatatatatatataaaatatatatatat -ataaaatatatatatataaaatatatatatataaaatatatatatatataaaatatatat -atataaaatatatatatataaaatatatatatatataatatatatatataaaatatatat -atataaaaaatatatataaaatatatatatataaaatatatatataatatatatatataa -aatatatatatataatatatatatataaaatatatatatataaaatatatatatatataa -aatatatatatatataaaatatatatat ->ref_chr20:35580586-35580856 -gcagtgagccgagatcgcgccactgcagcctaggcagcagagtgagactctgtcttaaaa -tatatattatggtttattttattttatggttaaaggccatatatatatatatataaaata -tatatatataaaatatatataaaatatatatatataaaatatatatat------aatata -tatatataaaatatatatatat------aatatatatatataaaatatatatatataaaa -tatatatatatataaaatatatatatatataaaatatatatat----------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_73dc8432c7f7e8affaa891ff7c4d68ac.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_73dc8432c7f7e8affaa891ff7c4d68ac.msa deleted file mode 100644 index b35e4943..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_73dc8432c7f7e8affaa891ff7c4d68ac.msa +++ /dev/null @@ -1,275 +0,0 @@ ->syndip_1_chr20:62057573-62059139 -cagtgatgcccagtgggggacacaaagggcccagcaagacctcaggaaggacggacacag -gtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcagg -aaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctca -gcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcg -gggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccaca -gacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggcctac -acaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggac -ggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaaga -cctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggc -caacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaat -ggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca -ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca -ggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcag -gaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacctc -agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc -ggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccac -agacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtct -acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga -cggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaag -acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggg -ccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaa -tggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacac -caggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggaca -caggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctca -ggaaggacggacacaggtctacac------------------------------------ --------------------------------------accaggccacagacaatggggct -cgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccac -agacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggccta -cacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaagga -cggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaa -gacctcaggaaggacggacacaggtctacacaccaggccacagacagtggggctcggggg -gccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagaca -atggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac -caggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggac -acaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacct -caggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaac -ctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatgggg -ctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggc -cacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacagg -tctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaa -ggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcag -caagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgg -gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga -caatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacac -accaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgga -cacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacc -tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggcca -acctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatgg -ggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccagg -ccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacagg -tctacacaccaggccacagacaatggggctcggggggccaacctctccagtccccaaaca -cagtccccaacagacaacttctcctgtccccacatgcggctcccaacaaacaatttctcc -tgccctcacacgcggttcccaacgacaacttctgctccacaacatgacacccacggtggg -aga ->syndip_2_chr20:62057573-62059139 -cagtgatgcccagtgggggacacaaagggcccagcaagacctcaggaaggac-------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -ggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaaga -cctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc-gggggc -caacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaat -ggggctcgggggccaacctcagcaagacctcaggaaggacggac---------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------a -caggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctca -ggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacct -cagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggct -cgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccac -agacaatggggctcg--------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------ggggccaacctctccagtccccaaaca -cagtccccaacagacaacttctcctgtcctcacatgcggctcccaacaaacaatttctcc -tgccctcacacgcggttcccaacgacaacttctgctccacaacatgacacccacggtggg -aga ->p:HG002_1_chr20:62057573-62059139 -cagtgatgcccagtgggggacacaaagggcccagcaagacctcaggaaggac-------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -ggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaaga -cctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc-gggggc -caacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaat -ggggctcgggggccaacctcagcaagacctcaggaaggacggac---------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------a -caggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctca -ggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacct -cagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggct -cgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccac -agacaatggggctcg--------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------ggggccaacctctccagtccccaaaca -cagtccccaacagacaacttctcctgtcctcacatgcggctcccaacaaacaatttctcc -tgccctcacacgcggttcccaacgacaacttctgctccacaacatgacacccacggtggg -aga ->p:HG002_2_chr20:62057573-62059139 -cagtgatgcccagtgggggacacaaagggcccagcaagacctcaggaaggacggacacag -gtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcagg -aaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctca -gcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcg -gggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccaca -gacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggcctac -acaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggac -ggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaaga -cctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggc -caacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaat -ggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca -ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca -ggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcag -gaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacctc -agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc -ggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccac -agacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtct -acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga -cggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaag -acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggg -ccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaa -tggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacac -caggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggaca -caggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctca -ggaaggacggacacaggtctacac------------------------------------ --------------------------------------accaggccacagacaatggggct -cgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccac -agacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggccta -cacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaagga -cggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaa -gacctcaggaaggacggacacaggtctacacaccaggccacagacagtggggctcggggg -gccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagaca -atggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac -caggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggac -acaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacct -caggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaac -ctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatgggg -ctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggc -cacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacagg -tctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaa -ggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcag -caagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgg -gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga -caatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacac -accaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgga -cacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacc -tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggcca -acctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatgg -ggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccagg -ccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacagg -tctacacaccaggccacagacaatggggctcggggggccaacctctccagtccccaaaca -cagtccccaacagacaacttctcctgtccccacatgcggctcccaacaaacaatttctcc -tgccctcacacgcggttcccaacgacaacttctgctccacaacatgacacccacggtggg -aga ->ref_chr20:62057573-62059139 -cagtgatgcccagtgggggacacaaagggcccagcaagacctcaggaaggacggacacag -gcctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcagg -aaggacggacacaggcctacacaccaggccacagacaatggggctcg------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------gggggccaacctcagcaagacctcaggaaggacggacacaggcctac -acaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggac -ggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaaga -cctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggc -caacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaat -ggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca -ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca -ggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcag -gaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacctc -agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc -ggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccac -agacaatggggctcggggggccaacctcagcaagacctcaggaaggacggac-------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------a -caggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctca -ggaaggacggacacaggtctacac------------------------------------ --------------------------------------accaggccacagacaatggggct -cgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccac -agacaatggggctcg--------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------gggggccaacctcagcaagacctcaggaa -ggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcag -caagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgg -gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga -caatggggctcgggggccaacctcagcaagacctcaggaaggacgga------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------cacaggtctacacaccagg -ccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacagg -tctacacaccaggccacagacaatggggctcggggggccaacctctccagtccccaaaca -cagtccccaacagacaacttctcctgtccccacatgcggctcccaacaaacaatttctcc -tgccctcacacgcggttcccaacgacaacttctgctccacaacatgacacccacggtggg -aga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_74f977ac65710362132c1bd4c4f85390.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_74f977ac65710362132c1bd4c4f85390.msa deleted file mode 100644 index bc9c1724..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_74f977ac65710362132c1bd4c4f85390.msa +++ /dev/null @@ -1,65 +0,0 @@ ->syndip_1_chr20:63559288-63559963 -ggcaggcacgagggtctgctgagcctcgcagaagtccaggaggctacgccagagggggca -gcagcgcagaaggaggtggtctcctgtgagggtgggagtcagatgggagtcagtcagggt -caggtgggaggagtcagggtcaggtgggag------------------------------ -----------tcagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcaga -gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggt---cggagtcagg -gtcaggtgggaggagtcagggtcaggtgggagtcagtcagggtcaggtgggagg------ ------------------------------------------------------------- -------------agtcagggtcaggtgggaggagtcagggtcaggtgggaggagtcaggg -tcagatgggagtcagtcagagtcaggtgggaggagtcagggtcaggtgggaggagtcagg -gtcaggtcggagtcagggtcaggcaggagtcggcagctccctagcccagccctggcctca -cctgtgttcccaccctggaagagcccagccccgccctcaccgatcaggcagagcccctcc -tgggcccgcgtgacag ->syndip_2_chr20:63559288-63559963 -ggcaggcacgagggtctgctgagcctcgcagaagtccaggaggctacgccagagggggca -gcagcgcagaaggaggtggtctcctgtgagggtgggagtcagatgggagtcagtcagggt -caggtggga--------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------ggagtcagg -gtcaggtgggaggagtcagggtcaggtgggagtc-------------------------- ------------------------------------------------------------- -------------agtcagggtcaggtgggaggagtcagggtcaggtgggaggagtcaggg -tcagatgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgggaggagtcagg -gtcaggtcggagtcagggtcaggcaggagtcggcagctccctagcccagccctggcctca -cctgtgttcccaccctggaagagcccagccccgccctcaccgatcaggcagagcccctcc -tgggcccgcgtgacag ->p:HG002_1_chr20:63559288-63559963 -ggcaggcacgagggtctgctgagcctcgcagaagtccaggaggctacgccagagggggca -gcagcgcagaaggaggtggtctcctgtgagggtgggagtcagatgggagtcagtcagggt -caggtggga--------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------ggagtcagg -gtcaggtgggaggagtcagggtcaggtgggagtc-------------------------- ------------------------------------------------------------- -------------agtcagggtcaggtgggaggagtcagggtcaggtgggaggagtcaggg -tcagatgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgggaggagtcagg -gtcaggtcggagtcagggtcaggcaggagtcggcagctccctagcccagccctggcctca -cctgtgttcccaccctggaagagcccagccccgccctcaccgatcaggcagagcccctcc -tgggcccgcgtgacag ->p:HG002_2_chr20:63559288-63559963 -ggcaggcacgagggtctgctgagcctcgcagaagtccaggaggctacgccagagggggca -gcagcgcagaaggaggtggtctcctgtgagggtgggagtcagatgggagtcagtcagggt -caggtgggaggagtcagggtcaggtgggag------------------------------ -----------tcagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcaga -gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggt---cggagtcagg -gtcaggtgggaggagtcagggtcaggtgggagtcagtcagggtcaggtgggagg------ ------------------------------------------------------------- -------------agtcagggtcaggtgggaggagtcagggtcaggtgggaggagtcaggg -tcagatgggagtcagtcagagtcaggtgggaggagtcagggtcaggtgggaggagtcagg -gtcaggtcggagtcagggtcaggcaggagtcggcagctccctagcccagccctggcctca -cctgtgttcccaccctggaagagcccagccccgccctcaccgatcaggcagagcccctcc -tgggcccgcgtgacag ->ref_chr20:63559288-63559963 -ggcaggcacgagggtctgctgagcctcgcagaagtccaggaggctacgccagagggggca -gcagcgcagaaggaggtggtctcctgtgagggtgggagtcagatgggagtcagtcagggt -caggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtgggagtcagtcaggg -tcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcaga -gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtgggaggagtcagg -gtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcag -ggtcaggtgggaggagtcagggtcaggtcggagtcagggtcaggtgggaggagtcagggt -caggtgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgggaggagtcaggg -tcagatgggagtcagtcagagtcaggtgggaggagtcagggtcaggtgggaggagtcagg -gtcaggtcggagtcagggtcaggcaggagtcggcagctccctagcccagccctggcctca -cctgtgttcccaccctggaagagcccagccccgccctcaccgatcaggcagagcccctcc -tgggcccgcgtgacag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_76652f704e7f5d8065ba92e110437e4d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_76652f704e7f5d8065ba92e110437e4d.msa deleted file mode 100644 index 9b27e60f..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_76652f704e7f5d8065ba92e110437e4d.msa +++ /dev/null @@ -1,250 +0,0 @@ ->syndip_1_chr20:62057502-62058868 -tacctggctacgctcctctcacaactttgagatcaagatgccacgtgtgccttcctcaca -tcggcgctttccagtgatgcccagtgggggacacaaagggcccagcaagacctcaggaag -gacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcagc -aagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctc-gg -gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga -caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctaca -caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg -acacaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaagac -ctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggcca -acctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatgg -ggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccag -gccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacag -gtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga -aggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctca -gcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcg -ggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacag -acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctac -acaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggac -ggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaaga -cctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggcc -aacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatg -gggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacacca -ggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacac -aggcctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcag -gaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctc -agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc -gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca -gacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggcctac -acaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggac -ggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaag -acctcaggaaggacggacacaggtctacacaccaggccacagacagtggggctcgggggg -ccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaa -tggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc -aggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggaca -caggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctc -aggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacc -tcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggc -tcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggcc -acagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggt -ctacacaccaggccacagacaatggggctc-gggggccaacctcagcaagacctcaggaa -ggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcag -caagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgg -gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga -caatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacac -accaggccacagacaatggggctc-gggggccaacctcagcaagacctcaggaaggacgg -acacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagac -ctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggcc -aacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatg -gggctcgggggccaacctcagcaagacctcagg ->syndip_2_chr20:62057502-62058868 -tacctggctacgctcctctcacaactttgagatcaagatgccacgtgtgccttcctcaca -tcggcgctttccagtgatgcccagtgggggacacaaagggcccagcaagacctcaggaag -gacggacacaggtctacacaccaggccacagacaatggggctc-gggggccaacctcagc -aagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc-gg -gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga -caatggggctc-gggggccaacctcagcaagacctcaggaaggacggacacaggcctaca -caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg -acacaggtctacacaccaggccacagacaatggggctc-gggggccaacctcagcaagac -ctcagg------------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------- ->p:HG002_1_chr20:62057502-62058868 -tacctggctacgctcctctcacaactttgagatcaagatgccacgtgtgccttcctcaca -tcggcgctttccagtgatgcccagtgggggacacaaagggcccagcaagacctcaggaag -gacggacacaggtctacacaccaggccacagacaatggggctc-gggggccaacctcagc -aagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggg -gggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacaga -caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctaca -caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg -acacaggtctacacaccaggccacagacaatggggctc-gggggccaacctcagcaagac -ctcagg------------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------- ->p:HG002_2_chr20:62057502-62058868 -tacctggctacgctcctctcacaactttgagatcaagatgccacgtgtgccttcctcaca -tcggcgctttccagtgatgcccagtgggggacacaaagggcccagcaagacctcaggaag -gacggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagc -aagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc-gg -gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga -caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctaca -caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg -acacaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaagac -ctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggcca -acctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatgg -ggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccag -gccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacag -gtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga -aggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctca -gcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcg -ggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacag -acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctac -acaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggac -ggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaaga -cctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggcc -aacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatg -gggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacacca -ggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacac -aggcctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcag -gaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctc -agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc -gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca -gacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggcctac -acaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggac -ggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaag -acctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggg -ccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaa -tggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc -aggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggaca -caggcctacacaccaggccacagacaatggggctc-gggggccaacctcagcaagacctc -aggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacc -tcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggc -tcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggcc -acagacaatggggctc-gggggccaacctcagcaagacctcaggaaggacggacacaggt -ctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaa -ggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcag -caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg -gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga -caatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacac -accaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacgg -acacaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaagac -ctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctc-gggggcc -aacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatg -gggctcgggggccaacctcagcaagacctcagg ->ref_chr20:62057502-62058868 -tacctggctacgctcctctcacaactttgagatcaagatgccacgtgtgccttcctcaca -tcggcgctttccagtgatgcccagtgggggacacaaagggcccagcaagacctcaggaag -gacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcagc -aagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcggg -gggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacaga -caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctaca -caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg -acacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagac -ctcagg------------------------------------------------------ ------------------------------------------------------------- ----------------------------------aaggacggacacaggcctacacaccag -gccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacag -gtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga -aggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctca -gcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcg -ggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacag -acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctac -acaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggac -ggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaaga -cctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggcc -aacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatg -gggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacacca -ggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacac -aggcctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcag -gaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctc -agcaagacctcagg---------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_786136b3c2690bd2db0b1ed0059f1abd.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_786136b3c2690bd2db0b1ed0059f1abd.msa deleted file mode 100644 index 9be2c94a..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_786136b3c2690bd2db0b1ed0059f1abd.msa +++ /dev/null @@ -1,60 +0,0 @@ ->syndip_1_chr20:2240860-2241390 -ctcagtgttgttatctacaaatgggagaatcaaggcaccctcctacaagcggcggctcat -cagctcacttggaaaatgtagtcatcttctcaaagttttctttttctttctttctttttc -ctttctttctttctttttctttctttctctctctctccttccttccttctttccttccct -ccctcccttccttttttcttctttctttcattttctttctttctctctttcttctttctc -ttcctttc---------------------------------------------------- ----ttctttcttttcctcctt-------cctcccttcttt--------------ccttcc -cttccttcttccctccctccctctttgtttctttctttctctccctc------------- ------------------------------------------------------------- -----------------------cttccctccctccctttctttctcctt----------- -ttcttccttccctccctgcctgtctccctctttctttctcttttttcttttccttccttc -cgtctttttcctcccttctttcctccctcctccctccctccctcctccctctttttctt ->syndip_2_chr20:2240860-2241390 -ctcagtgttgttatctacaaatgggagaatcaaggcaccctcctacaagcggcggctcat -cagctcacttggaaaatgtagtcatcttctcaaagttttctt------------------ --tttctttctttctttttctttctttctctctctctccttccttccttctttccttccct -ccctcccttccttttttcttcttcctttcattttctttctttctctctttcttctttctc -ttcctttc---------------------------------------------------- ----ttctttcttttcctcctt-------cctcccttcttt--------------ccttcc -cttccttcttccctccctccctctttgtttctttctttctctccctccttccctccctcc -ctttcttccttctttccttatccctcccttctttccttccttccctttgtttctctttct -ttctttctttctctctctcttccttccttccctccctccctccctccttcctcccttctt -tccttccctccctgcctctctgtctccctctttctttctcttttttcttttccttccttc -cgtctttttcctcccttctttcctccctcctccctccctccctcctccctctttttctt ->p:HG002_1_chr20:2240860-2241390 -ctcagtgttgttatctacaaatgggagaatcaaggcaccctcctacaagcggcggctcat -cagctcacttggaaaatgtagtcatcttctcaaagttttctttttctttctttctttttc -ctttctttctttctttttctttctttctctctctctccttccttccttctttccttccct -ccctcccttccttttttcttctttctttcattttctttctttctctctttcttctttctc -ttcctttctttccttccgtccctcccttccttccttttttcttcttcctttcattttctt -tctttctctctttcttctttcctccctttcttccttctttccttatccctcccttcttcc -tttcttctttcttttcctccttcctcccttctttccttcccttcctt------------- ------------------------------------------------------------- -----------------------cttccctccctccctctttgtttctttctttctctccc -tccttccctccctccctttctgtctccctctttctttctcttttttcttttccttccttc -cgtctttttcctcccttctttcctccctcctccctccctccctcctccctctttttctt ->p:HG002_2_chr20:2240860-2241390 -ctcagtgttgttatctacaaatgggagaatcaaggcaccctcctacaagcggcggctcat -cagctcacttggaaaatgtagtcatcttctcaaagttttctttttctttctttctttttc -ctttctttctttctttttctttctttctctctctctccttccttccttctttccttccct -ccctcccttccttttttcttctttctttcattttctttctttctctctttcttctttctc -ttcctttc---------------------------------------------------- ----ttctctctttcttctttc---------------------------------tcttcc -tttcttctttcttttcctccttcctcccttctttccttcccttcctt------------- ------------------------------------------------------------- -----------------------cttccctccctccctctttgtttctttctttctctccc -tccttccctccctccctttctgtctccctctttctttctcttttttcttttccttccttc -cgtctttttcctcccttctttcctccctcctccctccctccctcctccctctttttctt ->ref_chr20:2240860-2241390 -ctcagtgttgttatctacaaatgggagaatcaaggcaccctcctacaagcggcggctcat -cagctcacttggaaaatgtagtcatcttctcaaagttttctttttctttctttctttttc -ctttctttctttctttttctttctttctctctctctccttccttccttctttccttccct -ccctcccttccttttttcttctttctttcattttctttctttctctctttcttctttctc -ttcctttctttccttccgtccctcccttccttccttttttcttcttcctttcattttctt -tctttctctctttcttctttc---------------------------------tcttcc -tttcttctttcttttcctccttcctcccttctttccttcccttcctt------------- ------------------------------------------------------------- -----------------------cttccctccctccctctttgtttctttctttctctccc -tccttccctccctccctttctgtctccctctttctttctcttttttcttttccttccttc -cgtctttttcctcccttctttcctccctcctccctccctccctcctccctctttttctt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_7a076a28a734c11d216a268762b93b02.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7a076a28a734c11d216a268762b93b02.msa deleted file mode 100644 index 7b6c062a..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_7a076a28a734c11d216a268762b93b02.msa +++ /dev/null @@ -1,210 +0,0 @@ ->syndip_1_chr20:55943719-55946007 -tgttcttcaaatgtctcctttggggagccttgcatgaaacccccaggaagaattaaggac -aattttgaacacaactctagatcaggccaacatcttctctgtgctgggtactgtcccagt -cctcctacctgtttacctcacttccacccttgcctccttccaagtcaatcccatgggaac -cagcattttctgaaactcaataaaattagctagcatttcagccaggtgcagtggctcaag -cctgtaatcccagcactttgggaggccaaggtgggtggatcacttgaggttaggagtttg -agaccagcctggccaacatggtgaaacctcgcctctactaaaaatacaaaaattagctgg -gcatgctggcatgtgcctgtaatcccagctactcaggaggctgaggcaggagaactgctt -gagcctgggaggcagaggttgcagtgagctgagatggcaccactgcattccagctgggca -acagagagagactctttcttaaatatatatattttatatatatatagatacacacacaca -cacacacacacacac----------------------------------atatatatata -tatatatatatatatatatatatgcatgcatgccagatgcagtggctcacgcctgtaatc -ccagcactttgagaggccaaggtgggcagatcatctgaggtcaggagttccagaccagcc -tagccaacatggtgaaactccatctctactaaaaatacaaaattagctggctgtggtggc -tcatgctggtaatcccagctacttgggaggctgaggcaggagaatcacttgaacctggga -ggtggaggttgcagtgagccgagatcacaccactgcactccagcctggatgacagagcga -gactccattaaaaaaatatatctatatctatagatatctatagatatatatctagatata -gatctatgagtatatatctatagatatctagatatatatttatagatagatatatctata -gatatctatatatttctatcgatagagatatctatagatatctatcaatatatctataga -tttctagagatatgtatctagatataaatctatagacatagatatagatatatagatatt -taactgccaatgtcctaaacactttatactcaacacattttttataaaaaaaaatagata -tcggtctagatagtatctatctagatatcggtctagatagtatctatctagatatctgtg -tagatgtctagatatctatctagatattatctatctagatatct--gtcgctatctagat -atctatctagatatctgtcgctatctagatatctatctagatatctgtcgctatctagat -atctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctat -ctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgt -cgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagt -atctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatcta -gatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatc -tatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatcta -gatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgc -tatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatc -tgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagat -agtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctat -ctagatagtatctgtcgctatctagatatctagatagtatctgtcgctatctagatatct -agatagtatctgtctagatagctatctagatagtatctgtctagatagctatctagatag -tatctgtccagatatctgtagctatctagattgtatctgtctagatatctgtagatatct -agatatctatatctatctggatatctatagatatttaactgccgggcaatgtcctaaacc -ctttacactcaacacatttcattttataacaaaatatgaggtagatattattatttccct -caactcacagagaagaaaaaaatgaagcatatggagcccatgggctagtgacagagctgg -tatataaataaggattgaatttggctgaaaaaccccaaataacaatgactgaaatatgca -gtatcggttcacaagtagacagtc ->syndip_2_chr20:55943719-55946007 -tgttcttcaaatgtctcctttggggagccttgcatgaaacccccaggaagaattaaggac -aattttgaacacaactctagatcaggccaacatcttctctgtgctgggtactgtcccagt -cctcctacctgtttacctcacttccacccttgcctccttccaagtcaatcccatgggaac -cagcattttctgaaactcaataaaattagctagcatttcagccaggtgcagtggctcaag -cctgtaatcccagcactttgggaggccaaggtgggtggatcacttgaggttaggagtttg -agaccagcctggccaacatggtgaaacctcgcctctactaaaaatacaaaaattagctgg -gcatgctggcatgtgcctgtaatcccagctactcaggaggctgaggcaggagaactgctt -gagcctgggaggcagaggttgcagtgagctgagatggcaccactgcattccagctgggca -acagagagagactctttcttaaatatatatattttatatatatatagatacacacacaca -cacacacacacacacacacacacacacacacacacatatatatatatatatatatatata -tatatatatatatatatatatatgcatgcatgccagatgcagtggctcacgcctgtaatc -ccagcactttgagaggccaaggtgggcagatcatctgaggtcaggagttccagaccagcc -tagccaacatggtgaaactccatctctactaaaaatacaaaattagctggctgtggtggc -tcatgctggtaatcccagctacttgggaggctgaggcaggagaatcacttgaacctggga -ggtggaggttgcagtgagccgagatcacaccactgcactccagcctggatgacagagcga -gactccattaaaaaaatatatctatatctatagatatctatagatatatatctagatata -gatctatgagtatatatctatagatatctagatatatatttatagatagatatatctata -gatatctatatatttctatcgatagagatatctatagatatctatcaatatatctataga -tttctagagatatgtatctagatataaatctatagacatagatatagatatatagatatt -taactgccaatgtcctaaacactttatactcaacacattttttataaaaaaaaatagata -tcggtctagatagtatctatctagatatcggtctagatagtatctatctagatatcgg-- -------------------tctagatagtatctatctagatatctgcgtagatgtctagat -atctatctagatat---------------tatctatctaga------------------- ------------------------------------------------------------- ---------------------tatctgtcgctatctagatatctatctaga---tatctgt -cgctatctagatatctatctaga------------------------------------- ---------------------------------tatctgtcgctatctagatatctatcta -gatatcatctgtcgctatctagatatctatctagatatcatctgtcgctatctagatatc -tatctagatatcatctgtcgctatctagatatctatctagatatcatctgtcgctatcta -gatatctatctagatatcatctgtcgctatctagatatctatctagatagtatctgtcgc -tatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatc -tgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagat -agtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctat -ctagatagtatctgtcgctatctagatatctagatagtatctgtcgctatctagatatct -agatagtatctgtctagatagctatctagatagtatctgtctagatagctatctagatag -tatctgtccagatatctgtagctatctagattgtatctgtctagatatctgtagatatct -agatatctatatctatctggatatctatagatatttaactgccgggcaatgtcctaaacc -ctttacactcaacacatttcattttataacaaaatatgaggtagatattattatttccct -caactcacagagaagaaaaaaatgaagcatatggagcccatgggctagtgacagagctgg -tatataaataaggattgaatttggctgaaaaaccccaaataacaatgactgaaatatgca -gtatcggttcacaagtagacagtc ->p:HG002_1_chr20:55943719-55946007 -tgttcttcaaatgtctcctttggggagccttgcatgaaacccccaggaagaattaaggac -aattttgaacacaactctagatcaggccaacatcttctctgtgctgggtactgtcccagt -cctcctacctgtttacctcacttccacccttgcctccttccaagtcaatcccatgggaac -cagcattttctgaaactcaataaaattagctagcatttcagccaggtgcagtggctcaag -cctgtaatcccagcactttgggaggccaaggtgggtggatcacttgaggttaggagtttg -agaccagcctggccaacatggtgaaacctcgcctctactaaaaatacaaaaattagctgg -gcatgctggcatgtgcctgtaatcccagctactcaggaggctgaggcaggagaactgctt -gagcctgggaggcagaggttgcagtgagctgagatggcaccactgcattccagctgggca -acagagagagactctttcttaaatatatatattttatatatatatagatacacacacaca -cacacacacacacacacacacacacacacacacacatatatatatatatatatatatata -tatatatatatatatatatatatgcatgcatgccagatgcagtggctcacgcctgtaatc -ccagcactttgagaggccaaggtgggcagatcatctgaggtcaggagttccagaccagcc -tagccaacatggtgaaactccatctctactaaaaatacaaaattagctggctgtggtggc -tcatgctggtaattccagctacttgggaggctgaggcaggagaatcacatgaacctggga -ggtggaggttgcagtgagccgagatcacaccactgcactccagcctggatgacagagcga -gactccattaaaaaaatatatctatatctatagatatctatagatatatatctagatata -gatctatgagtatatatctatagatatctagatatatatttatagatagatatatctata -gatatctatatatttctatcgatagagatatctatagatatctatcaatatatctataga -tttctagagatatgtatctagatataaatctatagacatagatatagatatatagatatt -taactgccaatgtcctaaacactttatactcaacacattttttataaaaaaaaatagata -tcggtctagatagtatctatctagatatcggtctagatagtatctatctagatatcgg-- -------------------tctagatagtatctatctagatatctgcgtagatgtctagat -atctatctagatat---------------tatctatctaga------------------- ------------------------------------------------------------- ---------------------tatctgtcgctatctagatatctatctaga---tatctgt -cgctatctagatatctatctaga------------------------------------- ---------------------------------tatctgtcgctatctagatatctatcta -gatatcatctgtcgctatctagatatctatctagatatcatctgtcgctatctagatatc -tatctagatatcatctgtcgctatctagatatctatctagatatcatctgtcgctatcta -gatatctatctagatatcatctgtcgctatctagatatctatctagatagtatctgtcgc -tatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatc -tgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagat -agtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctat -ctagatagtatctgtcgctatctagatatctagatagtatctgtcgctatctagatatct -agatagtatctgtctagatagctatctagatagtatctgtctagatagctatctagatag -tatctgtccagatatctgtagctatctagattgtatctgtctagatatctgtagatatct -agatatctatatctatctggatatctatagatatttaactgccgggcaatgtcctaaacc -ctttacactcaacacatttcattttataacaaaatatgaggtagatattattatttccct -caactcacagagaagaaaaaaatgaagcatatggagcccatgggctagtgacagagctgg -tatataaataaggattgaatttggctgaaaaatcccaaataacaatgactgaaatatgca -gtatcggttcacaagtagacagtc ->p:HG002_2_chr20:55943719-55946007 -tgttcttcaaatgtctcctttggggagccttgcatgaaacccccaggaagaattaaggac -aattttgaacacaactctagatcaggccaacatcttctctgtgctgggtactgtcccagt -cctcctacctgtttacctcacttccacccttgcctccttccaagtcaatcccatgggaac -cagcattttctgaaactcaataaaattagctagcatttcagccaggtgcagtggctcaag -cctgtaatcccagcactttgggaggccaaggtgggtggatcacttgaggttaggagtttg -agaccagcctggccaacatggtgaaacctcgcctctactaaaaatacaaaaattagctgg -gcatgctggcatgtgcctgtaatcccagctactcaggaggctgaggcaggagaactgctt -gagcctgggaggcagaggttgcagtgagctgagatggcaccactgcattccagctgggca -acagagagagactctttcttaaatatatatattttatatatatatagatacacacacaca -cacacacacacacac----------------------------------atatatatata -tatatatatatatatatatatatgcatgcatgccagatgcagtggctcacgcctgtaatc -ccagcactttgagaggccaaggtgggcagatcatctgaggtcaggagttccagaccagcc -tagccaacatggtgaaactccatctctactaaaaatacaaaattagctggctgtggtggc -tcatgctggtaatcccagctacttgggaggctgaggcaggagaatcacttgaacctggga -ggtggaggttgcagtgagccgagatcacaccactgcactccagcctggatgacagagcga -gactccattaaaaaaatatatctatatctatagatatctatagatatatatctagatata -gatctatgagtatatatctatagatatctagatatatatttatagatagatatatctata -gatatctatatatttctatcgatagagatatctatagatatctatcaatatatctataga -tttctagagatatgtatctagatataaatctatagacatagatatagatatatagatatt -taactgccaatgtcctaaacactttatactcaacacattttttataaaaaaaaatagata -tcggtctagatagtatctatctagatatcggtctagatagtatctatctagatatctgtg -tagatgtctagatatctatctagatattatctatctagatatct--gtcgctatctagat -atctatctagatatctgtcgctatctagatatctatctagatatctgtcgctatctagat -atctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctat -ctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgt -cgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagt -atctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatcta -gatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatc -tatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatcta -gatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgc -tatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatc -tgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagat -agtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctat -ctagatagtatctgtcgctatctagatatctagatagtatctgtcgctatctagatatct -agatagtatctgtctagatagctatctagatagtatctgtctagatagctatctagatag -tatctgtccagatatctgtagctatctagattgtatctgtctagatatctgtagatatct -agatatctatatctatctggatatctatagatatttaactgccgggcaatgtcctaaacc -ctttacactcaacacatttcattttataacaaaatatgaggtagatattattatttccct -caactcacagagaagaaaaaaatgaagcatatggagcccatgggctagtgacagagctgg -tatataaataaggattgaatttggctgaaaaaccccaaataacaatgactgaaatatgca -gtatcggttcacaagtagacagtc ->ref_chr20:55943719-55946007 -tgttcttcaaatgtctcctttggggagccttgcatgaaacccccaggaagaattaaggac -aattttgaacacaactctagatcaggccaacatcttctctgtgctgggtactgtcccagt -cctcctacctgtttacctcacttccacccttgcctccttccaagtcaatcccatgggaac -cagcattttctgaaactcaataaaattagctagcatttcagccaggtgcagtggctcaag -cctgtaatcccagcactttgggaggccaaggtgggtggatcacttgaggttaggagtttg -agaccagcctggccaacatggtgaaacctcgcctctactaaaaatacaaaaattagctgg -gcatgctggcatgtgcctgtaatcccagctactcaggaggctgaggcaggagaactgctt -gagcctgggaggcagaggttgcagtgagctgagatggcaccactgcattccagctgggca -acagagagagactctttcttaaatatatatattttatatatatatagatacacacacaca -cacacacacacacac----------------------------------atatatatata -tatatatatatatatatatatatgcatgcatgccagatgcagtggctcacgcctgtaatc -ccagcactttgagaggccaaggtgggcagatcatctgaggtcaggagttccagaccagcc -tagccaacatggtgaaactccatctctactaaaaatacaaaattagctggctgtggtggc -tcatgctggtaatcccagctacttgggaggctgaggcaggagaatcacttgaacctggga -ggtggaggttgcagtgagccgagatcacaccactgcactccagcctggatgacagagcga -gactccattaaaaaaatatatctatatctatagatatctatagatatatatctagatata -gatctatgagtatatatctatagatatctagatatatatttatagatagatatatctata -gatatctatatatttctatcgatagagatatctatagatatctatcaatatatctataga -tttctagagatatgtatctagatataaatctatagacatagatatagatatatagatatt -taactgccaatgtcctaaacactttatactcaacacattttttataaaaaaaaatagata -tcggtctagatagtatctatctagatatcggtctagatagtatctatctagatatctgtg -tagatgtctagatatctatctagatattatctatctagatatct--gtcgctatctagat -atctatctagatatctgtcgctatctagatatctatctaga------------------- ------------------------------------------------------------- ---------------------tatctgtcgctatctagatatctatctagatagtatctgt -cgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagt -atctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatcta -gatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatc -tatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatcta -gatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgc -tatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatc -tgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagat -agtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctat -ctagatagtatctgtcgctatctagatatctagatagtatctgtcgctatctagatatct -agatagtatctgtctagatagctatctagatagtatctgtctagatagctatctagatag -tatctgtccagatatctgtagctatctagattgtatctgtctagatatctgtagatatct -agatatctatatctatctggatatctatagatatttaactgccgggcaatgtcctaaacc -ctttacactcaacacatttcattttataacaaaatatgaggtagatattattatttccct -caactcacagagaagaaaaaaatgaagcatatggagcccatgggctagtgacagagctgg -tatataaataaggattgaatttggctgaaaaaccccaaataacaatgactgaaatatgca -gtatcggttcacaagtagacagtc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_7addaa77bbf47f3c503354c9a7c534ba.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7addaa77bbf47f3c503354c9a7c534ba.msa deleted file mode 100644 index b06769a6..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_7addaa77bbf47f3c503354c9a7c534ba.msa +++ /dev/null @@ -1,85 +0,0 @@ ->syndip_1_chr20:5041731-5042478 -agcccagaggaccctgcgtgaaggttcagtgttggagcctgcagatgctgacagtgcctg -cagctttcctgcctattttaggacttgctagaagcttggcatgtcctaaaaacccttttt -caagagtctctccccagctgctgctagcgggattttttttttaactctctatcctattta -acctcctcactgatgaccttttaatgcgtaac---------------------------- -ttttttttttttttttttttttgagacggagtctcgctctcccaggctggagtgcagtgg -tgtgatctcggctcactgcaacctgtgcctcccaggttcaagcgatctcctgcctcagcc -tccccagtacctaggattacaggtgcgcgcctccagcatagctaatgtttgtatttttag -tagagacggggtttcaccatgttggccaggctggttatgcataactttttatcacagatg -tttgatctcagttttaatcttttcaacatttgtaaacccttggttcattgtgcttctccc -tttattactc------------tttt---------------------------------- ------------------------------------------------------------- ---------------------------------------------------tttttttttt -ttgagacggagtttcgctcttgttgcccaggctggagtgcagtggcgcactctcggttca -ctgcaatctccacctcataggttcaagcgattctcctgcctcagcctcctgagtagctgg -gattacaggcacacgccaccatgcctggctaatttttctttttcttttttgtatttttag -tagagatggggtttcactat ->syndip_2_chr20:5041731-5042478 -agcccagaggaccctgcgtgaaggttcagtgttggagcctgcagatgctgacagtgcctg -cagctttcctgcctattttaggacttgctagaagcttggcatgtcctaaaaacccttttt -caagagtctctccccagctgctgctagcgggattttttttttaactctctatcctattta -acctcctcactgatgaccttttaatgcgtaactttttttttttttttttttttttttttt -ttttttttttttttttttttttgagacggagtctcgctctcccaggctggagtgcagtgg -tgtgatctcggctcactgcaacctgtgcctcccaggttcaagcgatctcctgcctcagcc -tccccagtacctaggattacaggtgcgcgcctccagcatagctaatgtttgtatttttag -tagagacggggtttcaccatgttggccaggctggttatgcataactttttatcacagatg -tttgatctcagttttaatcttttcaacatttgtaaacccttggttcattgtgcttctccc -tttattactctttttttttttttttt---------------------------------- ------------------------------------------------------------- ---------------------------------------------------tttttttttt -ttgagacggagtttcgctcttgttgcccaggctggagtgcagtggcgcactctcggttca -ctgcaatctccacctcataggttcaagcgattctcctgcctcagcctcctgagtagctgg -gattacaggcacacgccaccatgcctggctaatttttctttttcttttttgtatttttag -tagagatggggtttcactat ->p:HG002_1_chr20:5041731-5042478 -agcccagaggaccctgcgtgaaggttcagtgttggagcctgcagatgctgacagtgcctg -cagctttcctgcctattttaggacttgctagaagcttggcatgtcctaaaaacccttttt -caagagtctctccccagctgctgctagcgggattttttttttaactctctatcctattta -acctcctcactgatgaccttttaatgcgtaactttttttttttttttttttttttttttt -ttttttttttttttttttttttgagacggagtctcgctctcccaggctggagtgcagtgg -tgtgatctcggctcactgcaacctgtgcctcccaggttcaagcgatctcctgcctcagcc -tccccagtacctaggattacaggtgcgcgcctccagcatagctaatgtttgtatttttag -tagagacggggtttcaccatgttggccaggctggttatgcataactttttatcacagatg -tttgatctcagttttaatcttttcaacatttgtaaacccttggttcattgtgcttctccc -tttattactctttttttttttttttt---------------------------------- ------------------------------------------------------------- ---------------------------------------------------tttttttttt -ttgagacggagtttcgctcttgttgcccaggctggagtgcagtggcgcactctcggttca -ctgcaatctccacctcataggttcaagcgattctcctgcctcagcctcctgagtagctgg -gattacaggcacacgccaccatgcctggctaatttttctttttcttttttgtatttttag -tagagatggggtttcactat ->p:HG002_2_chr20:5041731-5042478 -agcccagaggaccctgcgtgaaggttcagtgttggagcctgcagatgctgacagtgcctg -cagctttcctgcctattttaggacttgctagaagcttggcatgtcctaaaaacccttttt -caagagtctctccccagctgctgctagcgggattttttttttaactctctatcctattta -acctcctcactgatgaccttttaatgcgtaac---------------------------- -ttttttttttttttttttttttgagacggagtctcgctctcccaggctggagtgcagtgg -tgtgatctcggctcactgcaacctgtgcctcccaggttcaagcgatctcctgcctcagcc -tccccagtacctaggattacaggtgcgcgcctccagcatagctaatgtttgtatttttag -tagagacggggtttcaccatgttggccaggctggttatgcataactttttatcacagatg -tttgatctcagttttaatcttttcaacatttgtaaacccttggttcattgtgcttctccc -tttattactcttttttttttttttttgagacggagtttcgctcttgttgcccaggctgga -gtgcagtggagcactctcggttcactgcaacctccacctcataggttcaagcgattctcc -tgcctcagcctcctgagtagctgggattacaggtgcccaccaccatgccctttttttttt -ttgagacggagtttcgctcttgttgcccaggctggagtgcagtggcgcactctcggttca -ctgcaatctccacctcataggttcaagcgattctcctgcctcagcctcctgagtagctgg -gattacaggcacacgccaccatgcctggctaatttttctttttcttttttgtatttttag -tagagatggggtttcactat ->ref_chr20:5041731-5042478 -agcccagaggaccctgcgtgaaggttcagtgttggagcctgcagatgctgacagtgcctg -cagctttcctgcctattttaggacttgctagaagcttggcatgtcctaaaaacccttttt -caagagtctctccccagctgctgctagcgggattttttttttaactctctatcctattta -acctcctcactgatgaccttttaatgcgtaac---------------------------- -ttttttttttttttttttttttgagacggagtctcgctctcccaggctggagtgcagtgg -tgtgatctcggctcactgcaacctgtgcctcccaggttcaagcgatctcctgcctcagcc -tccccagtacctaggattacaggtgcgcgcctccagcatagctaatgtttgtatttttag -tagagacggggtttcaccatgttggccaggctggttatgcataactttttatcacagatg -tttgatctcagttttaatcttttcaacatttgtaaacccttggttcattgtgcttctccc -tttattactctttttttttttttttt---------------------------------- ------------------------------------------------------------- ---------------------------------------------------tttttttttt -ttgagacggagtttcgctcttgttgcccaggctggagtgcagtggcgcactctcggttca -ctgcaatctccacctcataggttcaagcgattctcctgcctcagcctcctgagtagctgg -gattacaggcacacgccaccatgcctggctaatttttctttttcttttttgtatttttag -tagagatggggtttcactat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_7bb50c57d657828978076072c80f8a1f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7bb50c57d657828978076072c80f8a1f.msa deleted file mode 100644 index 79860f7c..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_7bb50c57d657828978076072c80f8a1f.msa +++ /dev/null @@ -1,135 +0,0 @@ ->syndip_1_chr20:18209039-18210234 -tacagttatttccaaataaaaaataagcagaaaggaaaagctaatcatctccccctattc -cagtcccccaggcatgtatccttccgtagcttctccacacctacacgaacctagacgatt -ccttccacaccttccccacacccacacgaacctagacgattccttccacaccttccccac -acccacacgaacctagatgaattccttccacaccttctccacacccacacgaacctagac -gattccttccacaccttccccacacccattctccacacccacacgaacctagacgattcc -ttccacacctccacacccacacgaacctagatgaattccttccacaccttccccacaccc -acacaaacctagacgattccttccacaccttctccacacccacacgaacctagacgaatt -ccttccagaccttctccacacccacacagacctagacgattccttccacacctccacacc -cacacgaacctagacgaattccttccacaccttgtgcacacccacacgaacctagacgaa -ttccttccacaccttctccacacccacacgaacctagacgaattccttccacaccttctc -cacacccacacgaacctagacgattccttccacactttccccacacccacacgaacctag -acg-attccttccacac---ctccacacccacacgaacctagatgaattccttccacacc -ttccccacacccacacaaacctagacgattccttccacaccttctccacacccacacaaa -cctagacaattccttccacacacacatgaacctagatgaattccttccacaccttctcca -cacccacatgaacctagacgattccttccacaccttctccacacccacacacacctagat -gaattccttccacaccttccccacacccacacagacctagacgaattccttgcacacctt -ctccacacccacacgaacctagacgaattccttccacaccttctccatacccacacgaac -ctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttccaca -ccttctccacacccacacgaacctaaacgattccttccacaccttctccacacccacaca -cacctagatgaattccttccacaccttccccacacccacacagacctagacgaattcctt -ccacaccttctccacacccacacgaacctagacgattccttccacaccttctccataccc -acacgaacctagacaattccttccacaccttctcacacccacacaaacctagatgaattc -cttccacaccttccccacacccacacagacctagacgaattccttccacaccttct---- --------------------------------------ccacacccacacgaacctagaca -attccttgcacaccttctcacacccacacaaacctagacgaattccttccacaccttctc -cacacccacacaaacct ->syndip_2_chr20:18209039-18210234 -tacagttatttccaaataaaaaataagcagaaaggaaaagctaatcatctccccctattc -cagtcccccaggcatgtatccttccgtagcttctccacacctacacgaacctagacgatt -ccttccacaccttccccacacccacacgaacctagacgattccttccacaccttccccac -acccacacgaacctagatgaattccttccacaccttctccacacccacacgaacctagac -gattccttccacaccttccccacacccattctccacacccacacgaacctagacgattcc -ttccacacctccacacccacacgaacctagatgaattccttccacaccttccccacaccc -acacaaacctagacgattccttccacaccttctccacacccacacgaacctagacgaatt -ccttccagaccttctccacacccacacagacctagacgattccttccacacctccacacc -cacacgaacctagacgaattccttccacaccttgtgcacacccacacgaacctagacgaa -ttccttccacaccttctccacacccacacgaacctagacgaattccttccacaccttctc -cacacccacacgaacctagacgattccttccacactttccccacacccacaagaacctag -acg-attccttccacac---ctccacacccacacgaacctagatgaattccttccacacc -ttccccacacccacacaaacctagacgattccttccacaccttctccacacccacacaaa -cctagacaattccttccacacacacatgaacctagatgaattccttccacaccttctcca -cacccacatgaacctagacgattccttccacaccttctccacacccacacacacctagat -gaattccttccacaccttccccacacccacacagacctagacgaattccttgcacacctt -ctccacacccacacgaacctagacgaattccttccacaccttctccatacccacacgaac -ctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttccaca -ccttctccacacccacacgaacctaaacgattccttccacaccttctccacacccacaca -cacctagatgaattccttccacaccttccccacacccacacagacctagacgaattcctt -ccacaccttctccacacccacacgaacctagacgattccttccaca------------cc -acacgaacctagacaattccttccacaccttctcacacccacacaaacctagatgaattc -cttccacaccttccccacacccacacagacctagacgaattccttccacaccttct---- --------------------------------------ccacacccacacgaacctagaca -attccttgcacaccttctcacacccacacaaacctagacgaattccttccacaccttctc -cacacccacacaaacct ->p:HG002_1_chr20:18209039-18210234 -tacagttatttccaaataaaaaataagcagaaaggaaaagctaatcatctccccctattc -cagtcccccaggcatgtatccttccgtagcttctccacacctacacgaacctagacgatt -ccttccacaccttccccacacccacacgaacctagacgattccttccacaccttccccac -acccacacgaacctagatgaattccttccacaccttctccacacccacacgaacctagac -gattccttccacaccttccccacacccattctccacacccacacgaacctagacgattcc -ttccacacctccacacccacacgaacctagatgaattccttccacaccttccccacaccc -acacaaacctagacgattccttccacaccttctccacacccacacgaacctagacgaatt -ccttccagaccttctccacacccacacagacctagacgattccttccacacctccacacc -cacacgaacctagacgaattccttccacaccttgtgcacacccacacgaacctagacgaa -ttccttccacaccttctccacacccacacgaacctagacgaattccttccacaccttctc -cacacccacacgaacctagacgattccttccacaccttccccacacccacacagacctag -acgaattccttgcacaccttctccacacccacacgaacctagacgaattccttccacacc -ttctccatacccacacgaacctagacaattccttccacaccttctccacacccacacaaa -cctagacaattccttccacacccacacaaacctagatgaattccttccacaccttctcca -cacccacacgaacctaaacgattccttccacaccttctccacacccacacacacctagat -gaattccttccacaccttccccacacccacacagacctagacgaattccttccacacctt -ctccacacccacacgaacctagacg-attccttccacaccttctccatacccacacgaac -ctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttccaca -ccttctccacacccacacgaacctaaacgattccttccacaccttctccacacccacaca -cacctagatgaattccttccacaccttccccacacccacacagacctagacgaattcctt -ccacaccttctccacacccacacgaacctagacgattccttccaca------------cc -acacgaacctagacaattccttccacaccttcccacacccacacagacctagacgaattc -cttccacaccttctccacacccacacgaacctagacg-attccttccacaccttcc---- --------------------------------------ccacacccacacgaacctagaca -attccttgcacaccttctcacacccacacaaacctagacgaattccttccacaccttctc -cacacccacacaaacct ->p:HG002_2_chr20:18209039-18210234 -tacagttatttccaaataaaaaataagcagaaaggaaaagctaatcatctccccctattc -cagtcccccaggcatgtatccttccgtagcttctccacacctacacgaacctagacgatt -ccttccacaccttccccacacccacacgaacctagacgattccttccacaccttccccac -acccacacgaacctagatgaattccttccacaccttctccacacccacacgaacctagac -gattccttccacaccttccccacacccattctccacacccacacgaacctagacgattcc -ttccacacctccacacccacacgaacctagatgaattccttccacaccttccccacaccc -acacaaacctagacgattccttccacaccttctccacacccacacgaacctagacgaatt -ccttccagaccttctccacacccacacagacctagacgattccttccacacctccacacc -cacacgaacctagacgaattccttccacaccttgtgcacacccacacgaacctagacgaa -ttccttccacaccttctccacacccacacgaacctagacgaattccttccacaccttctc -cacacccacacgaacctagacgattccttccacactttccccacacccacacgaacctag -acg-attccttccacac---ctccacacccacacgaacctagatgaattccttccacacc -ttccccacacccacacaaacctagacgattccttccacaccttctccacacccacacaaa -cctagacaattccttccacacacacatgaacctagatgaattccttccacaccttctcca -cacccacatgaacctagacg---------------------------------------- ---attccttccacaccttccccacacccacacagacctagacgaattccttgcacacctt -ctccacacccacacgaacctagacgaattccttccacaccttctccatacccacacgaac -ctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttccaca -ccttctccacacccacacgaacctaaacgattccttccacaccttctccacacccacaca -cacctagatgaattccttccacaccttccccacacccacacagacctagacgaattcctt -ccacaccttctccacacccacacgaacctagacgattccttccacaccttctccataccc -acacgaacctagacaattccttccacaccttctcacacccacacaaacctagatgaattc -cttccacaccttccccacacccacacagacctagacgaattccttccacaccttctccac -acccacacgaacctagacgattccttccacaccttccccacacccacacgaacctagaca -attccttgcacaccttctcacacccacacaaacctagacgaattccttccacaccttctc -cacacccacacaaacct ->ref_chr20:18209039-18210234 -tacagttatttccaaataaaaaataagcagaaaggaaaagctaatcatctccccctattc -cagtcccccaggcatgtatccttccgtagcttctccacacct------------------ ------------------------acacgaacctagacgattccttccacaccttccccac -acccacacgaacctagatgaattccttccacaccttctccacacccacacgaacctagac -gattccttccacaccttccccacacccattctccacacccacacgaacctagacgattcc -ttccacacctccacacccacacgaacctagatgaattccttccacaccttccccacaccc -acacaaacctagacgattccttccacaccttctccacacccacacgaacctagacgaatt -ccttccagaccttctccacacccacacagacctagacgattccttccacacctccacacc -cacacgaacctagacgaattccttccacaccttgtgcacacccacacgaacctagacgaa -ttccttccacaccttctccacacccacacgaacctagacgaattccttccacaccttctc -cacacccacacgaacctagacgattccttccacaccttccccacacccacacagacctag -acgaattccttgcacaccttctccacacccacacgaacctagacgaattccttccacacc -ttctccatacccacacgaacctagacaattccttccacaccttct--------------- -----------------cacacccacacaaacctagatgaattccttccacaccttctcca -cacccacacgaacctaaacgattccttccacaccttctccacacccacacacacctagat -gaattccttccacaccttccccacacccacacagacctagacgaattccttccacacctt -ctccacacccacacgaacctagacg-attccttccacaccttctccatacccacacgaac -ctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttccaca -ccttccccacacccacacag---------------------------------------- --acctagacgaattccttccacaccttctccacacccacacgaacctagacg-attcctt -ccacaccttccccacac-----------------------------------------cc -acacgaacctagacaattccttgcacaccttctcacacccacacaaacctagacgaattc -cttccacaccttctccacacccacacaaacct---------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------ diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_7bd1639cc4586510073da802bd13f55b.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7bd1639cc4586510073da802bd13f55b.msa deleted file mode 100644 index 39d6c662..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_7bd1639cc4586510073da802bd13f55b.msa +++ /dev/null @@ -1,100 +0,0 @@ ->syndip_1_chr20:23155304-23156175 -ttcctggctcttctatcacgtgcctaccttatctaagaaagtttgaatgtttagccaatc -aggactagtttagattgtgtggtccaaccccagtcaatgggggaaagacacagaggtaga -atctgcgttaggaataaaaaccgctactctccgttgttctgtgtgcttttgcagtcatga -ttgatgcaggcagcacccttctgcagaagtaaattttgccctgcagcacaaaagaggaag -gaaagcaagggaagggaaggggaggggaggaagggaaggggaggggaggaagggaagggg -aggggaggaaggcgaggtgaggggaggagaggtgaggggagggggggaggggaggggagg -gagagtgaggaagagagagagaaagggagagaggaaggaaagaagaaaggaaggaaggaa -agaaggaaggaagggagggagggagggaggaaagaaggaaggaaaggagggaggaaggga -gggaaagagagagagaggaaaagagagagaaagagaaagagagaaagagaggaaggaagg -aaggaaggagagagagaaagaaagaaggaaagaggaaggaaggaagaaagaaaagaaaga -aagaaaaaagaaagaaaggaaggagagaaagaaatgaaagagaaagaaagaaagaaagaa -agaaagaaagaaaggagagaaaaaggaaaaacaaagaaagagaaaagaaggagagaagga -aaggaaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaagaaagaagaaagaaag -aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacaccttggtaatt -tttgtgctcttccctggactttggactttgcagccttagggagacagagctctttaatgt -acactttcccatcaggcactgcatggccaagaacctgcctgcaaagcccccactgaaggg -agggtttctccaaggagctctcccctttaaaggcccaggattgctcctgagagtgtctac -tctgccatcaataccataaagatttcatcag ->syndip_2_chr20:23155304-23156175 -ttcctggctcttctatcacgtgcctaccttatctaagaaagtttgaatgtttagccaatc -aggactagtttagattgtgtggtccaaccccagtcaatgggggaaagacacagaggtaga -atctgcgttaggaataaaaaccgctactctccgttgttctgtgtgcttttgcagtcatga -ttgatgcaggcagcacccttctgcagaagtaaattttgccctgcagcacaaaagaggaag -gaaagcaag-------------------ggaagggaaggggaggggaggaagggaagggg -aggggaggaaggcgaggtgaggggaggagaggtgaggggagggggggaggggaggggagg -gagagtgaggaagagagagagaaagggagagaggaaggaaagaagaaaggaaggaaggaa -agaaggaaggaagggagggagggagggaggaaagaaggaaggaaaggagggaggaaggga -gggaaagagagagagaggaaaagagagagaaagagaaagagagaaagagaggaaggaagg -aaggaaggagagagagaaagaaagaaggaaagaggaaggaaggaagaaagaaaagaaaga -aagaaaaaagaaagaaaggaaggagagaaagaaatgaaag----agaaagaaagaaagaa -agaaagaaagaaaggagagaaaaaggaaaaacaaagaaagagaaaagaaggagagaagga -aaggaaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaagaaag----------- --------------aagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacaccttggtaatt -tttgtgctcttccctggactttggactttgcagccttagggagacagagctctttaatgt -acactttcccatcaggcactgcatggccaagaacctgcctgcaaagcccccactgaaggg -agggtttctccaaggagctctcccctttaaaggcccaggattgctcctgagagtgtctac -tctgccatcaataccataaagatttcatcag ->p:HG002_1_chr20:23155304-23156175 -ttcctggctcttctatcacgtgcctaccttatctaagaaagtttgaatgtttagccaatc -aggactagtttagattgtgtggtccaaccccagtcaatgggggaaagacacagaggtaga -atctgcgttaggaataaaaaccgctactctccgttgttctgtgtgcttttgcagtcatga -ttgatgcaggcagcacccttctgcagaagtaaattttgccctgcagcacaaaagaggaag -gaaagcaag-------------------ggaagggaaggggaggggaggaagggaagggg -aggggaggaaggcgaggtgaggggaggagaggtgaggggagggggggaggggaggggagg -gagagtgaggaagagagagagaaagggagagaggaaggaaagaagaaaggaaggaaggaa -agaaggaaggaagggagggagggagggaggaaagaaggaaggaaaggagggaggaaggga -gggaaagagagagagaggaaaagagagagaaagagaaagagagaaagagaggaaggaagg -aaggaaggagagagagaaagaaagaaggaaagaggaaggaaggaagaaagaaaagaaaga -aagaaaaaagaaagaaaggaaggagagaaagaaatgaaag----agaaagaaagaaagaa -agaaagaaagaaaggagagaaaaaggaaaaacaaagaaagagaaaagaaggagagaagga -aaggaaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaagaaag----------- --------------aagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacaccttggtaatt -tttgtgctcttccctggactttggactttgcagccttagggagacagagctctttaatgt -acactttcccatcaggcactgcatggccaagaacctgcctgcaaagcccccactgaaggg -agggtttctccaaggagctctcccctttaaaggcccaggattgctcctgagagtgtctac -tctgccatcaataccataaagatttcatcag ->p:HG002_2_chr20:23155304-23156175 -ttcctggctcttctatcacgtgcctaccttatctaagaaagtttgaatgtttagccaatc -aggactagtttagattgtgtggtccaaccccagtcaatgggggaaagacacagaggtaga -atctgcgttaggaataaaaaccgctactctccgttgttctgtgtgcttttgcagtcatga -ttgatgcaggcagcacccttctgcagaagtaaattttgccctgcagcacaaaagaggaag -gaaagcaagggaagggaaggggaggggaggaagggaaggggaggggaggaagggaagggg -aggggaggaaggcgaggtgaggggaggagaggtgaggggagggggggaggggaggggagg -gagagtgaggaagagagagagaaagggagagaggaaggaaagaagaaaggaaggaaggaa -agaaggaaggaagggagggagggagggaggaaagaaggaaggaaaggagggaggaaggga -gggaaagagagagagaggaaaagagagagaaagagaaagagagaaagagaggaaggaagg -aaggaaggagagagagaaagaaagaaggaaagaggaaggaaggaagaaagaaaagaaaga -aagaaaaaagaaagaaaggaaggagagaaagaaatgaaagagaaagaaagaaagaaagaa -agaaagaaagaaaggagagaaaaaggaaaaacaaagaaagagaaaagaaggagagaagga -aaggaaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaagaaagaagaaagaaag -aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacaccttggtaatt -tttgtgctcttccctggactttggactttgcagccttagggagacagagctctttaatgt -acactttcccatcaggcactgcatggccaagaacctgcctgcaaagcccccactgaaggg -agggtttctccaaggagctctcccctttaaaggcccaggattgctcctgagagtgtctac -tctgccatcaataccataaagatttcatcag ->ref_chr20:23155304-23156175 -ttcctggctcttctatcacgtgcctaccttatctaagaaagtttgaatgtttagccaatc -aggactagtttagattgtgtggtccaaccccagtcaatgggggaaagacacagaggtaga -atctgcgttaggaataaaaaccgctactctccgttgttctgtgtgcttttgcagtcatga -ttgatgcaggcagcacccttctgcagaagtaaattttgccctgcagcacaaaagaggaag -gaaagcaag-------------------ggaagggaaggggaggggaggaaggga----- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------aggaaaagagagagaaagagaaagagagaaagagaggaaggaagg -aaggaaggagagagagaaagaaagaaggaaagaggaaggaaggaagaaagaaaagaaaga -aagaaaaaagaaagaaaggaaggagagaaagaaatgaaag--------agaaagaaagaa -agaaagaaagaaaggagagaaaaaggaaaaacaaagaaagagaaaagaaggagagaagga -aaggaaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaagaaag----------- --aagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtcttaacaccttggtaatt -tttgtgctcttccctggactttggactttgcagccttagggagacagagctctttaatgt -acactttcccatcaggcactgcatggccaagaacctgcctgcaaagcccccactgaaggg -agggtttctccaaggagctctcccctttaaaggcccaggattgctcctgagagtgtctac -tctgccatcaataccataaagatttcatcag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_7e6940eaf18dc93c36902592639eaf66.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7e6940eaf18dc93c36902592639eaf66.msa deleted file mode 100644 index b2c11da8..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_7e6940eaf18dc93c36902592639eaf66.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:41196210-41196648 -ttctccctttaattctgtcatttctgtttcatatgttttggagctctgttaggggtatat -atatatataatatatataaataaatatataaaaataaatatatatttataataaatatat -ttttatttcatatataaatatatatcttataaatatatatatttatataacataaatata -tatttatatatattata------------------------aatatatattatatataat -atatatttatataaatatatatattatatataatatatttatatataatatatatttata -tattataaatatatattatatataatatatatttatataaatatatattatatataaata -tatattatatataatatatatttatataaatatatattatatattatataaatattatat -ataatatatatttatataaatatatattatatattataaatatatattatatattatata -ttatataaatattatatataatatatattatatataatatatataaaaatatatatattt -atatatataaatattttatcaatataatatccttgtctcttgtaacctttcttgatttaa ->syndip_2_chr20:41196210-41196648 -ttctccctttaattctgtcatttctgtttcatatgttttggagctctgttaggggtatat -atatatataatatatataaataaatatataaaaataaatatatatttataataaatatat -ttttatttcatatataaatatatatcttataaatatatatatttatataacataaatata -tatttatatatattatataacataaatatatatttatatatattatatattatatataat -atatatttatataaatatatatattatatataatatatttatatataatatatatttata -tattataaatatatattatatataatatatatttatataaatatatattatatat----- -------------------------tataaatatatattatatattatataaatattatat -ataatatatatttatataaatatataatatatattataaatatatattatatattatata -ttatataaatattatatataatatatattatatataatatatataaaaatatatatattt -atatatataaatattttatcaatataatatccttgtctcttgtaacctttcttgatttaa ->p:HG002_1_chr20:41196210-41196648 -ttctccctttaattctgtcatttctgtttcatatgttttggagctctgttaggggtatat -atatatataatatatataaataaatatataaaaataaatatatatttataataaatatat -ttttatttcatatataaatatatatcttataaatatatatatttatataacataaatata -tatttatatatattatataacataaatatatatttatatatattatatattatatataat -atatatttatataaatatatatattatatataatatatttatatataatatatatttata -tattataaatatatattatatataatatatatttatataaatatatattatatat----- -------------------------tataaatatatattatatattatataaatattatat -ataatatatatttatataaatatataatatatattataaatatatattatatattatata -ttatataaatattatatataatatatattatatataatatatataaaaatatatatattt -atatatataaatattttatcaatataatatccttgtctcttgtaacctttcttgatttaa ->p:HG002_2_chr20:41196210-41196648 -ttctccctttaattctgtcatttctgtttcatatgttttggagctctgttaggggtatat -atatatataatatatataaataaatatataaaaataaatatatatttataataaatatat -ttttatttcatatataaatatatatcttataaatatatatatttatataacataaatata -tatttatatatattata------------------------aatatatattatatataat -atatatttatataaatatatatattatatataatatatttatatataatatatatttata -tattataaatatatattatatataatatatatttatataaatatatattatatataaata -tatattatatataatatatatttatataaatatatattatatattatataaatattatat -ataatatatatttatataaatatatattatatattataaatatatattatatattatata -ttatataaatattatatataatatatattatatataatatatataaaaatatatatattt -atatatataaatattttatcaatataatatccttgtctcttgtaacctttcttgatttaa ->ref_chr20:41196210-41196648 -ttctccctttaattctgtcatttctgtttcatatgttttggagctctgttaggggtatat -atatatataatatatataaataaatatataaaaataaatatatatttataataaatatat -ttttatttcatatataaatatatatcttataaatatatatatttatataacataaatata -tatttatatat------------------------------attatatattatatataat -atatatttatataaatatatatattatatataatatatttatatataatatatatttata -tattataaatatatat-------------------------------------------- ------------------------------------------------------------- ----------------------------tatatattataaatatatattatatattatata -ttatataaatattatatataatatatattatatataatatatataaaaatatatatattt -atatatataaatattttatcaatataatatccttgtctcttgtaacctttcttgatttaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_7f1194fc13d76299565e488d1bdc67b9.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7f1194fc13d76299565e488d1bdc67b9.msa deleted file mode 100644 index 1ae04243..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_7f1194fc13d76299565e488d1bdc67b9.msa +++ /dev/null @@ -1,135 +0,0 @@ ->syndip_1_chr20:55627144-55628650 -agaaaaagaaaatctgataaatcaatttcctcctcaacgaaaaggaaaattattatttta -tacttcttaatcttgccgtgatatgcatatattgtaggctgtatcagctatccactacat -acttagaaatttggctaattatcataacataaattaacattttatggctgtgaaaagaga -atagaaatggattttagaatgtcaagtatttatcactagtatgtgttaatataaatagct -taataaaaatagggcatttatatgtatatatgtgggtgttcatgtatatatttttatatg -tatatatgtgggtgtgcatgtatacattaaatgatgaatttatatgtatatattaaatgt -atatattatatgtatatattacatatatacatattgtatattacatatacataatacata -aaatgtttaatacatacataatatatacataatataatattgtatattattaaattatac -atgtatatatgtatactatatgtatatatgtatacaaaatatgtatataatatatacaaa -aatatgtgtatttttgtacatatattgtacaaaaatatgtatattatatatacaaaatat -gtatataatatatacatatattatgtaatataatatatacataatgtgtattacatacat -tatatgtaatatatacatatattatata---atatatatgtatatattatatacatatat -attatatacatatatgtatatattatata-----------------catatatgtataca -ttatatattatgtatacatatatgtatatatgtatacattatatattatgtatacatata -tgtatatatgtatacattatatattatgtatacatatatgtatatatgtatacattatat -attatgtatacatatatgtatatatgtatacattatatattatgtatacatatatgtata -tatgtatacattatatattatgtatacatatatgtatatatgtatacattatatattatg -tatacatatatgtata-------------------------------------------- ---------------------------------------------------tatgtataca -tgtatatacatatatacgtatacacatatatacgtg--------tatatacgtatataca -cgtatatattaaatgataaatttatatgtatatatgcgtgtgtgcacacacacacgagat -atgttggttttgtgtaatgcaaccaaataaattaagtatacataggagagagtcactgcc -ctgactcttaaatgtaacccttattaaagaaaatattttagttcattttttatctatcaa -ccttttttatctatcaactctgaaatctgcaatcaatcatatttggttatgagcaaaata -acatgaatgataatctaaaatttctggccaaataacactgggataattgcattattacct -ctagtactcttagaaatttcatttgccag ->syndip_2_chr20:55627144-55628650 -agaaaaagaaaatctgataaatcaatttcctcctcaacgaaaaggaaaattattatttta -tacttcttaatcttgccgtgatatgcatatattgtaggctgtatcagctatccactacat -acttagaaatttggctaattatcataacataaattaacattttatggctgtgaaaagaga -atagaaatggattttagaatgtcaagtatttatcactagtatgtgttaatataaatagct -taataaaaatagggcatttatatgtatatatgtgggtgttcatgtatatatttttatatg -tatatatgtgggtgtgcatgtatacattaaatgatgaatttatatgtatatattaaatgt -atatattatatgtatatattacatatatacatattgtatattacatatacataatacata -aaatgtttaatacatacataatatatacataatataatattgtatattattaaattatac -atgtatatatgtatac-----------atgtatacaaaatatgtatataatatatacaaa -aa-atgtgtatttttgtacatatattgtacaaaaatatgtatattatatatacaaaatat -gtatataatatatacatatattatgtaatataatatatacgtaatgtgtattacatacat -tatatgtaatatatacatatatattatatacatatatatgtatatattatatacatatat -attatatacatatatgtatatattatatattatgtatacacatatgtatatatgtatata -ttatatattatgtatacacatatgtatatatgtatatattatatattatgtatacac--- ------atatgtatatattatatattatgtatacacatatgtatatatgtatatattatat -attatgtatac--------acatatgtatatattatatattatgtatacacatatgtata -tatgtatatattatatattatgtatacacatatgtatat--------attatatattatg -tatacacatatgtatatattatatat---------------------------------- ---------------------------------------------------tatgtataca -cgtatatacatatatacgtatacacgtatatacgta--tatacgtatatacgtatataca -cgtatatattaaatgataaatttatatgtatatatgcgtgtgtgcacacacacacgagat -atgttggttttgtgtaatgcaaccaaataaattaagtatacataggagagagtcactgcc -ctgactcttaaatgtaacccttattaaagaaaatattttagttcattttttatctatcaa -ccttttttatctatcaactctgaaatctgcaatcaatcatatttggttatgagcaaaata -acatgaatgataatctaaaatttctggccaaataacactgggataattgcattattacct -ctagtactcttagaaatttcatttgccag ->p:HG002_1_chr20:55627144-55628650 -agaaaaagaaaatctgataaatcaatttcctcctcaacgaaaaggaaaattattatttta -tacttcttaatcttgccgtgatatgcatatattgtaggctgtatcagctatccactacat -acttagaaatttggctaattatcataacataaattaacattttatggctgtgaaaagaga -atagaaatggattttagaatgtcaagtatttatcactagtatgtgttaatataaatagct -taataaaaatagggcatttatatgtatatatgtgggtgttcatgtatatatttttatatg -tatatatgtgggtgtgcatgtatacattaaatgatgaatttatatgtatatattaaatgt -atatattatatgtatatattacatatatacatattgtatattacatatacataatacata -aaatgtttaatacatacataatatatacataatataatattgtatattattaaattatac -atgtatatatgtatac-----------atgtatacaaaatatgtatataatatatacaaa -aa-atgtgtatttttgtacatatattgtacaaaaatatgtatattatatatacaaaatat -gtatataatatatacatatattatgtaatataatatatacgtaatgtgtattacatacat -tatatgtaatatatacatatatattatatacatatatatgtatatattatatacatatat -attatatacatatatgtatatattatatattatgtatacacatatgtatatatgtatata -ttatatattatgtatacacatatgtatatatgtatatattatatattatgtatacac--- ------atatgtatatattatatattatgtatacacatatgtatatatgtatatattatat -attatgtatac--------acatatgtatatattatatattatgtatacacatatgtata -tatgtatatattatatattatgtatacacatatgtatat--------attatatattatg -tatacacatatgtatatattatatat---------------------------------- ---------------------------------------------------tatgtataca -cgtatatacatatatacgtatacacgtatatacgta--tatacgtatatacgtatataca -cgtatatattaaatgataaatttatatgtatatatgcgtgtgtgcacacacacacgagat -atgttggttttgtgtaatgcaaccaaataaattaagtatacataggagagagtcactgcc -ctgactcttaaatgtaacccttattaaagaaaatattttagttcattttttatctatcaa -ccttttttatctatcaactctgaaatctgcaatcaatcatatttggttatgagcaaaata -acatgaatgataatctaaaatttctggccaaataacactgggataattgcattattacct -ctagtactcttagaaatttcatttgccag ->p:HG002_2_chr20:55627144-55628650 -agaaaaagaaaatctgataaatcaatttcctcctcaacgaaaaggaaaattattatttta -tacttcttaatcttgccgtgatatgcatatattgtaggctgtatcagctatccactacat -acttagaaatttggctaattatcataacataaattaacattttatggctgtgaaaagaga -atagaaatggattttagaatgtcaagtatttatcactagtatgtgttaatataaatagct -taataaaaatagggcatttatatgtatatatgtgggtgttcatgtatatatttttatatg -tatatatgtgggtgtgcatgtatacattaaatgatgaatttatatgtatatattaaatgt -atatattatatgtatatattacatatatacatattgtatattacatatacataatacata -aaatgtttaatacatacataatatatacataatataatattgtatattattaaattatac -atgtatatatgtatactatatgtatatatgtatacaaaatatgtatataatatatacaaa -aatatgtgtatttttgtacatatattgtacaaaaatatgtatattatatatacaaaatat -gtatataatatatacatatattatgtaatataatatatacataatgtgtattacatacat -tatatgtaatatatacatatattatata---atatatatgtatatattatatacatatat -attatatacatatatgtatatattatata-----------------catatatgtataca -ttatatattatgtatacatatatgtatatatgtatacattatatattatgtatacatata -tgtatatatgtatacattatatattatgtatacatatatgtatatatgtatacattatat -attatgtatacatatatgtatatatgtatacattatatattatgtatacatatatgtata -tatgtatacattatatattatgtatacatatatgtatatatgtatacattatatattatg -tatacatatatgtata-------------------------------------------- ---------------------------------------------------tatgtataca -tgtatatacatatatacgtatacacatatatacgtg--------tatatacgtatataca -cgtatatattaaatgataaatttatatgtatatatgcgtgtgtgcacacacacacgagat -atgttggttttgtgtaatgcaaccaaataaattaagtatacataggagagagtcactgcc -ctgagtcttaaatgtaacccttattaaagaaaatattttagttcattttttatctatcaa -ccttttttatctatcaactctgaaatctgcaatcaatcatatttggttatgagcaaaata -acatgaatgataatctaaaatttctggccaaataacactgggataattgcattattacct -ctagtactcttagaaatttcatttgccag ->ref_chr20:55627144-55628650 -agaaaaagaaaatctgataaatcaatttcctcctcaacgaaaaggaaaattattatttta -tacttcttaatcttgccgtgatatgcatatattgtaggctgtatcagctatccactacat -acttagaaatttggctaattatcataacataaattaacattttatggctgtgaaaagaga -atagaaatggattttagaatgtcaagtatttatcactagtatgtgttaatataaatagct -taataaaaatagggcatttatatgtatatatgtgggtgttcatgtatatatttttatatg -tatatatgtgggtgtgcatgtatacattaaatgatgaatttatatgtatatattaaatgt -atatattatatgtatatattacatatatacatattgtatattacatatacataatacata -aaatgtttaatacatacataatatatacataatataatattgtatattattaaattatac -atgtatatatgtatac-----------atgtatacaaaatatgtatataatatatacaaa -aa-atgtgtatttttgtacatatattgtacaaaaatatgtatattatatatacaaaatat -gtatataatatatacatatattatgtaatataatatatacataatgtgtattacatacat -tatatgtaatatatacatatatattatatacatatatat-tatata-catatatgtatat -attatatacatatatgtatatattatatattatgtatacacatatgtatatatgtatata -ttatatattatgtatacacatatgtatatatgtatatattatatattatgtatacacata -tgtatatatgtatatattatatattatgtatacacatatgtatatatgtatatattatat -attatgtatacatatatgtatatatgtatatattatatattatgtatacatatatgtata -tatgtatatattatatattatgtatacatatatgtatat--------attatatattatg -tatacatatatgtatatattatatattatgtatacatatatgtatatattatatattatg -tatacatatatgtatatattatatattatgtatacatatatgtatatatgtatgtataca -tgtatatacatatatacgtatacacatatatacgtgtatatacatatatacgtatataca -cgtatatattaaatgataaatttatatgtatatatgcgtgtgtgcacacacacacgagat -atgttggttttgtgtaatgcaaccaaataaattaagtatacataggagagagtcactgcc -ctgactcttaaatgtaacccttattaaagaaaatattttagttcattttttatctatcaa -ccttttttatctatcaactctgaaatctgcaatcaatcatatttggttatgagcaaaata -acatgaatgataatctaaaatttctggccaaataacactgggataattgcattattacct -ctagtactcttagaaatttcatttgccag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_7f9d6dcbf25e736ccea5efaead6993c2.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7f9d6dcbf25e736ccea5efaead6993c2.msa deleted file mode 100644 index b6bec417..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_7f9d6dcbf25e736ccea5efaead6993c2.msa +++ /dev/null @@ -1,70 +0,0 @@ ->syndip_1_chr20:62830440-62830907 -gcatggggggcggcacacccagacgggccagacccgacagggtatgggcactgacgagcc -aggacctccttccccagggccagaagggcagcatgggagaccccggccttccaggccccc -agggcctccgaggtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccct -gcaccccctctacccatgtaccacagtcccccaccccccaccgtgctccacc-------- -----------------------------------ccccaccacagtcccccaccccccac -cccagtccccaaacccctaccacagtcccccaa-ccccaccacagtcccccaccccctac -cacagtcccccaccccctaccacagtcccccaacccccaccacagtcccccacccccacc -acagtccgccaacccccatgacagtccctca--------------------acccccacc -acagtcccccaacccccatgacagtcccccaacccccaccacagtcccccaacccccacc -acagtccccaccccctaccacagtcccccaacccccaccacagtcccccaccccctacca -caatcccccaccccccaccacagtcccctgggacgcagacagggagaggcccttgcagct -cccagtgggaaatctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcag -ggccccg ->syndip_2_chr20:62830440-62830907 -gcatggggggcggcacacccagacgggccagacccgacagggtatgggcactgacgagcc -aggacctccttccccagggccagaagggcagcatgggagaccccggccttccaggccccc -agggcctccgaggtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccct -gcaccccctctacccatgtaccacagtcccccaccccccaccacagtcccccacccccca -ccccagtccccaaacccctaccacagtcccccaaccccaccacagtcccccaccccctac -cacagtcccccaacccctaccacagtcccccaacccccaccacagtcccccaccccc-ac -cacagtccgccaacccccatgacagtcccccaacccccaccacagtcccccacccccacc -acagtccgccaacccccatgacagtcccccaacccccaccacagtcccccaacccccatg -acagtcccccaacccccaccacagtcccccaacccctaccacagtcccccaacccccacc -acagtccccaccccctaccacagtcccccaacccccaccacagtcccccaccccctacca -caatcccccaccccccaccacagtcccctgggacgcagacagggagaggcccttgcagct -cccagtgggaaatctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcag -ggccccg ->p:HG002_1_chr20:62830440-62830907 -gcatggggggcggcacacccagacgggccagacccgacagggtatgggcactgacgagcc -aggacctccttccccagggccagaagggcagcatgggagaccccggccttccaggccccc -agggcctccgaggtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccct -gcaccccctctacccatgtaccacagtcccccaccccccaccacagtcccccacccccca -ccccagtccccaaacccctaccacagtcccccaaccccaccacagtcccccaccccctac -cacagtcccccaacccctaccacagtcccccaacccccaccacagtcccccaccccc-ac -cacagtccgccaacccccatgacagtcccccaacccccaccacagtcccccacccccacc -acagtccgccaacccccatgacagtcccccaacccccaccacagtcccccaacccccatg -acagtcccccaacccccaccacagtcccccaacccctaccacagtcccccaacccccacc -acagtccccaccccctaccacagtcccccaacccccaccacagtcccccaccccctacca -caatcccccaccccccaccacagtcccctgggacgcagacagggagaggcccttgcagct -cccagtgggaaatctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcag -ggccccg ->p:HG002_2_chr20:62830440-62830907 -gcatggggggcggcacacccagacgggccagacccgacagggtatgggcactgacgagcc -aggacctccttccccagggccagaagggcagcatgggagaccccggccttccaggccccc -agggcctccgaggtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccct -gcaccccctctacccatgtaccacagtcccccaccccccaccgtgctccacc-------- -----------------------------------ccccaccacagtcccccaccccccac -cccagtccccaaacccctaccacagtcccccaa-ccccaccacagtcccccaccccctac -cacagtcccccaccccctaccacagtcccccaacccccaccacagtcccccacccccacc -acagtccgccaacccccatgacagtccccca--------------------acccccacc -acagtcccccaacccccatgacagtcccccaacccctaccacagtcccccaacccccacc -acagtccccaccccctaccacagtcccccaacccccaccacagtcccccaccccctacca -caatcccccaccccccaccacagtcccctgggacgcagacagggagaggcccttgcagct -cccagtgggaaatctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcag -ggccccg ->ref_chr20:62830440-62830907 -gcatggggggcggcacacccagacgggccagacccgacagggtatgggcactgacgagcc -aggacctccttccccagggccagaagggcagcatgggagaccccggccttccaggccccc -agggcctccgaggtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccct -gcaccccctctacccatgtaccacagtccccc---------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------acccccatg -acagtcccccaacccccaccacagtcccccaacccctaccacagtcccccaacccccacc -acagtccccaccccctaccacagtcccccaacccccaccacagtcccccaccccctacca -caatcccccaccccccaccacagtcccctgggacgcagacagggagaggcccttgcagct -cccagtgggaaatctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcag -ggccccg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_7fa21bb9ea93a0a76522c86d42bdac86.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7fa21bb9ea93a0a76522c86d42bdac86.msa deleted file mode 100644 index 5a165f3c..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_7fa21bb9ea93a0a76522c86d42bdac86.msa +++ /dev/null @@ -1,130 +0,0 @@ ->syndip_1_chr20:21720974-21721935 -aggcaaaacctttcagccttagtttcctcatccgtttaatggaaattatacctctctccc -tgggctgctgtgagaactaaatgtaataatatacataaagagtagggacttgctttgggt -cacagtcagcttttattagtgttattattgttgctgttttcttctttttctttgtacatc -aacgttttatggtgaattaaatcgtgttttaaccttgtagaccacattggctattacata -tatatatataatatatatgtaatatatatatgtaatgtatattatatatgtaatgtatat -aatatatgtaatgtatataatatatatgtaatacatatatattatatatgtatataatac -atatatatgtatatatatgtatgtatatatatatgtatatatgtatatatatatgtatat -aatacatatatatacatatatattatatatgtaatacatatataatatatatgtaatgta -tatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgtatat -aatatatatgtaatacatatataatatatatgtaatgtatattatatatgtaatgtatat -aatatgtatgtaatacatatattatatatgtaatgtatattatatatgtattacatatat -gtattacatatataacatatatgtattacatatatgtattacatatataacatatatgta -ttacatatatgtattacatatataacatatatgtattacatatatgtattacatatataa -catatatgtaatacatatatgtattacatatataacatatatgtattacatatatgtatt -acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca -tatatgtattacatatataacatatatgtattacatatatgtattacatatataacatat -atgtattacatatatgtaatacatatataacatatatgtattacatatatgtaatacata -tataacatatatgtattacatatatgtaatacatatataacatatatgtattacatatat -gtaatacatatataac----atgtattacatatatgtaatacatatataac--------- ------------------atgtattacatatatgtaatacatatataacatgtattacata -tatgtaatacacatataatatatatgttatatatatatatatatataaaattttttaaaa -aattgtttcttgagatagggtctcactctgtcacccaggctggagtataatggtttgatc -atagttcactgcagccttgaacttctagactcaggtgatcctcccacctcaacctcctga -gtagctacaactacagccatgcaccaccacacctggctaattttttaatttttaattttt -tgtagagatgcagtcttgctatgttgcccaggctggt ->syndip_2_chr20:21720974-21721935 -aggcaaaacctttcagccttagtttcctcatccgtttaatggaaattatacctctctccc -tgggctgctgtgagaactaaatgtaataatatacataaagagtagggacttgctttgggt -cacagtcagcttttattagtgttattattgttgctgttttcttctttttctttgtacatc -aacgttttatggtgaattaaatcgtgttttaaccttgtagaccacattggctattacata -tatatatataatatatatgtaatatatatatgtaatgtatattatatatgtaatgtatat -aatatatgtaatgtatataatacatatgtaatacatatatattatatatgtatataatac -atatatatgtatatatatgtatgtatatatatatgtatatatgtatatatatatgtatat -aatacatatatatacatatatattatatatgtaatacatatataatatatatgtaatgta -tatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgtatat -aatatatatgtaatacatatataatatatatgtaatgtatattatatatgtaatgtatat -aatatgtatgtaatacatatattatatatgtaatgtatattatatatgtattacatatat -gtattacatatataacatatatgtattacatatatgtattacatatataacatatatgta -ttacatatatgtattacatatataacatatatgtattacatatatgtattacatatataa -catatatgtattacatatatgtattacatatataacatatatgtattacatatatgtatt -acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca -tatatgtattacatatataacatatatgtattacatatatgtattacatatataacatat -atgtattacatatatgtattacatatataacatatatgtattacatatatgtattacata -tataacatatatgtattacatatatgtattacatatataacatatatgtattacatatat -gtaatacatatataacatatatgtattacatatatgtaatacatatataacatatatgta -atacatatataacatatatgtattacatatatgtaatacatatataacatgtattacata -tatgtaatacacatataatatatatgttatatatatatatatatataaaattttttaaaa -aattgtttcttgagatagggtctcactctgtcacccaggctggagtataatggtttgatc -atagttcactgcagccttgaacttctagactcaggtgatcctcccacctcaacctcctga -gtagctacaactacagccatgcaccaccacacctggctaattttttaatttttaattttt -tgtagagatgcagtcttgctatgttgcccaggctggt ->p:HG002_1_chr20:21720974-21721935 -aggcaaaacctttcagccttagtttcctcatccgtttaatggaaattatacctctctccc -tgggctgctgtgagaactaaatgtaataatatacataaagagtagggacttgctttgggt -cacagtcagcttttattagtgttattattgttgctgttttcttctttttctttgtacatc -aacgttttatggtgaattaaatcgtgttttaaccttgtagaccacattggctattacata -tatatatataatatatatgtaatatatatatgtaatgtatattatatatgtaatgtatat -aatatatgtaatgtatataatacatatgtaatacatatatattatatatgtatataatac -atatatatgtatatatatgtatgtatatatatatgtatatatgtatatatatatgtatat -aatacatatatatacatatatattatatatgtaatacatatataatatatatgtaatgta -tatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgtatat -aatatatatgtaatacatatataatatatatgtaatgtatattatatatgtaatgtatat -aatatgtatgtaatacatatattatatatgtaatgtatattatatatgtattacatatat -gtattacatatataacatatatgtattacatatatgtattacatatataacatatatgta -ttacatatatgtattacatatataacatatatgtattacatatatgtattacatatataa -catatatgtattacatatatgtattacatatataacatatatgtattacatatatgtatt -acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca -tatatgtattacatatataacatatatgtattacatatatgtattacatatataacatat -atgtattacatatatgtattacatatataacatatatgtattacatatatgtattacata -tataacatatatgtattacatatatgtattacatatataacatatatgtattacatatat -gtaatacatatataacatatatgtattacatatatgtaatacatatataacatatatgta -atacatatataacatatatgtattacatatatgtaatacatatataacatgtattacata -tatgtaatacacatataatatatatgttatatatatatatatatataaaattttttaaaa -aattgtttcttgagatagggtctcactctgtcacccaggctggagtataatggtttgatc -atagttcactgcagccttgaacttctagactcaggtgatcctcccacctcaacctcctga -gtagctacaactacagccatgcaccaccacacctggctaattttttaatttttaattttt -tgtagagatgcagtcttgctatgttgcccaggctggt ->p:HG002_2_chr20:21720974-21721935 -aggcaaaacctttcagccttagtttcctcatccgtttaatggaaattatacctctctccc -tgggctgctgtgagaactaaatgtaataatatacataaagagtagggacttgctttgggt -cacagtcagcttttattagtgttattattgttgctgttttcttctttttctttgtacatc -aacgttttatggtgaattaaatcgtgttttaaccttgtagaccacattggctattacata -tatatatataatatatatgtaatatatatatgtaatgtatattatatatgtaatgtatat -aatatatgtaatgtatataatatatatgtaatacatatatattatatatgtatataatac -atatatatgtatatatatgtatgtatatatatatgtatatatgtatatatatatgtatat -aatacatatatatacatatatattatatatgtaatacatatataatatatatgtaatgta -tatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgtatat -aatatatatgtaatacatatataatatatatgtaatgtatattatatatgtaatgtatat -aatatgtatgtaatacatatattatatatgtaatgtatattatatatgtattacatatat -gtattacatatataacatatatgtattacatatatgtattacatatataacatatatgta -ttacatatatgtattacatatataacatatatgtattacatatatgtattacatatataa -catatatgtaatacatatatgtattacatatataacatatatgtattacatatatgtatt -acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca -tatatgtattacatatataacatatatgtattacatatatgtattacatatataacatat -atgtattacatatatgtaatacatatataacatatatgtattacatatatgtaatacata -tataacatatatgtattacatatatgtaatacatatataacatatatgtattacatatat -gtaatacatatataac----atgtattacatatatgtaatacatatataac--------- ------------------atgtattacatatatgtaatacatatataacatgtattacata -tatgtaatacacatataatatatatgttatatatatatatatatataaaattttttaaaa -aattgtttcttgagatagggtctcactctgtcacccaggctggagtataatggtttgatc -atagttcactgcagccttgaacttctagactcaggtgatcctcccacctcaacctcctga -gtagctacaactacagccatgcaccaccacacctggctaattttttaatttttaattttt -tgtagagatgcagtcttgctatgttgcccaggctggt ->ref_chr20:21720974-21721935 -aggcaaaacctttcagccttagtttcctcatccgtttaatggaaattatacctctctccc -tgggctgctgtgagaactaaatgtaataatatacataaagagtagggacttgctttgggt -cacagtcagcttttattagtgttattattgttgctgttttcttctttttctttgtacatc -aacgttttatggtgaattaaatcgtgttttaaccttgtagaccacattggctattacata -tatatatataatatatatgtaatatatatatgtaatgtatattatatatgtaatgtatat -aatatatgtaatgtatataatatatatgtaatacatatatattatatatgtatataatac -atatatatgtatatatatgtatgtatatatatatgtatatatgtatatatatatgtatat -aatacatatatatacatatatattatatatgtaatacatatataatatatatgtaatgt- ------------------------------------------atatatatgtaatgtatat -aatatatatgtaatacatatataatatatatgtaatgtatattatatatgtaatgtatat -aatatgtatgtaatacatatattatatatgtaatgtatattatatatgtattacatatat -gtattacatatataacatatatgtattacatatatgtattacatatataacatat----- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------atgtattacata -tatgtaatacacatataatatatatgttatatatatatatatatataaaattttttaaaa -aattgtttcttgagatagggtctcactctgtcacccaggctggagtataatggtttgatc -atagttcactgcagccttgaacttctagactcaggtgatcctcccacctcaacctcctga -gtagctacaactacagccatgcaccaccacacctggctaattttttaatttttaattttt -tgtagagatgcagtcttgctatgttgcccaggctggt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_83155236e9083623b05cf9812a722f73.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_83155236e9083623b05cf9812a722f73.msa deleted file mode 100644 index f2792d3f..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_83155236e9083623b05cf9812a722f73.msa +++ /dev/null @@ -1,40 +0,0 @@ ->syndip_1_chr20:45600569-45600746 -ctaaatattccactgtctttgactgctatacctctctctcttttctttcaccaagcctct -ctctttgctttccttctggtaaaagcagtctctctctctctctctctctctctctctctc -tctctctatccccccctccctccctccttccctccctccctctctctctctctctccctt -tctctgtctctccctctctctctctctctctccctctctctctctttctccctctctctc -cctctctctctctctctctccctctctctctctttctccctctctctccctctctccccc -tctctctccctctctccctctctccctctctctccctctctctctacccctgaatctggc -ctttctaaacaccctcaact ->syndip_2_chr20:45600569-45600746 -ctaaatattccactgtctttgactgctatacctctctctcttttctttcaccaagcctct -ctctttgctttccttctggtaaaagcag--tctctctctctctctctctctctctctctc -tctctctatccccccctccctccctccttccctccctccctctctctctctctctccctt -tctctgtctctccctctctctctctctctctccctctctct------------------- ----------------------------------------------------------ccc -tctctccccctctctctccctctctccctctctccctctctctctacccctgaatctggc -ctttctaaacaccctcaact ->p:HG002_1_chr20:45600569-45600746 -ctaaatattccactgtctttgactgctatacctctctctcttttctttcaccaagcctct -ctctttgctttccttctggtaaaagcag--tctctctctctctctctctctctctctctc -tctctctatccccccctccctccctccttccctccctccctctctctctctctctccctt -tctctgtctctccctctctctctctctctctccctctctct------------------- ----------------------------------------------------------ccc -tctctccccctctctctccctctctccctctctccctctctctctacccctgaatctggc -ctttctaaacaccctcaact ->p:HG002_2_chr20:45600569-45600746 -ctaaatattccactgtctttgactgctatacctctctctcttttctttcaccaagcctct -ctctttgctttccttctggtaaaagcagtctctctctctctctctctctctctctctctc -tctctctatccccccctccctccctccttccctccctccctctctctctctctctccctt -tctctgtctctccctctctctctctctctctccctctctctctctttctccctctctctc -cctctctctctctctctctccctctctctctctttctccctctctctccctctctccccc -tctctctccctctctccctctctccctctctctccctctctctctacccctgaatctggc -ctttctaaacaccctcaact ->ref_chr20:45600569-45600746 -ctaaatattccactgtctttgactgctatacctctctctcttttctttcaccaagcctct -ctctttgctttccttctggtaaaagcagtctctctctctctctctctctctctctctcta -tccccccctctccctctctctctacccct------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------gaatctggc -ctttctaaacaccctcaact diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_84fcaabd79e4fdafcadb7d8053cbaad8.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_84fcaabd79e4fdafcadb7d8053cbaad8.msa deleted file mode 100644 index 77677139..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_84fcaabd79e4fdafcadb7d8053cbaad8.msa +++ /dev/null @@ -1,95 +0,0 @@ ->syndip_1_chr20:5041857-5042709 -tctctccccagctgctgctagcggga-ttttttttttaactctctatcctatttaacctc -ctcactgatgaccttttaatgcataac------------------------------ttt -tttttttttttttttttgagacggagtctcgctctcccaggctggagtgcagtggtgtga -tctcggctcactgcaacctgtgcctcccaggttcaagcgatctcctgcctcagcctcccc -agtacctaggattacaggtgcgcgcctccagcatagctaatgtttgtatttttagtagag -acggggtttcaccatgttggccaggctggttatgcataactttttatcacagatgtttga -tctcagttttaatcttttcaacatttgtaaacccttggttcattgtgcttctccctttat -tactc----------------ttttttttttttttttgagacggagtttcgctcttgttg -cccaggctggagtgcagtggcgcactctcggttcactgcaatctccacctcataggttca -agcgattctcctgcctcagcctcctgagtagctgggattacaggcacacgccaccatgcc -tggctaattt-------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------ttctttttcttttt -tgtatttttagtagagatggggtttcactatgttggccagactggtcttgaactcctgac -ctcgtgatctgcccacctcagactcccaaagtgctgggattacaggtgtgagccaccgtg -cctggcctaattttgtatttttagtagagacggggtttctccatgttggtcaggctggtc -tcgaactcctgacctcaggtgatctgctcgtcttggcctcccaaagtgttgggattatag -gcataagccaccacaaccgacc ->syndip_2_chr20:5041857-5042709 -tctctccccagctgctgctagcggga-ttttttttttaactctctatcctatttaacctc -ctcactgatgaccttttaatgcgtaacttttttttttttttttttttttttttttttttt -tttttttttttttttttgagacggagtctcgctctcccaggctggagtgcagtggtgtga -tctcggctcactgcaacctgtgcctcccaggttcaagcgatctcctgcctcagcctcccc -agtacctaggattacaggtgcgcgcctccagcatagctaatgtttgtatttttagtagag -acggggtttcaccatgttggccaggctggttatgcataactttttatcacagatgtttga -tctcagttttaatcttttcaacatttgtaaacccttggttcattgtgcttctccctttat -tactcttttttttttttttttttttttttttttttttgagacggagtttcgctcttgttg -cccaggctggagtgcagtggcgcactctcggttcactgcaatctccacctcataggttca -agcgattctcctgcctcagcctcctgagtagctgggattacaggcacacgccaccatgcc -tggctaattt-------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------ttctttttcttttt -tgtatttttagtagagatggggtttcactatgttggccagactggtcttgaactcctgac -ctcgtgatctgcccacctcagactcccaaagtgctgggattacaggtgtgagccaccgtg -cctggcctaattttgtatttttagtagagacggggtttctccatgttggtcaggctggtc -tcgaactcctgacctcaggtgatctgctcgtcttggcctcccaaagtgttgggattatag -gcataagccaccacaaccgacc ->p:HG002_1_chr20:5041857-5042709 -tctctccccagctgctgctagcgggatttttttttttaactctctatcctatttaacctc -ctcactgatgaccttttaatgcgtaacttttttttttttttttttttttttttttttttt -tttttttttttttttttgagacggagtctcgctctcccaggctggagtgcagtggtgtga -tctcggctcactgcaacctgtgcctcccaggttcaagcgatctcctgcctcagcctcccc -agtacctaggattacaggtgcgcgcctccagcatagctaatgtttgtatttttagtagag -acggggtttcaccatgttggccaggctggttatgcataactttttatcacagatgtttga -tctcagttttaatcttttcaacatttgtaaacccttggttcattgtgcttctccctttat -tactcttttttttttttttttttttttttttttttttgagacggagtttcgctcttgttg -cccaggctggagtgcagtggcgcactctcggttcactgcaatctccacctcataggttca -agcgattctcctgcctcagcctcctgagtagctgggattacaggcacacgccaccatgcc -tggctaattt-------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------ttctttttcttttt -tgtatttttagtagagatggggtttcactatgttggccagactggtcttgaactcctgac -ctcgtgatctgcccacctcagactcccaaagtgctgggattacaggtgtgagccaccgtg -cctggcctaattttgtatttttagtagagacggggtttctccatgttggtcaggctggtc -tcgaactcctgacctcaggtgatctgctcgtcttggcctcccaaagtgttgggattatag -gcatgagccaccacaaccgacc ->p:HG002_2_chr20:5041857-5042709 -tctctccccagctgctgctagcggga-ttttttttttaactctctatcctatttaacctc -ctcactgatgaccttttaatgcataac------------------------------ttt -tttttttttttttttttgagacggagtctcgctctcccaggctggagtgcagtggtgtga -tctcggctcaccgcaacctgtgcctcccaggttcaagtgatctcctgcctcagcctcccc -agtacctaggattacaggtgcgcgcctccagcatagctaatgtttgtatttttagtagaa -acggggtttcaccatgttggccaggatggttatgcataactttttatcacagatgtttga -tctcagttttaatcttttcaacatttgtaaacccttggttcattgtgcttctccctttat -tactc----------------ttttttttttttttttgagacggagtttcgctcttgttg -cccaggctggagtgcagtggagcactctcggttcactgcaacctccacctcataggttca -agcgattctcctgcctcagcctcctgagtagctgggattacaggtgcccaccaccatgcc -cagctaatttttttttttgagagtctcacactgtcgcccaggctggagtgcaatggcact -atcttgactcactgcaacctcctcctgtgttcacgtgattctcctgcctcagcctcctga -gtagctgggattacaggcacatgccaccatgcccggctaatttttctttttttttttttt -tgtatttttagtagagatggggtttcactatgttggccagactggtcttgaactcctgac -ctcgtgatctgcccgcctcggactcccaaagtgctgggattacaggtgtgagccaccgtg -cccggcctaattttgtatttttagtagagacggggtttctccatgttggtcaggctggtc -tcgaactcccgatctcaggtgatccgctcgtcttggcctcccaaagtgttgggattacag -gcatgagccaccacacccagcc ->ref_chr20:5041857-5042709 -tctctccccagctgctgctagcggga-ttttttttttaactctctatcctatttaacctc -ctcactgatgaccttttaatgcgtaac----------------------------ttttt -tttttttttttttttttgagacggagtctcgctctcccaggctggagtgcagtggtgtga -tctcggctcactgcaacctgtgcctcccaggttcaagcgatctcctgcctcagcctcccc -agtacctaggattacaggtgcgcgcctccagcatagctaatgtttgtatttttagtagag -acggggtttcaccatgttggccaggctggttatgcataactttttatcacagatgtttga -tctcagttttaatcttttcaacatttgtaaacccttggttcattgtgcttctccctttat -tactct----tttttttttttttttttttttttttttgagacggagtttcgctcttgttg -cccaggctggagtgcagtggcgcactctcggttcactgcaatctccacctcataggttca -agcgattctcctgcctcagcctcctgagtagctgggattacaggcacacgccaccatgcc -tggctaattt-------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------ttctttttcttttt -tgtatttttagtagagatggggtttcactatgttggccagactggtcttgaactcctgac -ctcgtgatctgcccacctcagactcccaaagtgctgggattacaggtgtgagccaccgtg -cctggcctaattttgtatttttagtagagacggggtttctccatgttggtcaggctggtc -tcgaactcctgacctcaggtgatctgctcgtcttggcctcccaaagtgttgggattatag -gcataagccaccacaaccgacc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_85836283fdfecd2a963f6b695137738c.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_85836283fdfecd2a963f6b695137738c.msa deleted file mode 100644 index a2467e55..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_85836283fdfecd2a963f6b695137738c.msa +++ /dev/null @@ -1,130 +0,0 @@ ->syndip_1_chr20:62349541-62349926 -aagagggaggacaaaacagccgttttcagacaattccggatagactgtcatggaatagaa -aaactacagggtgcatttcaggaaggaggaagcagcaacccaggggatggggatggggat -ggggatggggatggtgggggtgatgggggtgatgatggtgatggtgatggtgatggtgat -ggtgatggtgatggtgggggtggtgat---------ggtgggggtgggggtggtgatggt -gggggtgggggtgatgatggtgatggtgggggtgatgacggtggggctgggggtgatgat -ggtgggggtgatgacggtgatgatgggggtggaggggtgatgacggtgatgatgggggtg -ggggggtgatgacggtgatgtgggggtgatgacggtgggggtgggggtgatgacggtgat ----------------------ggtgggggtgatgacggtgggggtgggggtgatgacggt -gggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgat -ggtgatggtgggggtgatgatggtgggggtgggggtgatgatggtgagggtgatgatggt -gggggtaatgacggtggggtgggggtgatgacggtgggagtgggggtgatgacggtgatg -gtgggggtgatgacggtgatggtgggggtgatgacggtgatggcggtgggggtgatgacg -gtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatg -acggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtg -atgacggtgggggtgggggtgatgacggtgatggtagaggtgatgatggtgggggtgatg -gtgggggtgggggtggg---------ggtgggggtgatgatggtgatggtgggggtgatg -atggtgagggtgatgatggtgggggtgatggtgggggtgggggtg--------------g -gggtgggggtgatgacggtgatggtgggggtgatgatggtgggagtgggctggtagtggg -ggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcag------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------aaaattgctggctg ->syndip_2_chr20:62349541-62349926 -aagagggaggacaaaacagccgttttcagacaattccggatagactgtcatggaatagaa -aaactacagggtgcatttcaggaaggaggaagcagcaaccca------ggggatggggat -ggggatggggatggggatggtgggggtgatgggggtgatgatggtgatggtgggggtgat -gatggtgatggtgatggtgatggtgat---------------ggtgggggtggtgatggt -gggggtgggggtgatgatggtgatggtgggggtgatgacggtggggctgggggtgatgat -ggtgggggtgatgacggtgatgatgggggtggaggggtgatgacggtgatgatgggggtg -ggggggtgatgacggtgatgtgggggtgatgacggtgggggtgggggtgatgacggtgat -ggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggt -gggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgat -ggtgatggtgggggtgatgatggtgggggtgggggtgatgatggtgagggtgatgatggt -gggggtaatgacggtggggtgggggtgatgacggtgggggtgggggtgatgacggtgatg -gtgggggtgatgacgatgatggtgggggtgatgacggtgatggcggtgggggtgatgacg -gtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatg -acggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtg -atgacggtgggggtgggggtgatgacggtgatggtagaggtgatgatggtgggggtgggg -gtgggggtgggggtgagggtgatgatggtgggggtgatgatggtgatggtgggggtgatg -atggtgagggtgatgatggtgggggtgatggtgggggtgggggtgggggtaatgacggtg -gggtgggggtaatgacggtgggggtgggggtgatgacggtgggagtggg--ggtgatgac -ggtgatggtgggggtgatgac--ggtgatggtgggggtgatgacggtgatggcggtgggg -gtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtg -ggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatg -gtagaggtgatgatggtgggggtgatggtgggggtgggggtgggggtgggggtgatgatg -gtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtgggggtgggg -gtgggggtgggggtgatgatggtgggagtgggctggtagtgggggtgatggtttgggtgg -gagtaaggtgatggtggaggtaaagaggcagaaaattgctggctg ->p:HG002_1_chr20:62349541-62349926 -aagagggaggacaaaacagccgttttcagacaattccggatagactgtcatggaatagaa -aaactacagggtgcatttcaggaaggaggaagcagcaaccca------ggggatggggat -ggggatggggatggtgggggtgatgggggtgatgatggtgatggtgatggtgatggtgat -ggtgatggtgatggtgggggtggtgat--------------gggtgggggtgatgacggt -gggagtgggggtgatgacggtgatggtgggggtgatgacggtgatggtgggggtgatgat -ggtgggggtgatgacggtgatgatgggggtggaggggtgatgacggtgatgatgggggtg -ggggggtgatgacggtgatgtgggggtgatgacggtgggggtgggggtgatgacggtgat -ggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggt -gggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgat -ggtgatggtgggggtgatgatggtgggggtgggggtgatgatggtgagggtgatgatggt -gggggtaatgacggtggggtgggggtgatgacggtgggggtgggggtgatgacggtgatg -gtgggggtgatgacgatgatggtgggggtgatgacggtgatggcggtgggggtgatgacg -gtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatg -acggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtg -atgacggtgggggtgggggtgatgacggtgatggtagaggtgatgatggtgggggtgggg -gtgggggtgggggtgagggtgatgatggtgggggtgatgatggtgatggtgggggtgatg -atggtgagggtgatgatggtgggggtgatggtgggggtgggggtgggggtaatgacggtg -gggtgggggtaatgacggtgggggtgggggtgatgacggtgggggtggg--ggtgatgac -ggtgatggtgggggtgatgac--gatgatggtgggggtgatgacggtgatggcggtgggg -gtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtg -ggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatg -gtagaggtgatgatggtgggggtgatggtgggggtgggggtgggggtgggggtgatgatg -gtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtgggggtggcg -gtgatggtgggggtgatgatggtgggagtgggctggtagtgggggtgatggtttgggtgg -gagtaaggtgatggtggaggtaaagaggcagaaaattgctggctg ->p:HG002_2_chr20:62349541-62349926 -aagagggaggacaaaacagccgttttcagacaattccggatagactgtcatggaatagaa -aaactacagggtgcatttcaggaaggaggaagcagcaaccca------ggggatggggat -ggggatggggatggtgggggtgatgggggtgatgatggtgatggtgatggtgatggtgat -ggtgatggtgatggtgggggtggtgatggtggtgatggtgggggtgggggtggtgatggt -gggggtgggggtgatgatggtgatggtgggggtgatgacggtggggctgggggtgatgat -ggtgggggtgatgacggtgatgatgggggtggaggggtgatgacggtgatgatgggggtg -ggggggtgatgacggtgatgtgggggtgatgacggtgggggtgggggtgatgacggtgat ----------------------ggtgggggtgatgacggtgggggtgggggtgatgacggt -gggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgat -ggtgatggtgggggtgatgatggtgggggtgggggtgatgatggtgagggtgatgatggt -gggggtaatgacggtggggtgggggtgatgacggtgggggtgggggtgatgacggtgatg -gtgggggtgatgacgatgatggtgggggtgatgacggtgatggcggtgggggtgatgacg -gtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatg -acggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtg -atgacggtgggggtgggggtgatgacggtgatggtagaggtgatgatggtgggggtgatg -gtgggggtgggggtggg---------ggtgggggtgatgatggtggtgggggtgatgacg -gtgggagtgggggtgatgacggtgatggtgggggtgatgacggtg--------------a -tggtgggggtgatgacggtgatggtgggggtgatgatggtgggagtgggctggtagtggg -ggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcag------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------aaaattgctggctg ->ref_chr20:62349541-62349926 -aagagggaggacaaaacagccgttttcagacaattccggatagactgtcatggaatagaa -aaactacagggtgcatttcaggaaggaggaagcagcaaccca------ggggatggggat -ggggatggggatggtgggggtgatgggggtgatgatggtgatggtgatggtgatggtgat -ggtgatggtgatggtgggggtggtgat--------------gggtgggggtgatgacggt -gggagtgggggtgatgacggtgatggtgggggtgatgacggtgatggtgggggtgatgac -ggtgatggtgggggtgatgatggtgggagtgggctggtagtgggggtgatggtttgggtg -ggagtaaggtgatggtggaggtaaagaggcag---------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------aaaattgctggctg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_87c0f9c83d535bef7d6a1ec41e7cfa49.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_87c0f9c83d535bef7d6a1ec41e7cfa49.msa deleted file mode 100644 index 76167b7d..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_87c0f9c83d535bef7d6a1ec41e7cfa49.msa +++ /dev/null @@ -1,30 +0,0 @@ ->syndip_1_chr20:10802676-10802958 -tttgggggacataacccacaatgtcctctgaatatatatatatatatcctccc------- ----atatatatatatatcctccc--atatatatatatatat------------------- --------------------------------------------------atatatatata -tatgtcctcccatatatatatatatcctcccatatatatatctatcctccc----atata -tatatatatatattttcaatgtatccctttattcaagtgattt ->syndip_2_chr20:10802676-10802958 -tttgggggacataacccacaatgtcctctgaatatatatatatatatcctcccatatata -tatatatatatatatatcctccc--atatatatatatatatatatatatcctcccatata -tatatatatatatatatcctcccatatatatatatatatatgtcctcccatatatatata -tatatcctcccatatatatatatatcctcccatatatatatctatcctcccatatatata -tatatatatatattttcaatgtatccctttattcaagtgattt ->p:HG002_1_chr20:10802676-10802958 -tttgggggacataacccacaatgtcctctgaatatatatatatatatcctcccatatata -tatatatatatatatatcctccc--atatatatatatatatatatatatcctcccatata -tatatatatatatatatcctcccatatatatatatatatatgtcctcccatatatatata -tatatcctcccatatatatatatatcctcccatatatatatctatcctcccatatatata -tatatatatatattttcaatgtatccctttattcaagtgattt ->p:HG002_2_chr20:10802676-10802958 -tttgggggacataacccacaatgtcctctgaatatatatatatatatcctccc------- ----atatatatatatatcctccc--atatatatatatatat------------------- --------------------------------------------------atatatatata -tatgtcctcccatatatatatatatcctcccatatatatatctatcctccc----atata -tatatatatatattttcaatgtatccctttattcaagtgattt ->ref_chr20:10802676-10802958 -tttgggggacataacccacaatgtcctctgaatatatatatatatatcctcccatatata -tatatatatatatatatcctcccatatatatatatatatatatatatatcctcccatata -tatatatatatatatatcctcccatatatatatatatatatgtcctcccatatatatata -tatatcctcccatatatatatatatcctcccatatatatatctatcctcccatatatata -tatatatatatattttcaatgtatccctttattcaagtgattt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_88defe82879155d5712cdad2147ce335.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_88defe82879155d5712cdad2147ce335.msa deleted file mode 100644 index 086443cc..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_88defe82879155d5712cdad2147ce335.msa +++ /dev/null @@ -1,125 +0,0 @@ ->syndip_1_chr20:38123589-38124213 -agctttgtgatctcaggcctgtcctgtaacctctctgggcctcagaaacctctctctctc -tctatatatatatatatataataatatataataataatatataatatgtataataataat -atataatatttataataataatatatataatatgtatatataatatacatatacctatta -tatataatatacctattatatataatatacatatacctattatatataatatacctatta -tatataagatacctattatatataatatacatatacctattatatatataatatacct-- ---------------attatatat-------atataatatacctattatatatataatata -cctat--tatatatataatatacctattatatatataatatacctattatatatataata -tacctat--tatatataatatacctattatatataa-------aatatacctattatata -taatatacctattatatacattatatataatatacctattatatgcattatatataatat -acctattatatgcattatatataatatacctattatatgcattatatataatatacctat -tatatgcattatatataatatacctattatatgcattatataatatattatatataatat -gc--atattatatgtattatatattatatattatatatataatatacatattatatgtat -tatatattatatattatatatataatatacatattatatgtattatatattatatataat -atacatattatatattatatattatatacatattatatattatatattatatacatatta -tatattatatacatattatatattatatattatatacatattatacattatatatatcta -aaatatataatacacattatatattatataatacacattatatataatatataatacaca -ttatatattatatataatacacattatatattatatataatacacattatatat------ ------------------tatataatacacattatatattatatataatacacattatata -ttatatataatacacattatatattatatataatacacattatatattatataatacaca -ttatatattatatataatacacattatatatataatacacattatatattatatataata -cataatacacattatatattatatataatacacattatatataatatataacacacatta -tatataatatataacacacattatatattatatataatacacattatatattatatataa -tacacatatattatatataatacacattatatattatatataatacacatatattatata -taatacacattatatattatatataatacacattatatataatata ->syndip_2_chr20:38123589-38124213 -agctttgtgatctcaggcctgtcctgtaacctctctgggcctcagaaacctctctctctc -tctatatatatatatatataataatatataataataatatataatatgtataataataat -atataatatttataataataatatatataatatgtatatataatatacatatacctatta -tatataatatacctattatatataatatacatatacctattatatataatatacctatta -tatataagatacctattatatataatatacatatacctattatatatataatatacct-- ---------------attatatat-------atataatatacctattatatatataatata -cctat--tatatatataatatacctattatatatataatatacctattatatatataata -tacctat--tatatataatatacctattatatataa-------aatatacctattatata -taatatacctattatata---------------------------cattatatataatat -acctattatatgcattatatataatatacctattatatgcattatatataatatacctat -tatatgcattatatataatatacctattatatgcattatataatatattatatataatat -gc--atattatatgtattatatattatatattatatatataatatacatattatatgtat -tatatattatatattatatatataatatacatattatatgtattatatattatatataat -atacatattatatattatatattatatacatattatatattatatattatatacatatta -tatattatatacatattatatattatatattatatacatattatacattatatatatcta -aaatatataatacacattatatattatataatacacattatatataatatataatacaca -ttatatattatatataatacacattatatattatatataatacacattatatattatata -atacacattatatattatatataatacacattatatattatatataatacacattatata -ttatatataatacacattatatattatatataatacacattatatattatataatacaca -ttatatattatatataatacacattatatatataatacacattatatattatatataata -cataatacacattatatattatatataatacacattatatataatatataacacacatta -tatataatatataacacacattatatattatatataatacacattatatattatatataa -tacacatatattatatataatacacattatatattatatataatacacatatattatata -taatacacattatatattatatataatacacattatatataatata ->p:HG002_1_chr20:38123589-38124213 -agctttgtgatctcaggcctgtcctgtaacctctctgggcctcagaaacctctctctctc -tctatatatatatatatataataatatataataataatatataatatgtataataataat -atataatatttataataataatatatataatatgtatatataatatacatatacctatta -tatataatatacctattatatataatatacataaacctattatatataatatacctatta -tatataagatacctattatatataatatacctatacctattatatatataagatacct-- ---------------attatatataatatacatacctattacctattatatatataatata -cctattatatatatataatatacctattatatatataatatacctat-----------ta -tacctat--tatatataatatacctattatatatat-------aatatacctattatata -taatatacctattatata---------------------------cattatatataatat -acctattatatgcattatatataatatacctattatatgcattatatataatatacctat -tatatgcattatatataatatacctattatatgcattatataatatattatatataatat -gc--atattatatgtattatatattatatattatatatataatatacatattatatgtat -tatatattatatattatatatataatatacatattatatgtattatatattatatataat -atacatattatatattatatattatatacatattatatattatatattatatacatatta -tatattatatacatattatatattatatattatatacatattatacattatatatatcta -aaatatataatacacattatatattatataatacacattatatataatatataatacaca -ttatatattatatataatacacattatatattatatataatacacattatatattatata -atacacattatatattatatataatacacattatatattatatataatacacattatata -ttatatataatacacattatatattatatataatacacattatatattatataatacaca -ttatatattatatataatacacattatatatataatacacattatatattatatataata -cataatacacattatatattatatataatacacattatatataatatataacacacatta -tatataatatataacacacattatatattatatataatacacattatatattatatataa -tacacatatattatatataatacacattatatattatatataatacacatatattatata -taatacacattatatattatatataatacacattatatataatata ->p:HG002_2_chr20:38123589-38124213 -agctttgtgatctcaggcctgtcctgtaacctctctgggcctcagaaacctctctctctc -tctatatatatatatatataataatatataataataatatataatatgtataataataat -atataatatttataataataatatatataatatgtatatataatatacatatacctatta -tatataatatacctattatatataatatacataaacctattatatataatatacctatta -tatataagatacctattatatataatatacctatacctattatatatataatatacctta -tatataagatacctattatatataatatacata-----tacctattatatatataatata -cctattatatatatataatatacctattatatatataatatacctattatatatataata -tacctat--tatatatataatacctattatatataatatacctattatatacattatata -taatatacctattatatg---------------------------cattatatataatat -acctattatatgcattatatataatatacctattatatgcattatatataatatacctat -tatatgcattatatataatatacctattatatgcattatataatatattatatataatat -gc--atattatatgtattatatattatatattatatatataatatacatattatatgtat -tatatattatatattatatatataatatacatattatatgtattatatattatatataat -atacatattatatattatatattatatacatattatatattatatattatatacatatta -tatattatatacatattatatattatatattatatacatattatacattatatatatcta -aaatatataatacacattatatattatataatacacattatatataatatataatacaca -ttatatattatatataatacacattatatattatatataatacacattatatat------ ------------------tatataatacacattatatattatatataatacacattatata -ttatatataatacacattatatattatatataatacacattatatattatataatacaca -ttatatattatatataatacacattatatatataatacacattatatattatatataata -cataatacacattacctattatatataatacacattatatataatatataacacacatta -tatataatatataacacacattatatattatatataatacacattatatattatatataa -tacacatatattatatataatacacattatatattatatataatacacatatattatata -taatacacattatatattatatataatacacattatatataatata ->ref_chr20:38123589-38124213 -agctttgtgatctcaggcctgtcctgtaacctctctgggcctcagaaacctctctctctc -tctatatatatatatatataataatatataataataatatataatatgtataataataat -atataatatttataataataatatatataatatgtatatataatatacatatacctatta -tatataatatacctattatatataatatacataaacctattatatataatatacctatta -tatataagatacctattatatataatatacctat--------tatatataagatacct-- ---------------attatatataatatacata-----tacctattatatatataatata -cctattatatatatataatatacctattatatatataatatacctattatatatataata -tacctattatatatataatatacctattatatataa-----------tacacattatata -taata----tataacaca---------------------------cattatatataata- ----tataacacacattatatattata----tataatacacattatatattatatataata -cacatatattatatataatacac----------------attatatattatatataatac -acatatattatatataatacacattatatattatatata----atacacattatatataa -tata-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_8a21396bcfb498d1e7e1cb7424870b13.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_8a21396bcfb498d1e7e1cb7424870b13.msa deleted file mode 100644 index 2d39a3da..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_8a21396bcfb498d1e7e1cb7424870b13.msa +++ /dev/null @@ -1,305 +0,0 @@ ->syndip_1_chr20:62057373-62059339 -gaccttcttactgcagggccctcattctaaaacctaatgtcaaatttgatagacagaaaa -aactgtttctggggtttcctgactattcggaaatggtccctccaagatccatgtacccca -acaccaccctacctggctacgctcctctcacaactttgagatcaagatgccacgtgtgcc -ttcctcacatcggcgctttccagtgatgcccagtgggggacacaaagggcccagcaagac -ctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggcc -aacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatg -gggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccag -gccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacaca -ggcctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagg -aaggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctc -agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc -gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca -gacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggccta -cacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggac -ggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaaga -cctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggc -caacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaat -ggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca -ggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacac -aggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca -ggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacct -cagcaagacctcaggaaggacggacacaggtc---------------------------- ---------------------------------------------tacacaccaggccaca -gacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctac -acaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggac -ggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaag -acctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggc -caacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaat -ggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca -ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca -ggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagg -aaggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctc -agcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctc -ggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccac -agacagtggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtct -acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga -cggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaa -gacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggg -gccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagaca -atggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac -caggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggac -acaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacct -caggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaac -ctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatgggg -ctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggc -cacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggt -ctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaag -gacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagca -agacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggg -ggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagac -aatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacac -accaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgga -cacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacct -caggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaa -cctctccagtccccaaacacagtccccaacagacaacttctcctgtccccacatgcggct -cccaacaaacaatttctcctgccctcacacgcggttcccaacgacaacttctgctccaca -acatgacacccacggtgggagaagctgggggcacttcactacatcatcctgcacactgca -gcatggcctgctccaggcagaaggcaggcctggagaagagcctgggaccaccgcggactg -accaacagcggacaccaggtactttctcaaatgggagaggggcctcatggtggacaacat -gtatctctttgtttttcgaaagctgtacatctttggtgcaaa ->syndip_2_chr20:62057373-62059339 -gaccttcttactgcagggccctcattctaaaacctaatgtcaaatttgatagacagaaaa -aactgtttctggggtttcctgactattcggaaatggtccctccaagatccatgtacccca -acaccaccctacctggctacgctcctctcacaactttgagatcaagatgccacgtgtgcc -ttcctcacatcggcgctttccagtgatgcccagtgggggacacaaagggcccagcaagac -ctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc-------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------gggggccaacctcagcaagacctca -ggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacct -cagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggct -cgggggccaacctcagcaagacctcaggaaggacggacacaggt---------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------ctacacaccaggccacagacaatggggctcgggggc -caacctcagcaagacctcaggaaggacg-------------------------------- ------------------------------------------gacacaggtctacacacca -ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca -ggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagg -aaggacggacacaggtctacacaccaggccacagacaatggggctc-------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------gggggccaa -cctctccagtccccaaacacagtccccaacagacaacttctcctgtcctcacatgcggct -cccaacaaacaatttctcctgccctcacacgcggttcccaacgacaacttctgctccaca -acatgacacccacggtgggagaagctgggggcacttcactacatcatcctgcacactgca -gcatggcctgctccaggcagaaggcaggcctggagaagagcctgggaccaccgcggactg -accaacagcggacaccaggtactttctcaaatgggagaggggcctcatggtggacaacat -gtatctctttgtttttcgaaagctgtacatctttggtgcaaa ->p:HG002_1_chr20:62057373-62059339 -gaccttcttactgcagggccctcattctaaaacctaatgtcaaatttgacagacagaaaa -aactgtttctggggtttcctgactattcggaaatggtccctccaagatccatgtacccca -acaccaccctacctggccacgctcctctcacaactttgagatcaagatgccacgtgtgcc -ttcctcacatcggcgctttccagtgatgcccagtgggggacacaaagggcccagcaagac -ctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc-------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------gggggccaacctcagcaagacctca -ggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacct -cagcaagacctcaggaaggacggacacaggtc---------------------------- ---------------------------------------------tacacaccaggccaca -gacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggt---- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------ctacacaccaggccacagacaatggggctcgggggc -caacctcagcaagacctcaggaaggacg-------------------------------- ------------------------------------------gacacaggtctacacacca -ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca -ggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagg -aaggacggacacaggtctacacaccaggccacagacaatggggctc-------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------gggggccaa -cctctccagtccccaaacacagtccccaacagacaacttctcctgtcctcacatgcggct -cccaacaaacaatttctcctgccctcacacgcggttcccaacgacaacttctgctccaca -acatgacacccacggtgggagaagctgggggcacttcactacatcatcctgcacactgca -gcatggcctgctccaggcagaaggcaggcctggagaagagcctgggaccaccgcggactg -accaacagcggacaccaggtactttctcaaatgggagaggggcctcatggtggacaacat -gtatctctttgtttttcgaaagctgtacatctttggtgcaaa ->p:HG002_2_chr20:62057373-62059339 -gaccttcttactgcagggccctcattctaaaacctaatgtcaaatttgatagacagaaaa -aactgtttctagggtttcctgactattcggaaatggtccctccaagatccatgtacccca -acaccaccctacctggctacgctcctctcacaactttgagatcaagatgccacgtgtgcc -ttcctcacatcggcgctttccagtgatgcccagtgggggacacaaagggcccagcaagac -ctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggcc -aacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatg -gggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccag -gccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacaca -ggcctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagg -aaggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctc -agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc -gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca -gacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggccta -cacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggac -ggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaaga -cctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggc -caacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaat -ggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca -ggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacac -aggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca -ggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacct -cagcaagacctcaggaaggacggacacaggtc---------------------------- ---------------------------------------------tacacaccaggccaca -gacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctac -acaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggac -ggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaag -acctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggc -caacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaat -ggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca -ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca -ggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagg -aaggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctc -agcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctc -ggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccac -agacagtggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtct -acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga -cggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaa -gacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggg -gccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagaca -atggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac -caggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggac -acaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacct -caggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaac -ctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatgggg -ctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggc -cacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggt -ctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaag -gacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagca -agacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggg -ggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagac -aatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacac -accaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgga -cacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacct -caggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaa -cctctccagtccccaaacacagtccccaacagacaacttctcctgtccccacatgcggct -cccaacaaacaatttctcctgccctcacacgcggttcccaacgacaacttctgctccaca -acatgacacccacggtgggagaagctgggggcacttcactacatcatcctgcacactgca -gcatggcctgctccaggcagaaggcaggcctggagaagagcctgggaccaccgcggactg -accaacagcggacaccaggtactttctcaaatgggagaggggcctcatggtggacaacat -gtatctctttgtttttcgaaagctgtacatctttggtgcaaa ->ref_chr20:62057373-62059339 -gaccttcttactgcagggccctcattctaaaacctaatgtcaaatttgatagacagaaaa -aactgtttctggggtttcctgactattcggaaatggtccctccaagatccatgtacccca -acaccaccctacctggctacgctcctctcacaactttgagatcaagatgccacgtgtgcc -ttcctcacatcggcgctttccagtgatgcccagtgggggacacaaagggcccagcaagac -ctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggggcc -aacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatg -gggctcg----------------------------------------------------- ------------------------------------------------------------- ----------------------------------gggggccaacctcagcaagacctcagg -aaggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctc -agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc -gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca -gacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggccta -cacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggac -ggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaaga -cctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggc -caacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaat -ggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca -ggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacac -aggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca -ggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacct -cagcaagacctcaggaaggacggacacaggtc---------------------------- ---------------------------------------------tacacaccaggccaca -gacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctac -acaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggac -ggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaag -acctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggc -caacctcagcaagacctcaggaaggacg-------------------------------- ------------------------------------------gacacaggtctacacacca -ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca -ggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagg -aaggacggacacaggtctacacaccaggccacagacaatggggctc-------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------ggggggccaa -cctctccagtccccaaacacagtccccaacagacaacttctcctgtccccacatgcggct -cccaacaaacaatttctcctgccctcacacgcggttcccaacgacaacttctgctccaca -acatgacacccacggtgggagaagctgggggcacttcactacatcatcctgcacactgca -gcatggcctgctccaggcagaaggcaggcctggagaagagcctgggaccaccgcggactg -accaacagcggacaccaggtactttctcaaatgggagaggggcctcatggtggacaacat -gtatctctttgtttttcgaaagctgtacatctttggtgcaaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_8e56bbd36144696ef61ad874334f0ede.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_8e56bbd36144696ef61ad874334f0ede.msa deleted file mode 100644 index c8497eb0..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_8e56bbd36144696ef61ad874334f0ede.msa +++ /dev/null @@ -1,85 +0,0 @@ ->syndip_1_chr20:20295955-20296565 -gagcccgcccttgcacaccaacgcctgcatgcttccctccttccttccttccttccctcc -tttccttccttctttcttttcttcctccctcccttcct---tcccttccttcccttcctt -ccctcctttt--cttccttctttccttccttccttccctccctccttcccttccttcctt -ccttcc-cttccttccttctctccttccttccttccctccctccttcccttccttccttc -tctccttccttcccttccttccttctctccttccttcccttccttccttctctccttcct -tcccttccttccttctctccttccttcccttccttccttctctccttccttcccttgctt -cctttcttccttcctttgcttccttgcttccttctttcctttcttcatccctccctccct -ccttccttcctttccttccttccctctatccttccttccttcctttctttctccctccct -tccttcccttccttccttccctcttttccttccatctttcctttcttcctccctccctcc -ctccttccctccttcattacttccttccctcctttccttccttcacctccttcccttctc -tcctcccttcatcccttccttcctttcttccttccctccctcttccttcctttcttcacc -cctcccccttccctcatcccttccctccttcccttccttccttccttccctccttccttc -ccttccttccttccttgcttccttccttctttcctttcttcatccctccttccctccctc -cctccttcctgccttccttctttctttcttttctttcttcctccctccctccttccttcc -ctccttcctgccttccttccttcctttctttttcctccctccctccttccttctttactc -ccttccttccttccttcctcccctcactcaatttgttcatcaaaaaatctagttccttg ->syndip_2_chr20:20295955-20296565 -gagcccgcccttgcacaccaacgcctgcatgcttccctccttccttccttccttccttcc --ttccttccttccttccttccttcctgcctgcctgcctgccttcctgccttcccttcctc -cctccctccctacctccctccctccttccttcccttcctccctccctcccttctttactt -ccttcctccttccctcctcctttcctccatccttccctcccttctttcctttcttcctcc -tgccct------ccctccttctttcccttcctccctcccttccttcccatcctccttccc -tccct--ccttccttcctgccttccttccttccctccatccttccttccttccttt-ctt -cctccctcccttccttcctcccttccttcccttccttccttccctcttttccttccatct -ttcctttcttcctccctccctccctccttccctccttcattcctttct---tccctcctt -tccttccttcacctccttcccttctctcctcccttcatcccttccttcctttcttccttc -cctccctcttccttcctttcttcacccctcccccttccctcatcccttccctccttccct -tccttccttccttccctccttccttcccttccttccttc--cttccctccttcctt---- ------cccttccttccttgcttccttccttccttcccttccttccttgcttccttccttc -cttcccttccttccttgcttccttccttctttcctttcttcatccctccttccctccctc -cctccttcctgccttccttctttctttcttttctttcttcctccctccctccttccttcc -ctccttcctgccttccttccttcctttctttttcctccctccctccttccttctttactc -ccttccttccttccttcctcccctcactcaatttgttcatcaaaaaatctagttccttg ->p:HG002_1_chr20:20295955-20296565 -gagcccgcccttgcacaccaacgcctgcatgcttccctccttccttccttccttccttcc --ttccttccttccttccttccttcctgcctgcctgcctgccttcctgccttcccttcctc -cctccctccctacctccctccctccttccttcccttcctccctccctcccttctttactt -ccttcctccttccctcctcctttcctccatccttccctcccttctttcctttcttcctcc -tgccct------ccctccttctttcccttcctccctcccttccttcccatcctccttccc -tccct--ccttccttcctgccttccttccttccctccatccttccttccttccttt-ctt -cctccctcccttccttcctcccttccttcccttccttccttccctcttttccttccatct -ttcctttcttcctccctccctccctccttccctccttcattcctttct---tccctcctt -tccttccttcacctccttcccttctctcctcccttcatcccttccttcctttcttccttc -cctccctcttccttcctttcttcacccctcccccttccctcatcccttccctccttccct -tccttccttccttccctccttccttcccttccttccttc--cttccctccttcctt---- ------cccttccttccttgcttccttccttccttcccttccttccttgcttccttccttc -cttcccttccttccttgcttccttccttctttcctttcttcatccctccttccctccctc -cctccttcctgccttccttctttctttcttttctttcttcctccctccctccttccttcc -ctccttcctgccttccttccttcctttctttttcctccctccctccttccttctttactc -ccttccttccttccttcctcccctcactcaatttgttcatcaaaaaatctagttccttg ->p:HG002_2_chr20:20295955-20296565 -gagcccgcccttgcacaccaacgcctgcatgcttccctccttccttccttccttccctcc -tttccttccttctttcttttcttcctccctcccttcct---tcccttccttcccttcctt -ccctcctttt--cttccttctttccttccttccttccctccctccttcccttccttcctt -ccttcc-cttccttccttctctccttccttccttccctccctccttcccttccttccttc -tctccttccttcccttccttccttctctccttccttcccttccttccttctctccttcct -tcccttccttccttctctccttccttcccttccttccttctctccttccttcccttgctt -cctttcttccttcctttgcttccttgcttccttctttcctttcttcatccctccctccct -ccttccttcctttccttccttccctctatccttccttccttcctttctttctccctccct -tccttcccttccttccttccctcttttccttccatctttcctttcttcctccctccctcc -ctccttccctccttcattacttccttccctcctttccttccttcacctccttcccttctc -tcctcccttcatcccttccttcctttcttccttccctccctcttccttcctttcttcacc -cctcccccttccctcatcccttccctccttcccttccttccttccttccctccttccttc -ccttccttccttccttgcttccttccttctttcctttcttcatccctccttccctccctc -cctccttcctgccttccttctttctttcttttctttcttcctccctccctccttccttcc -ctccttcctgccttccttccttcctttctttttcctccctccctccttccttctttactc -ccttccttccttccttcctcccctcactcaatttgttcatcaaaaaatctagttccttg ->ref_chr20:20295955-20296565 -gagc-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------ccgcccttgcacaccaacgcct -gcatgcttccctccttccttccttccttccctcctttccttccttctttcttttcttcct -ccctcccttccttcc--------------cttccttcccttccttccctccttttcttcc -ttctttccttccttccttccctccctccttcccttccttccttccttcctccctccctcc -ctccttccctccttcattccttccttccctcctttccttccttcacctccttcccttctc -tcctcccttcatcccttccttcctttcttccttccctccctcttccttcctttcttcacc -cctcccccttccctcatcccttccctccttcccttccttccttccttccctccttccttc -ccttccttccttccttgcttccttccttctttcctttcttcatccctccttccctccctc -cctccttcctgccttccttctttctttcttttctttcttcctccctccctccttccttcc -ctccttcctgccttccttccttcctttctttttcctccctccctccttccttctttactc -ccttccttccttccttcctcccctcactcaatttgttcatcaaaaaatctagttccttg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_8e593bfc608e33e76bb95b3f5bcca2c7.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_8e593bfc608e33e76bb95b3f5bcca2c7.msa deleted file mode 100644 index 27cb9183..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_8e593bfc608e33e76bb95b3f5bcca2c7.msa +++ /dev/null @@ -1,205 +0,0 @@ ->syndip_1_chr20:20337000-20337907 -tcatggcaaagaattgaaccctaggtcttctccttccttgcaaccgttaatgtcagaagc -tctgaagacacctgggacagagaagagagggagaaaagtttacgtggaagcatagggaag -gaagggatgtttgttgaggggtggtgtgatgcagcagaggaagaggaccagaggaaagca -gccactggaaataaggaaacagggtttaggaaggcctcactagacctgttaggatggatg -catggatggatggatggatggacagaatgggtgggtggatggatggatggatggatggat -ggatggatagatgggtgggtggatggatggatggatagatgggtggatggatagatgggt -ggatggataaatggatggatggatggatggatagatgggtgggtggatggatggatggat -ggatggatggatggatggatggatagatggatagatgggtgggtggatggatggatggat -ggatggatggatggatggatggatagatgggtgggtggatggatggatggatagatggat -agatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagat -ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat -agatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggat -ggatagatgggtggatggataaatggatggatggatggatggatagatgtgtgggtggat -ggatggatggatggatggatggatggatggatggatagatggatagatgggtgggtggat -ggatggatggatggatggatggatggatggatggatagatgggtggatggatggatagat -gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat -agatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggat -ggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat -ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat -ggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat -ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat -ggatggatggatggatggatggatggatagatgggtgggtggatggatggatggatagat -gggtgggtggatggatggatggatggatggatggatggatggatggatagatggatagat -gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatggat -agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat -ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat -agatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagat -gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat -agatgggtgggtggatggatggatggatggatggatagatggatagatgggtgggtggat -ggatggatggatagatgggtgggtggatggatggatggatggatggatggatggatggat -ggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat -ggatggatagatggatagatgggtgggtggatggatggatggatagatggatagatgggt -gggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggt -ggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggt -gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat -gggtgggtggatggatggatggatagatgggtgggtgggtggatggatggatggatggat -ggatagaataaaaagaaagctaggacatggttctagtgttcttagcagacgtcccaccat -ggaagaggtcatggagcacaggggctttgggaaaggtgtttacaatcctgcctgcctctc -acccagacctcttgccagggttggcacacccagatgcctgctgtgaccaatggagaggag -caattctggccagactggtgggaaagcaaggacgaaccacggaggccatccct ->syndip_2_chr20:20337000-20337907 -tcatggcaaagaattgaaccctaggtcttctccttccttgcaaccgttaatgtcagaagc -tctgaagacacctgggacagagaagagagggagaaaagtttacgtggaagcatagggaag -gaagggatgtttgttgaggggtggtgtgatgcagcagaggaagaggaccagaggaaagca -gccactggaaataaggaaacagggtttaggaaggcctcactagacctgttaggatggatg -catggatggatggatggatggacagaatgggtgggtggatggatggatggatggatggat -ggatggatggatagatgggtgggtggatggatggatggatagatgggtggatggataaat -ggatgg----atggatggatggatagatgggtgggtggatggatggatggatggatggat -ggatggatggatggatagatggatagatgggtgggtggatggatggatggatggatggat -ggatggatggatggatggatggatagatgggtgggtggatggatggatggatagatggat -agatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagat -ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat -agatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggat -ggatagatgggtggatggataaatggatggatggatggatggatagatgggtgggtggat -ggatggatggatggatggatggatagatggataga----------------tgggtgggt -ggatggatggatggatggatggatggatggatggatagatgggtggatggatggatagat -gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat -agatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggat -ggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat -ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat -ggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat -ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat -ggatggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat -gggtggg----tggatggatggatggatggatggatggatggatggatagatggatagat -gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatggat -agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat -ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat -a--------------------gatggatagatgggtgggtggatggatggatggatagat -gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat -agatgggtgggtggatggatggatggataga----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------t -gggtgggtgggtggatggatggatagatgggtgggtggatggatggatggatagatgggt -gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat -gggtgggtggatggatggatggatagatgggtgggtgggtggatggatggatggatggat -ggatagaataaaaagaaagctaggacatggttctagtgttcttagcagacgtcccaccat -ggaagaggtcatggagcacaggggctttgggaaaggtgtttacaatcctgcctgcctctc -acccagacctcttgccagggttggcacacccagatgcctgctgtgaccaatggagaggag -caattctggccagactggtgggaaagcaaggacgaaccacggaggccatccct ->p:HG002_1_chr20:20337000-20337907 -tcatggcaaagaattgaaccctaggtcttctccttccttgcaaccgttaatgtcagaagc -tctgaagacacctgggacagagaagagagggagaaaagtttacgtggaagcatagggaag -gaagggatgtttgttgaggggtggtgtgatgcagcagaggaagaggaccagaggaaagca -gccactggaaataaggaaacagggtttaggaaggcctcactagacctgttaggatggatg -catggatggatggatggatggacagaatgggtgggtggatggatggatggatggatggat -ggatggatggatagatgggtgggtggatggatggatggatagatgggtggatggataaat -ggatgg----atggatggatggatagatgggtgggtggatggatggatggatggatggat -ggatggatggatggatagatggatagatgggtgggtggatggatggatggatggatggat -ggatggatggatggatggatggatagatgggtgggtggatggatggatggatagatggat -agatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagat -ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat -agatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggat -ggatagatgggtggatggataaatggatggatggatggatggatagatgggtgggtggat -ggatggatggatggatggatggatagatggataga----------------tgggtgggt -ggatggatggatggatggatggatggatggatggatagatgggtggatggatggatagat -gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat -agatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggat -ggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat -ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat -ggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat -ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat -ggatggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat -gggtggg----tggatggatggatggatggatggatggatggatggatagatggatagat -gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatggat -agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat -ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat -a--------------------gatggatagatgggtgggtggatggatggatggatagat -gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat -agatgggtgggtggatggatggatggataga----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------t -gggtgggtgggtggatggatggatagatgggtgggtggatggatggatggatagatgggt -gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat -gggtgggtggatggatggatggatagatgggtgggtgggtggatggatggatggatggat -ggatagaataaaaagaaagctaggacatggttctagtgttcttagcagacgtcccaccat -ggaagaggtcatggggcacaggggctttgggaaaggtgtttacaatcctgcctccctctc -acccagacctcttgccagggttggcacacccagatgcctgctgtgaccaatggagaggag -caattctggccagactggtgggaaagcaaggacgaaccacggaggccatccct ->p:HG002_2_chr20:20337000-20337907 -tcatggcaaagaattgaaccctaggtcttctccttccttgcaaccgttaatgtcagaagc -tctgaagacacctgggacagagaagagagggagaaaagtttacgtggaagcatagggaag -gaagggatgtttgttgaggggtggtgtgatgcagcagaggaagaggaccagaggaaagca -gccactggaaataaggaaacagggtttaggaaggcctcactagacctgttaggatggatg -catggatggatggatggatggacagaatgggtgggtggatggatggatggatggatggat -ggatggatagatgggtgggtggatggatggatggatagatgggtggatggatagatgggt -ggatggataaatggatggatggatggatggatagatgggtgggtggatggatggatggat -ggatggatggatggatggatggatagatggatagatgggtgggtggatggatggatggat -ggatggatggatggatggatggatagatgggtgggtggatggatggatggatagatggat -agatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagat -ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat -agatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggat -ggatagatgggtggatggataaatggatggatggatggatggatagatgtgtgggtggat -ggatggatggatggatggatggatggatggatggatagatggatagatgggtgggtggat -ggatggatggatggatggatggatggatggatggatagatgggtggatggatggatagat -gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat -agatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggat -ggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat -ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat -ggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat -ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat -ggatggatggatggatggatggatggatagatgggtgggtggatggatggatggatagat -gggtgggtggatggatggatggatggatggatggatggatggatggatagatggatagat -gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatggat -agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat -ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat -agatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagat -gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat -agatgggtgggtggatggatggatggatggatggatagatggatagatgggtgggtggat -ggatggatggatagatgggtgggtggatggatggatggatggatggatggatggatggat -ggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat -ggatggatagatggatagatgggtgggtggatggatggatggatagatggatagatgggt -gggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggt -ggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggt -gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat -gggtgggtggatggatggatggatagatgggtgggtgggtggatggatggatggatggat -ggatagaataaaaagaaagctaggacatggttctagtgttcttagcagacgtcccaccat -ggaagaggtcatggggcacaggggctttgggaaaggtgtttacaatcctgcctccctctc -acccagacctcttgccagggttggcacacccagatgcctgctgtgaccaatggagaggag -caattctggccagactggtgggaaagcaaggacgaaccacggaggccatccct ->ref_chr20:20337000-20337907 -tcatggcaaagaattgaaccctaggtcttctccttccttgcaaccgttaatgtcagaagc -tctgaagacacctgggacagagaagagagggagaaaagtttacgtggaagcatagggaag -gaagggatgtttgttgaggggtggtgtgatgcagcagaggaagaggaccagaggaaagca -gccactggaaataaggaaacagggtttaggaaggcctcactagacctgttaggatggatg -catggatggatggatggatggacagaatgggtgggtggatggatggatggatagatggat -ggatggatggatggatggatggatggatggatggatggatagatgggtgggtgg----gt -ggatgg----atggatggatggatggatggatggatggatggatggatagatgggtgggt -ggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggt -gggtggatggatggatggatagatgggtggatggataaatggatggatggatggatggat -agatgggtgggtggatggatggatggatggatggatggatggatggatagat-------- -----------gtgggtggatggatggatggatagatgggtgggtgggtggatggatggat -ggatggatagatgggtgggtgggtggatggatggatggatggatagaataa--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------aaaagaaagctaggacatggttctagtgttcttagcagacgtcccaccat -ggaagaggtcatggagcacaggggctttgggaaaggtgtttacaatcctgcctgcctctc -acccagacctcttgccagggttggcacacccagatgcctgctgtgaccaatggagaggag -caattctggccagactggtgggaaagcaaggacgaaccacggaggccatccct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_930581c6929e0f46a955420b776d2ba5.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_930581c6929e0f46a955420b776d2ba5.msa deleted file mode 100644 index 6f8ea9b3..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_930581c6929e0f46a955420b776d2ba5.msa +++ /dev/null @@ -1,90 +0,0 @@ ->syndip_1_chr20:24407983-24408997 ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------tacccttcct -ctcagttatgttggagccacaggaggtgatatagggtgcttccggccctggccatagggt -acttctgggaggtgatatagggtatttccagccttggccatagggtacttctgggaggtg -atatagggtatttccagccttggccatagggtacttctgggaggtgatatagggtacttc -cagccttggccatagggtacttctgggaggtgatatagggtacttccagccctggccata -gggtacttctgggaggagatatagggtatttccagccttggccatagggtacttctggga -ggtgatatagggtatttccagccttggccatagggtacttctgggaggtgatatagggta -tttccagccttggccatagggtacttctgggaggtgatatagggtatttccagccctggc -catagggtacttctaggaggtgatatagggtacttccagccctggccatagggtacttct -gggaggtgatataggatacttccagccctgg----------------------------- ------------------ccatagggtacttctgggaggtgatataggatacttccag-cc -tggccatagggtacttctgggaggtgatataggatacttccagccctggccatagggtac -ttctgggaggtgatataggatacttccagccctggccatagggtacttctgggaggtgat -ataggatacttccagccttggccatctcctctcctttaagatacctacacttgtt ->syndip_2_chr20:24407983-24408997 -tacccttcctctcagttatgttggagccacaggaggtgatatagggtgcttccagccctg -gccatagggtacttctgggaggtgatatagggtatttccagccttggccatagggtactt -ctgggaggtgatatagggtatttccagccttggccatagggtacttctgggaggtgatat -agggtacttccagccttggccatagggtacttctgggaggtgatatagggtacttccagc -cctggccatagggtacttctgggaggagatatagggtatttccagccttggccatagggt -acttctgggaggtgatatagggtatttccagccttggccatagggtacttctgggaggtg -atatagggtatttccagccttggccatagggtacttctgggaggtgatatagggtacttc -cagccttggccatagggtacttctgggaggtgatatagggtacttccagccctggccata -gggtacttctgggaggagatatagggtatttccagccttggccatagggtacttctggga -ggtgatatagggtatttccagccttggccatagggtacttctgggaggtgatatagggta -tttccagccttggccatagggtacttctgggaggtgatatagggtatttccagccttggc -catagggtacttctaggaggtgatatagggtacttccagccctggccatagggtacttct -gggaggtgatataggatacttccagccctgg----------------------------- -------------------catagggtacttctgggaggtgatataggatacttccagccc -tggccatagggtacttctgggaggtgatataggatacttccagccctggccatagggtac -ttctgggaggtgatataggatacttccagccctggccatagggtacttctgggaggtgat -ataggatacttccagccttggccatctcctctcctttaagatacctacacttgtt ->p:HG002_1_chr20:24407983-24408997 -tacccttcctctcagttatgttggagccacaggaggtgatatagggtgcttccagccctg -gccatagggtacttctgggaggtgatatagggtatttccagccttggccatagggtactt -ctgggaggtgatatagggtatttccagccttggccatagggtacttctgggaggtgatat -agggtacttccagccttggccatagggtacttctgggaggtgatatagggtacttccagc -cctggccatagggtacttctgggaggagatatagggtatttccagccttggccatagggt -acttctgggaggtgatatagggtatttccagccttggccatagggtacttctgggaggtg -atatagggtatttccagccttggccatagggtacttctgggaggtgatatagggtacttc -cagccttggccatagggtacttctgggaggtgatatagggtacttccagccctggccata -gggtacttctgggaggagatatagggtatttccagccttggccatagggtacttctggga -ggtgatatagggtatttccagccttggccatagggtacttctgggaggtgatatagggta -tttccagccttggccatagggtacttctgggaggtgatatagggtatttccagccttggc -catagggtacttctaggaggtgatatagggtacttccagccctggccatagggtacttct -gggaggtgatataggatacttccagccctgg----------------------------- -------------------catagggtacttctgggaggtgatataggatacttccagccc -tggccatagggtacttctgggaggtgatataggatacttccagccctggccatagggtac -ttctgggaggtgatataggatacttccagccctggccatagggtacttctgggaggtgat -ataggatacttccagccttggccatctcctctcctttaagatacctacacttgtt ->p:HG002_2_chr20:24407983-24408997 ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------tacccttcct -ctcagttatgttggagccacaggaggtgatatagggtgcttccggccctggccatagggt -acttctgggaggtgatatagggtatttccagccttggccatagggtacttctgggaggtg -atatagggtatttccagccttggccatagggtacttctgggaggtgatatagggtacttc -cagccttggccatagggtacttctgggaggtgatatagggtacttccagccctggccata -gggtacttctgggaggagatatagggtatttccagccttggccatagggtacttctggga -ggtgatatagggtatttccagccttggccatagggtacttctgggaggtgatatagggta -tttccagccttggccatagggtacttctgggaggtgatatagggtatttccagccctggc -catagggtacttctaggaggtgatatagggtacttccagccctggccatagggtacttct -gggaggtgatataggatacttccagccctgg----------------------------- ------------------ccatagggtacttctgggaggtgatataggatacttccag-cc -tggccatagggtacttctgggaggtgatataggatacttccagccctggccatagggtac -ttctgggaggtgatataggatacttccagccctggccatagggtacttctgggaggtgat -ataggatacttccagccttggccatctcctctcctttaagatacctacacttgtt ->ref_chr20:24407983-24408997 -tacccttcctctcagttatgttggagccacaggaggtgatatagggtgcttccagccctg -gccatagggtacttctgggaggtgatatagggtatttccagccttggccatagggtactt -ctgggaggtgatatagggtacttccagccttggccatagggtacttctgggaggtgatat -agggtacttccagccttggccatagggtacttctgggaggtgatatagggtacttccagc -cctggccatagggtacttctgggaggagatatagggtatttccagccttggccatagggt -acttctgggaggtgatataggttatttccagccttggccatagggtacttctgggaggtg -atatagggtatttccagccttggccatagggtacttctgggaggtgatatagggtacttc -cagccctggccatagggtacttctgggaggtgatatagggtacttccagccctggccata -gggtacttctgggaggagatatagggtatttccagccttggccatagggtacttctggga -ggtgatatagggtatttccagccttggccatagggtacttctgggaggtgatatagggta -tttccagccttggccatagggtacttctgggaggtgatatagggtatttccagccttggc -catagggtacttctaggaggtgatatagggtacttccagccctggccatagggtacttct -gggaggtgatataggatacttccagccctggccatagggtacttctgggaggtgatatag -gatacttccagccctggccatagggtacttctgggaggtgatataggatacttccagccc -tggccatagggtacttctgggaggtgatataggatacttccagccctggccatagggtac -ttctgggaggtgatataggatacttccagccctggccatagggtacttctgggaggtgat -ataggatacttccagccttggccatctcctctcctttaagatacctacacttgtt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9365afe46e460f9ddc259fd58d9b4717.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_9365afe46e460f9ddc259fd58d9b4717.msa deleted file mode 100644 index d3ec0252..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9365afe46e460f9ddc259fd58d9b4717.msa +++ /dev/null @@ -1,35 +0,0 @@ ->syndip_1_chr20:21120212-21120539 -cagggttcttcagagaaacagaaccagtaggacacacacacacgcacacacacacacgtg -tgtgtatatatatgtgtgtatgtatatatatatatatatatttatatatatatatatatt -----tatatatatatatatttatatatatatatatatatatggagagagagagatttatt -tttaggaagtggttcatg------------------------------------------ ------------------------------------------------------------- -------------------------agattg ->syndip_2_chr20:21120212-21120539 -cagggttcttcagagaaacagaaccagtaggacacacacacacgcacacacacacacgtg -tgtgtatatatatgtgtgtatgtatatatatatatatatatttatatatatatatatatt -tatatatatatatatatatttatatatatatatatatatatggagagagagagatttatt -tttaggaagtggttcatg------------------------------------------ ------------------------------------------------------------- -------------------------agattg ->p:HG002_1_chr20:21120212-21120539 -cagggttcttcagagaaacagaaccagtaggacacacacacacgcacacacacacacgtg -tgtgtatatatatgtgtgtatgtatatatatatatatatatttatatatatatatatatt -tatatatatatatatatatttatatatatatatatatatatggagagagagagatttatt -tttaggaagtggttcatg------------------------------------------ ------------------------------------------------------------- -------------------------agattg ->p:HG002_2_chr20:21120212-21120539 -cagggttcttcagagaaacagaaccagtaggacacacacacacgcacacacacacacgtg -tgtgtatatatatgtgtgtatgtatatatatatatatatatttatatatatatatatatt -----tatatatatatatatttatatatatatatatatatatggagagagagagatttatt -tttaggaagtggttcatg------------------------------------------ ------------------------------------------------------------- -------------------------agattg ->ref_chr20:21120212-21120539 -cagggttcttcagagaaacagaaccagtaggacacacacacacgcacacacacacacgtg -tgtgtatatatatgtgtgtatg--tatatatatatatatatttatatatatatatattta -tatatatatatttatatatatatatttatatatatatatatttatatatatatatttata -tatatatatttatatatatatatatttatatatatatatatttatatatatatatttata -tatatatatatttatatatatatatttatatatatatatatttatatggagagagagaga -tttatttttaggaagtggttcatgagattg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_947f9c58eae63ff94c10ca8dcf36e629.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_947f9c58eae63ff94c10ca8dcf36e629.msa deleted file mode 100644 index 95b41e03..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_947f9c58eae63ff94c10ca8dcf36e629.msa +++ /dev/null @@ -1,190 +0,0 @@ ->syndip_1_chr20:63491747-63492600 -gagatggatggatggattggtggatggatggatggatggatggatgaggaggtagatgag -tggatggacagaaggatggatgggtaggaaggtgggtggatgaatggatggatggggagg -tggatggatagatggatggatggatggatggatggatggatggatggggggatagatgga -tggatggatggatggacggacggatggggagg--------tggatggatggatggatgga -tggatggatggatggatgaggagatgaacggatggatgagatggatggatggatgatgga -gggaaggatggctgggtggggagatggatggatagagaggtggatgggtggatggggaga -tggatggatggatggatggatggggaagtggatggatggggaggtggatggatggatagg -tggatgggtggatggacagaaggatgaatgggtagggagatggatggatggatggatgg- ----------ggagggatggatggatggatggatggatgggtggatggatagaaggatgga -tgggtggggaggtgggtgggtgg----gtggatggatggagagatggatagatggata-- ---gatggatggatggatggatggatggagagaaggatggatgggtggggaggtgggtggg -tgggtggatgggtggatggatggatgggtggggaggtggg----cgggtggatggatgga -tggatgcagaggtgggtggatggatggatggagagaaggatggatgggtggggaggtggg -tgggtggatggatggatgagtggggaggtgggtgggtgggtggatggatggatggatgga -tgcatggatggatgga-------------------------------------------- ------------------------------------------------------------- ------------tggagaggtgggtggacggatggatggattgggaggtgggtagatgggt -ggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatggatggatgggg -aggtggatggatggatggttagatggggaggtgggtggatgggtggatggacagaaggat -ggatgggtagggaggtaggtgagtggatggatggatggggagatggatggatggatagag -agaaggatggatgggtgggacaatggatggatggatggatagaaggatggacgggtgggg -agatggatggatggatggatggatggatggatggatggacagaaggatgtatgggtgggt -aggtgggtggatagatggatggatggatggatggataaatggatggatggaaggatggat -ggataggtaggtgggtggatggatggatggatggatgtacagaaggatggatgggtgggt -aggtgggtgagtggatgaatggatggatggatagatagaaggatggatgggtgggtcaat -agatggatggatagagagaaggatggatgggtggggagatggatggatggatggatggat -ggatggatggatggatggatagagagaaggatggatggttgagaca----atggatggat -ggatggatggagagatggatggatggacggatggacagaaggatggatgggtggggaggt -ggatggatggattgaaggatggatgggtgggga----catggatggatggatggatggat -ggatggatggatggacagaaggatgta--------tgggtggggaggtgggtggatagat -ggatggatggggaaatggatggatggaaggatggatggatagggaggtgggtggatggat -ggatggatggatgtacagaaggatggatgggtggggaggtgggtgagtggatgaatggat -ggatggatagatagaaggatggatgggtgggacaatagatggatggatagagagaaggat -ggatgggtggggagatagatggatggatggatggatggatggatagagagaaggatggat -ggttgagacaatggatggatggatggatggatggagagatggatggatggatggatggac -agaaggatggatgggtggggaggtggatggatggatggaaggatggatggatggatagag -agaaggatggatgggtgggacaatggatggatggatgcatggatg ->syndip_2_chr20:63491747-63492600 -gagatggatggatggattggtggatggatggatggatggatggatgaggaggtagatgag -tggatggacagaaggatggatgggtaggaaggtgggtggatgaatggatggatggggagg -tggatggatagatggatggatggatggatggatggatggatggatggggggatagatgga -tggatggatggatggacggacggatggggaggtggatggatggatggatggatggatgga -tggatggatggatggatgaggagatgaacggatggatgagatggatggatggatgatgga -gggaaggatggctgggtggggagatggatggatagagaggtggatgggtggatggggaga -tggatggatggatggatggatggggaagtggatggatggggaggtggatggatggatagg -tggatgggtggatggacagaaggatgaatgggtagggagatggatggatggatggatgc- ----------ggagggatggatggatggatggatggatgggtggatggatagaaggatgga -tgggtggggaggtgggtgggtgggtgcgtggatggatggagagatggatagatggataga -tggatggatggatggatggatggatggagagaaggatggatgggtggggaggtgggtggg -tgggtggatgggtggatggatggatgggtggggaggtggg----cgggtggatggatgga -tggatgcagaggtgggtggatggatggatggagagaaggatggatgggtggggaggtggg -tgggtggatggatggatgagtggggaggtgggtgggtggatggatggatggatggatgca -tggatggatggatggagaggtgggtggatgggtggatggacagaaggatggatgggtggg -gaggtgggtgagtgggtggatggatgaatggggaggtggatggatggatggatggatgaa -ggatggatgggtggggaggtgggtggacggatggatggattgggaggtgggtagatgggt -ggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatggatggatgggg -aggtggatggatggatggttagatggggaggtgggtggatgggtggatggacagaaggat -ggatgggtagggaggtaggtgagtggatggatggatggggagatggatggatggatagag -agaaggatggatgggtgggacaatggatggatggatggatagaaggatggacgggtgggg -a----gatggatggatggatggatggatggatggatggacagaaggatgtatgggtgggg -aggtgggtggatagatggatggatggatggatggggaaatggatggatggaaggatggat -ggatagggaggtgggtggatggatggatggatggatgtacagaaggatggatgggtgggg -aggtgggtgagtggatgaatggatggatggatagatagaaggatggatgggtgggacaat -agatggatggatagagagaaggatggatgggtgggga--------gatggatggatggat -ggatggatggatggatggatagagagaaggatggatggttgagacaatggatggatggat -ggatggatggagagatggatggatggatggatggacagaaggatggatgggtggggaggt -ggatggatggattgaaggatggacgggtggggagatggatggatggatggatggatggat -ggatggatggatggacagaaggatgtatgggtgggtaggtgggtggatagatggatggat -ggatggatggataaatggatggatggaaggatggatggataggtaggtgggtggatggat -ggatggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggatgaatggat -ggatggatagatagaaggatggatgggtgggtcaatagatggatggatagagagaaggat -ggatgggtggg----tagatggatggatggatggatggatggatagagagaaggatggat -ggttgagacaatggatggatggatggatggatggagagatggatggatggatggatggac -agaaggatggatgggtggggaggtggatggatggatggaaggatggatggatggatagag -agaaggatggatgggtgggacaatggatggatggatgcatggatg ->p:HG002_1_chr20:63491747-63492600 -gagatggatggatggattggtggatggatggatggatggatggatgaggaggtagatgag -tggatggacagaaggatggatgggtaggaaggtgggtggatgaatggatggatggggagg -tggatggatagatggatggatggatggatggatggatggatggatggggggatagatgga -tggatggatggatggacggacggatggggaggtggatggatggatggatggatggatgga -tggatggatggatggatgaggagatgaacggatggatgagatggatggatggatgatgga -gggaaggatggctgggtggggagatggatggatagagaggtggatgggtggatggggaga -tggatggatggatggatggatggggaagtggatggatggggaggtggatggatggatagg -tggatgggtggatggacagaaggatgaatgggtagggagatggatggatggatggatgc- ----------ggagggatggatggatggatggatggatgggtggatggatagaaggatgga -tgggtggggaggtgggtgggtgggtgcgtggatggatggagagatggatagatggataga -tggatggatggatggatggatggatggagagaaggatggatgggtggggaggtgggtggg -tgggtggatgggtggatggatggatgggtggggaggtggg----cgggtggatggatgga -tggatgcagaggtgggtggatggatggatggagagaaggatggatgggtggggaggtggg -tgggtggatggatggatgagtggggaggtgggtgggtggatggatggatggatggatgca -tggatggatggatggagaggtgggtggatgggtggatggacagaaggatggatgggtggg -gaggtgggtgagtgggtggatggatgaatggggaggtggatggatggatggatggatgaa -ggatggatgggtggggaggtgggtggacggatggatggattgggaggtgggtagatgggt -ggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatggatggatgggg -aggtggatggatggatggttagatggggaggtgggtggatgggtggatggacagaaggat -ggatgggtagggaggtaggtgagtggatggatggatggggagatggatggatggatagag -agaaggatggatgggtgggacaatggatggatggatggatagaaggatggacgggtgggg -a----gatggatggatggatggatggatggatggatggacagaaggatgtatgggtgggg -aggtgggtggatagatggatggatggatggatggggaaatggatggatggaaggatggat -ggatagggaggtgggtggatggatggatggatggatgtacagaaggatggatgggtgggg -aggtgggtgagtggatgaatggatggatggatagatagaaggatggatgggtgggacaat -agatggatggatagagagaaggatggatgggtgggga--------gatggatggatggat -ggatggatggatggatggatagagagaaggatggatggttgagacaatggatggatggat -ggatggatggagagatggatggatggatggatggacagaaggatggatgggtggggaggt -ggatggatggattgaaggatggacgggtggggagatggatggatggatggatggatggat -ggatggatggatggacagaaggatgtatgggtgggtaggtgggtggatagatggatggat -ggatggatggataaatggatggatggaaggatggatggataggtaggtgggtggatggat -ggatggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggatgaatggat -ggatggatagatagaaggatggatgggtgggtcaatagatggatggatagagagaaggat -ggatgggtggg----tagatggatggatggatggatggatggatagagagaaggatggat -ggttgagacaatggatggatggatggatggatggagagatggatggatggatggatggac -agaaggatggatgggtggggaggtggatggatggatggaaggatggatggatggatagag -agaaggatggatgggtgggacaatggatggatggatgcatggatg ->p:HG002_2_chr20:63491747-63492600 -gagatggatggatggattggtggatggatggatggatggatggatgaggaggtagatgag -tggatggacagaaggatggatgggtaggaaggtgggtggatgaatggatggatggggagg -tggatggatagatggatggatggatggatggatggatggatggatggggggatagatgga -tggatggatggatggacggacggatggggaggtggatggatggatggatggatggatgga -tggatggatggatggatgaggagatgaacggatggatgagatggatggatggatgatgga -gggaaggatggctgggtggggagatggatggatagagaggtggatgggtggatggggaga -tggatggatggatggatggatggggaagtggatggatggggaggtggatggatggatgta -tgggtgggtggatggacagaaggatgaatgggtagggagatggatggatggatggatgg- ----------ggagggatggatggatggatggatggatgggtggatggatagaaggatgga -tgggtggggaggtgggtgggtgg----gtggatggatggagagatggatagatggata-- ---gatggatggatggatggatggatggagagaaggatggatgggtggggaggtgggtggg -tgggtggatgggtggatggatggatgggtggggaggtggg----cgggtggatggatgga -tggatgcagaggtgggtggatggatggatggagagaaggatggatgggtggggaggtggg -tgggtggatggatggatgagtggggaggtgggtgggtgggtggatggatggatggatgga -tgcatggatggatgga-------------------------------------------- ------------------------------------------------------------- ------------tggagaggtgggtggacggatggatggattgggaggtgggtagatgggt -ggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatggatggatgggg -aggtggatggatggatggttagatggggaggtgggtggatgggtggatggacagaaggat -ggatgggtagggaggtaggtgagtggatggatggatggggagatggatggatggatagag -agaaggatggatgggtgggacaatggatggatggatggatagaaggatggacgggtgggg -agatggatggatggatggatggatggatggatggatggacagaaggatgtatgggtgggg -aggtgggtggatagatggatggatggatggatggggaaatggatggatggaaggatggat -ggatagggaggtgggtggatggatggatggatggatgtacagaaggatggatgggtgggg -aggtgggtgagtggatgaatggatggatggatagatagaaggatggatgggtgggacaat -agatggatggatagagagaaggatggatgggtggggagatggatggatggatggatggat -ggatggatggatggatggatagagagaaggatggatggttgagaca----atggatggat -ggatggatggagagatggatggatggacggatggacagaaggatggatgggtggggaggt -ggatggatggattgaaggatggatgggtgggga----catggatggatggatggatggat -ggatggatggatggacagaaggatgta--------taggtgggtggatagatggatggat -ggatggatggataaatggatggatggaaggatggatggataggtaggtgggtggatggat -ggatggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggatgaatggat -ggatggatagatagaaggatggatgggtgggtcaatagatggatggatagagagaaggat -ggatgggtggg----tagatggatggatggatggatggatggatagagagaaggatggat -ggttgagacaatggatggatggatggatggatggagagatggatggatggatggatggac -agaaggatggatgggtggggaggtggatggatggatggaaggatggatggatggatagag -agaaggatggatgggtgggacaatggatggatggatgcatggatg ->ref_chr20:63491747-63492600 -gagatggatggatggattggtggatggatggatggatggatggatgaggaggtagatgag -tggatggacagaaggatggatgggtaggaaggtgggtggatgaatggatggatggggagg -tggatggatagatggatggatggatggatggatggatggatggatggggggatagatgga -tggatggatggatggacggacggatggggaggtggatggatggatggatggatggatgga -tggatggatggatggatgaggagatgaacggatggatgagatggatggatggatgatgga -gggaaggatggctgggtggggagatggatggatagagaggtggatgggtggatggggaga -tggatggatggatggatggatggggaagtggatggatggggaggtggatggatggatgta -tgggtgggtaggtgggtggatagatggatggatggatggatggataaatggatggatgga -aggatggatggataggtaggtgggtggatggatggatggatggatgtacagaaggatgga -tgggtgggtaggtgggtgagtgg----atgaatggatggatggatagatagaaggatgga -tgggtgggtcaatagatggatggatagagagaaggatggatgggtgggtagatggatgga -tggatggatggatggatagagagaaggatggatggttgagacaatggatggatggatgga -tggatggagagatggatggatggatggatggacagaaggatggatgggtggggaggtgga -tggatggatggaaggatggatggatggatagagagaaggatggatgggtgggacaatgga -tggatggatgcatgga-------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------tg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_948efca46451b3b357a7493997fce3f2.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_948efca46451b3b357a7493997fce3f2.msa deleted file mode 100644 index cba725f7..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_948efca46451b3b357a7493997fce3f2.msa +++ /dev/null @@ -1,655 +0,0 @@ ->syndip_1_chr20:63693239-63693942 -gcattccccgaaggcagcgggcacagccggtcctggaccccactggtaaatggggcccca -ggtgggaccctcagactcctgcgtggaaggcagtgtgggccagagtcctgggctgcttgg -ggtgggcatcctcgggccctgcttggccccgcctctctgttcccctatgggagtgatggg -ggcctccacctccaccaccagcaccagcagcaccacctccaccttcaccaccaccacctc -caccaccacctccaccacctccacctccaccacctccaccacctccaccaccaccacctc -caccaccaccacctccaccaccaccaccaccaccacctccaccaccaccaccaccaccac -cacctccacctccaccacctccaccaccacctccacctccaccaccacctccacctccac -ctccaccaccaccacctccaccacctccaccacctccacctccaccaccacctccacctc -caccaccacctccacctccacctccacctccacctccaccaccaccacctccaccacctc -caccacctccacctccaccaccaccacctccacctccacctccaccacctccacctccac -cacctccacctccaccacctccaccaccaccaccaccaccaccaccacctccaccaccac -caccaccaccacctccaccacctccacctccaccacctccaccaccaccacctccaccac -cacctccaccaccacctccacctccaccacctccacctccaccacctccacctccacctc -caccaccacctccaccacctccaccaccacctccaccacctccacctccaccaccaccac -ctccaccaccaccaccaccaccacctccaccacctccacctccaccacctccaccaccac -cacctccaccaccacctccaccaccacctccacctccaccacctccacctccaccacctc -cacctccacctccaccaccacctccaccacctccaccaccacctccaccacctccaccac -ctccaccaccacctccaccacctccacctccaccaccaccacctccacctccaccaccac -cacctccaccaccacctccacctccaccaccaccacctccacctccaccaccaccacctc -caccaccacctccaccaccaccaccaccaccaccacctccacctccaccacctccaccac -caccaccaccacct---ccacctccaccacctccaccacctccaccaccaccaccaccac -ctccaccacctccaccaccacctccaccacctccacctccaccaccaccacctccaccac -caccacctccacctccacctccacctccacctccaccaccacctccacctccaccaccac -ctccaccaccacctccacctccaccacctccacctccacctccaccacctccaccaccac -caccaccaccaccaccaccaccaccacctccaccacctccacctccacctccaccaccac 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-ca---------------------------------------------------------- ------------------------------------------------------------- ---------------------------------ccaccaccacctccaccacctccaccac -cacctccaccacctccacctccacctccacct---------------------------- ------------------------------------------------ccacctccaccac -cacctccaccacctccaccaccacctccacctccaccacctccacctccacctccaccac -ctccaccaccaccacctccaccaccacctccaccaccaccacctccacctccaccaccac -ctccaccacctccaccacctccaccaccacctccaccacct------------------- ------------------------ccaccacctccaccaccaccaccaccacctccaccac -ctccaccaccacctccaccaccaccacctccacctccacctccaccacctccaccacctc -caccaccacctccaccacctccaccacctccaccacca---------------cctccac -cacctccaccacctccacctccaccaccaccacctccaccacctccaccaccacctccac -cacctccacctccacctccacctccacctccaccaccacctccacca------cctccac -caccacctccacctccaccacctccacctccacctccaccacctccacct---------- ---------ccacctccacctccaccaccaccacctccacctccacctccacctccaccac -gtccaccacctccaccacctccacct---------------------------ccacctc -cacctccacctccaccacct---ccacctccacctccaccacctccacctccacctccac -ctccaccacgtccaccaccaccacctccaccaccaccaccaccacctcca---------- ---------ccaccacctccacctccaccaccacctccaccaccacctccaccaccaccac -ctccacctccaccaccaccacctccacctccaccaccaccaccaccaccacctccaccac -cacctccacctccaccaccacctccacctccaccacctccaccaccagcaccaccaccac -ctccaccaccaccacctccacctccaccaccaccaccaccaccacctccacca------- ---------ccacctccacctcc-------------------------------------- ------------------------------------------------------------- --------------------------------------------------acctccacctc -caccaccacctccaccaccacctccaccacctccaccaccacctccacctccaccacctc -cacct------------------------------------------ccacctccaccac -ctccacctccacctccaccacctccacctccacctccacctccaccaccaccacctccac -ctccacctccacct---------------------------------ccaccacgtccac -cacctccaccacctccacctccacctccacctccacctccaccacctccacctccacctc -caccacctccacctccacctccacctccaccacgtccaccaccaccacctccaccaccac -caccaccacctccaccaccacctccacctccaccaccacctccaccaccacctccaccac -caccacctccacctccaccaccaccacctccacctccaccaccaccacca---------- ------ccaccacctccaccaccacctccacctccaccaccacctccacctccaccacctc -caccaccaccaccacctccacctccaccaccacca------------cctccacctccac -ctccacctccaccaccacctccaccaccacctccaccaccaccacctccacctccaccac -caccaccaccaccacctccaccaccacctccacctccaccaccacctcca---------- ------------------------------------------------------------- ------------------------------------ccaccacctccaccacctccaccac -caccaccacctccacctccaccaccaccacctccacctccaccaccaccacca------- ------------------------------------------ccaccacctccaccaccac -ctccacctccaccaccacctccaccacctccacctccacctccacctccacctccaccac -ctccacctccacctccaccaccaccaccacctccaccacctccaccaccacctccaccac -ctccacctccacctccacctcc---------------accaccacctccaccacctccac -caccacctccacca------------------------------------------cctc -caccacctccacctccaccaccacctccacctccacctccaccacctccaccaccacca- ------------ccaccaccacctccacca------------------------ccacctc -caccaccacctccacctccacctccaccacctccaccaccacctcca------------- ------ccaccaccaccacctccacctccaccacctccacctccacctccaccaccacctc -caccacctccaccaccaccaccaccacctccaccacctccacct---------------- ---------------------------------------------------------ccac -ctccacctccacctccaccacctccacctccacctcca---------------------- ---------------------------------------------------------ccac -caccaccacctccaccacctccaccaccacctccac------------------------ ------------------------------------------------------------- -------------cacctccacctccacctccacctccaccaccacctccaccacctccac -caccacctccaccacctccaccaccacctccacctccaccaccaccacctccacctccac -caccacctcca---------------ccaccaccacctccacctccaccaccacctccac -caccaccaccaccaccaccaccaccaccaccaccacctccaccaccaccacctgcaccac -cacctccacctccaccaccaccaccacctccacctccaccagcagcagcatcacttgttg -gggagaccctgtgcaactccatgcacagccctgtccctgccatagccccgacccctaagc -acagccctgtccaactgccacacgtcccctgcctcccatgcatggtcctggggggtcaac -tgcacacgccagggtcctagggtcctagacccctg ->p:HG002_2_chr20:63693239-63693942 -gcattccccgaaggcagcgggcacagccggtcctggaccccactggtaaatggggcccca -ggtgggaccctcagactcctgcgtggaaggcagtgtgggccagagtcctgggctgcttgg -ggtgggcatcctcgggccctgcttggccccgcctctctgttcccctatgggagtgatggg -ggcctccacctccaccaccagcaccagcagcaccacctccacctccacctccacctccac -ctccaccaccacctccacctccaccaccacctcctccaccaccaccacctccaccaccac -caccaccaccaccacctccacctccaccacctccacctccaccaccaccacctccacctc -caccaccaccacctccacctccaccaccacctccacctccaccaccacctccacctccac -ctccaccaccaccacctccaccacctccaccacctccacctccaccaccacctccacctc -caccaccacctccacctccacctccacctccacctccaccaccaccacctccaccacctc -caccacctccacctccaccaccaccacctccacctccacctccaccacctccacctccac -cacctccacctccaccacctccaccaccaccaccaccaccaccaccacctccaccaccac -caccaccaccacctccaccacctccacctccaccacctccaccaccaccacctccaccac -cacctccaccaccacctccacctccaccacctccacctccaccacctccacctccacctc -caccaccacctccaccacctccaccaccacctccaccacctccacctccaccaccaccac -ctccaccaccaccaccaccaccacctccaccacctccacctccaccacctccaccaccac -cacctccaccaccacctccaccaccacctccacctccaccacctccacctccaccacctc -cacctccacctccaccaccacctccaccacctccaccaccacctccaccacctccaccac -ctccaccaccacctccaccacctccacctccaccaccaccacctccacctccaccaccac -cacctccaccaccacctccacctccaccaccaccacctccacctccaccaccaccacctc -caccaccacctccaccaccaccaccaccaccaccacctccacctccaccacctccaccac -caccaccaccacct---ccacctccaccacctccaccacctccaccaccaccaccaccac -ctccaccacctccaccaccacctccaccacctccacctccaccaccaccacctccaccac -caccacctccacctccacctccacctccacctccaccaccacctccacctccaccaccac -ctccaccaccacctccacctccaccacctccacctccacctccaccacctccaccaccac -caccaccaccaccaccaccaccaccacctccaccacctccacctccacctccaccaccac -caccaccacctccaccaccaccaccaccacctccaccacctccaccaccacctccaccac -caccaccaccaccaccaccaccacctccaccacctccacctccacctccacctccaccac -ctccaccacctccaccaccacctccaccaccaccaccaccacctccaccaccacctccac -ctccaccaccacctccaccaccacctccacctccaccacctccacctccaccacctccac -cacctccacctccaccacctccacctccacctccaccacctccaccaccaccaccaccac -caccaccaccaccaccacctccaccaccaccacctccaccaccacctccaccacctccac -caccacctccaccaccaccaccaccaccaccaccaccaccaccacctccaccaccacctc -cacctccaccaccacctccaccaccacctccacctccaccacctccacctccaccacctc -caccacctccaccaccaccaccaccacctccaccaccacctccacctccaccaccaccac -caccaccaccacctccaccaccaccacctccaccaccacctccaccacctccaccaccac -ctccacctccaccacctccaccaccacctccaccaccacctccaccaccaccacctccac -caccacctccaccacctccaccaccacctccacctccaccacctccaccaccacctccac -caccacctccaccaccaccacctccaccaccacctccaccacctccaccaccacctccac -ctccaccacctccacctccacctccaccacctccaccaccaccaccaccaccaccaccac -caccaccaccaccaccaccaccacctccacctccacctccaccacctccacctccaccac -ctccaccaccacctccacctccaccacctccacctccacctccaccacctccacctccac -cacctccacctccacctccaccacctccaccaccaccacctccaccaccacctccaccac -ctccaccaccacctccacctccaccacctccaccaccacctccaccaccacctccaccac -caccacctccaccaccacctccaccacctccaccaccacctccacctccaccacctccac -ctccacctccaccacctccaccaccaccaccaccaccaccaccaccaccaccacctccac -caccaccacctccaccaccacctccaccaccaccaccaccacctccaccaccaccaccac -cacctccaccaccacctccaccacctccaccaccaccaccaccaccaccaccacctccac -caccacctccaccaccaccaccaccaccaccaccacctccaccacctccacctccaccac -caccaccacctccaccaccaccaccaccaccacctccacctccaccaccaccacctccac -caccaccaccacctccaccaccacctccaccaccaccaccaccaccaccaccaccacctc -caccacctccaccacctccaccaccacctccaccacctccaccaccaccaccaccacctc -caccaccacctccaccaccaccaccaccaccaccacctccacctccacctccaccacctc -cacctccaccacctccacctccaccacctccacctccacctccaccacctccaccaccac -ctccacctccaccaccacctcctccaccaccaccacctccaccaccacctccaccaccac -cacctccacctccaccacctccacctccaccaccaccacctccacctccaccaccaccac -ctccaccacctccaccaccacctccaccacctccacctccaccaccaccacctccaccac -caccacctccacctccaccaccaccaccaccaccacctccacctccaccaccacctccac -caccacctccacctccacctccaccacctccaccaccacctccaccacctccaccacctc -cacctccaccaccaccaccacctccaccaccaccaccaccacctctaccacctctaccac -caccaccaccacctccaccaccaccaccaccacctccaccaccaccaccaccaccacctc -caccaccacctccaccacctccaccaccaccaccaccacctctaccacctccacctccac -caccaccaccacctctaccaccaccaccaccacctccaccaccaccaccacctccaccac -caccaccacctccaccaccacctccaccaccacctccaccacctccaccaccaccaccac -ctccacctccaccacctccaccaccacctccaccaccaccaccaccaccacctccaccac -cacctccaccacctccaccaccaccaccaccacctctaccacctccacctccaccaccac -caccacctccacctccaccaccaccaccaccaccaccaccaccaccacctccaccaccac -caccaccaccacctctaccaccaccaccaccacctccaccaccaccaccacctccaccac -caccaccacctccaccaccacctccaccaccaccaccaccaccaccaccacctctaccac -caccaccaccacctccaccaccaccaccacctccaccaccaccaccacctccaccaccac -ctccaccaccaccaccacctccaccaccacctccaccaccacctccaccacctccaccac -caccaccaccacctccaccaccacctccacctccaccaccaccaccaccacctccaccac -caccaccaccaccaccacctccaccaccacctccaccaccacctccaccacctccaccac -caccaccaccacctccaccaccacctccacctccaccaccaccaccaccacctccaccac -cacctccaccaccaccaccaccaccacctccaccaccacctccaccacctccaccaccac -caccaccacctctaccacctctaccaccaccaccaccacctccaccaccaccaccacctc -caccaccaccaccacctccaccaccaccacctccacctccaccaccaccacctccaccac -ctccaccaccacctccaccaccaccacctccacctccaccaccaccacctccaccacctc -caccaccaccaccaccaccaccaccacctccaccaccaccaccaccaccacctccaccac -cacctccaccacctccaccaccaccaccaccacctctaccacctctaccaccaccaccac -cacctccaccaccaccaccacctccaccaccaccaccacctccaccaccacctccaccac -caccacctccacctccaccaccaccacctccaccaccaccacctccacctccaccaccac -cacctccaccacctccaccaccacctccaccaccaccacctccacctccaccaccaccac -ctccaccacctccaccaccaccacctccaccaccaccacctccaccacctccaccaccac -caccaccacctccaccacctccaccacctccaccaccaccaccaccacctccacctccac -ctccaccacctccaccaccaccacctccaccaccaccaccaccaccaccaccacctccac -ctccacctccaccacctccacctccaccaccaccaccaccaccaccaccaccaccaccac -ctccacctccacctccaccacctccaccaccaccacctccaccaccaccacctccacctc -ca---ccacctccaccaccacctccaccaccaccacctccacctc---caccaccaccac -ctccaccaccaccacctccacctccaccaccaccacctccaccacctccaccaccacctc -caccaccaccacctccacctccaccaccaccacctccaccacctccaccaccaccacctc -caccaccaccacctccaccacctccaccaccaccaccaccacctccaccacctccaccac -ctccaccaccaccaccaccacctccacctccacctccaccacctccaccaccaccacctc -caccaccaccaccaccaccacctccaccacctccaccaccaccaccaccacctccacctc -cacctccaccacctccaccaccaccacctccaccaccaccaccaccaccaccaccaccac -ctccacctccacctccaccacctccacctccaccaccaccaccaccaccaccacctccac -caccacctccacctccacctccaccacctccacctccaccaccaccaccaccaccaccac -caccaccaccacctccacctccacctccaccaccaccacctctaccaccacctccaccac -caccaccaccaccaccaccaccacctccaccacctccaccaccaccacctccaccaccac -cacctccacctccaccaccaccaccacct---ccaccacctccaccaccacctccacctc -cacctccaccacctccaccaccaccacctccaccaccaccaccaccaccaccacctccac -cacctccaccaccaccacctccaccaccaccacctccacctccaccacctccaccacctc -caccaccaccaccacctccaccaccaccaccaccaccacctccacctccaccacctctac -caccacctccaccaccaccaccaccaccacctccacctccaccacctccacctccaccac -ctctaccaccacctccaccaccaccacctccacctccacctccaccaccaccacctccac -ctccacctccaccaccaccaccaccaccaccacctccaccaccaccaccaccaccaccac -caccacctccacctccaccaccaccacctccaccaccaccacctccaccacctccaccac -cacctccacctccaccaccaccacctccacctccacctccaccaccaccaccaccacctc -caccaccaccacctccaccaccaacacctccacctccacctccaccaccaccaccaccac -ctccacctccaccaccacctccaccaccaccacctccacctccaccaccaccacctccac -caccacctccaccacctccaccaccaccacctccaccaccacctccaccaccaccaccac -caccacctccacctccacctccaccaccaccacctctaccaccacctccaccaccaccac -caccaccaccaccaccacctccacctccacctccaccacctccacctccaccaccaccac -caccaccaccacctccaccaccacctccacctccacctccaccacctccacctccaccac -caccaccaccaccaccaccaccaccaccacctccacctccacctccaccaccaccacctc -taccaccacctccaccaccaccaccaccaccaccaccaccacctccaccaccaccacctc -cacctccaccaccaccacctccacctccaccaccaccacctccacctccaccaccaccac -caccaccaccacctccaccaccaccacctccaccacctccaccaccacctccaccaccac -cacctccaccacctccaccaccacctccacctccaccaccaccacctccaccaccaccac -ctccacctccaccaccaccacctccacctccacctccaccacctccacctccaccacctc -caccaccaccacctccaccacctccaccaccacctccacctccaccaccaccacctccac -caccaccacctccaccacctccaccaccacctccacctccaccaccaccacctccacctc -cacctccaccaccaccaccaccacctccactaccaccacctccacctccaccaccaccac -ctccaccaccaacacctccacctccacctccacctccaccaccaccacctccacctccac -caccaccacctccaccaccaccacctccaccacctccacctccaccaccaccacctccac -caccacctccaccaccaccaccacctccaccaccacctccacctccaccaccacctccac -caccaccaccaccaccaccaccaccaccaccaccacctccaccaccaccacctgcaccac -cacctccacctccaccaccaccaccacctccacctccaccagcagcagcatcacttgttg -gggagaccctgtgcaactccatgcacagccctgtccctgccatagccccgacccctaagc -acagccctgtccaactgccacacgtcccctgcctcccatgcatggtcctggggggtcaac -tgcacacgccagggtcctagggtcctagacccctg ->ref_chr20:63693239-63693942 -gcattccccgaaggcagcgggcacagccggtcctggaccccactggtaaatggggcccca -ggtgggaccctcagactcctgcgtggaaggcagtgtgggccagagtcctgggctgcttgg -ggtgggcatcctcgggccctgcttggccccgcctctctgttcccctatgggagtgatggg -ggcctccacctccaccaccagcaccagcagcaccacctccacctccacctccacctccac -ctccaccaccacctccacctccaccaccacctcctccaccacc----------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----accacctccaccaccaccaccaccaccaccacctccacctccaccacctccacctc -caccaccaccacct---ccacctcca---------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- 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------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------ccaccaccac -ctccacctccaccaccacctccaccaccaccacctccacctccaccacca---------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------cctccac -caccaccaccaccaccaccaccaccaccaccaccacctccaccaccaccacctgcaccac -cacctccacctccaccaccaccaccacctccacctccaccagcagcagcatcacttgttg -gggagaccctgtgcaactccatgcacagccctgtccctgccatagccccgacccctaagc -acagccctgtccaactgccacacgtcccctgcctcccatgcatggtcctggggggtcaac -tgcacacgccagggtcctagggtcctagacccctg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_95a1ef556930ed45e8dd2d3a52eba9b6.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_95a1ef556930ed45e8dd2d3a52eba9b6.msa deleted file mode 100644 index 5ef1b039..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_95a1ef556930ed45e8dd2d3a52eba9b6.msa +++ /dev/null @@ -1,85 +0,0 @@ ->syndip_1_chr20:44763696-44764485 -aacccattggtcttttattattaacctctgagcttggtttggcccctggattttctgtgt -tcttgatggtgaaagaagtaactggctcacgcaggggtttgactccattctcttttccag -atggatcactcgtctcaacagcatcagaaattaaaaggttgcacagcccttgtggtgatt -ataggttatgtgattctcaaaggtttaggagtttacgggttccctgtccatccattcact -acatgctcacctatccatccatccatccatttatccatccatccatccacctatcacttc -atccatccatccatttatccatccatccatttatccatccatccatccatttatccatcc -atccatccatttatccatccatccatccatccatccacccatccatccgtccatccattt -atccatccatccatccatccatttatccatccatttatccatccatccatccatccatcc -atccatccatccatttatcc----atccatccatccatccacccatccatccatccgtcc -atccatttatccatccatccatccatccatccatccatccatccatttatccatccgtcc -atttatccatccatccatccacccacccatccatccatccatccacttatccatccaccc -atccatccatccgtccatccattcatccatccatccatcctcccacaaactcaccaagcc -tacaatacaatcaattctgctgtaacatgaaatatacatttctaaaaattactgtgcaac -gcaaaatcttgctataaaaatcacacagcttatgggaaaatggggtcagtgtcacatcaa -aaacagaaaaaggcaagaatgcagtaaaaatgaaagcatggttttaaatatgttaaatgc -tttagaaatgcacaaatactacaataaaaa ->syndip_2_chr20:44763696-44764485 -aacccattggtcttttattattaacctctgagcttggtttggcccctggattttctgtgt -tcttgatggtgaaagaagtaactggctcacgcaggggtttgactccattctcttttccag -atggatcactcgtctcaacagcatcagaaattaaaaggttgcacagcccttgtggtgatt -ataggttatgtgattctcaaaggtttaggagtttacgggttccctgtccatccattcact -acatgctcacctatccatccatccatccatttatccatccatccatccacctatcacttc -atccatccatccatttatccatccatccatttatccatccatccatccatttatccatcc -atccatccatttatccatccatccatccatccatccacccatccatccgtccatccattt -atccatccatccatccatccatttatccatccatttatccatccatccatccatccatcc -atccatccatccatccatccatttatccatccatccatccatccacccatccatccatcc -gtccatccatttatccatccatccatccatccatccatccatccatttatccatccgtcc -atttatccatccatccatccacccacccatccatccatccatccatttatccatccaccc -atccatccatccgtccatccattcatccatccatccatcctcccacaaactcaccaagcc -tacaatacaatcaattctgctgtaacatgaaatatacatttctaaaaattactgtgcaac -gcaaaatcttgctataaaaatcacacagcttatgggaaaatggggtcagtgtcacatcaa -aaacagaaaaaggcaagaatgcagtaaaaatgaaagcatggttttaaatatgttaaatgc -tttagaaatgcacaaatactacaataaaaa ->p:HG002_1_chr20:44763696-44764485 -aacccattggtcttttattattaacctctgagcttggtttggcccctggattttctgtgt -tcttgatggtgaaagaagtaactggctcacgcaggggtttgactccattctcttttccag -atggatcactcgtctcaacagcatcagaaattaaaaggttgcacagcccttgtggtgatt -ataggttatgtgattctcaaaggtttaggagtttacgggttccctgtccatccattcact -acatgctcacctatccatccatccatccatttatccatccatccatccacctatcacttc -atccatccatccatttatccatccatccatttatccatccatccatccatttatccatcc -atccatccatttatccatccatccatccatccatccacccatccatccgtccatccattt -atccatccatccatccatccatttatccatccatttatccatccatccatccatccatcc -atccatccatccatccatccatttatccatccatccatccatccacccatccatccatcc -gtccatccatttatccatccatccatccatccatccatccatccatttatccatccgtcc -atttatccatccatccatccacccacccatccatccatccatccatttatccatccaccc -atccatccatccgtccatccattcatccatccatccatcctcccacaaactcaccaagcc -tacaatacaatcaattctgctgtaacatgaaatatacatttctaaaaattactgtgcaac -gcaaaatcttgctataaaaatcacacagcttatgggaaaatggggtcagtgtcacatcaa -aaacagaaaaaggcaagaatgcagtaaaaatgaaagcatggttttaaatatgttaaatgc -tttagaaatgcacaaatactacaataaaaa ->p:HG002_2_chr20:44763696-44764485 -aacccattggtcttttattattaacctctgagcttggtttggcccctggattttctgtgt -tcttgatggtgaaagaagtaactggctcacgcaggggtttgactccattctcttttccag -atggatcactcgtctcaacagcatcagaaattaaaaggttgcacagcccttgtggtgatt -ataggttatgtgattctcaaaggtttaggagtttacgggttccctgtccatccattcact -acatgctcacctatccatccatccatccatttatccatccatccatccacctatcacttc -atccatccatccatttatccatccatccatttatccatccatccatccatttatccatcc -atccatccatttatccatccatccatccatccatccacccatccatccgtccatccattt -atccatccatccatccatccatttatccatccatttatccatccatccatccatccatcc -atccatccatccatttatcc----atccatccatccatccacccatccatccatccgtcc -atccatttatccatccatccatccatccatccatccatccatccatttatccatccgtcc -atttatccatccatccatccacccacccatccatccatccatccacttatccatccaccc -atccatccatccgtccatccattcatccatccatccatcctcccacaaactcaccaagcc -tacaatacaatcaattctgctgtaacatgaaatatacatttctaaaaattactgtgcaac -gcaaaatcttgctataaaaatcacacagcttatgggaaaatggggtcagtgtcacatcaa -aaacagaaaaaggcaagaatgcagtaaaaatgaaagcatggttttaaatatgttaaatgc -tttagaaatgcacaaatactacaataaaaa ->ref_chr20:44763696-44764485 -aacccattggtcttttattattaacctctgagcttggtttggcccctggattttctgtgt -tcttgatggtgaaagaagtaactggctcacgcaggggtttgactccattctcttttccag -atggatcactcgtctcaacagcatcagaaattaaaaggttgcacagcccttgtggtgatt -ataggttatgtgattctcaaaggtttaggagtttacgggttccctgtccatccattcact -acatgctcacctatccatccatccatccatttatccatccatccatccacctatcacttc -atccatccatccatttatccatccatccatttatccatccatccatccatttatccatcc -atccatccatttatccatccatccatccatccatccacccatccatccgtccatccattt -atccatccatccatccatccatttatgcatccatttatccatccatccatccatccatcc -atccatccatccatttatcc---------------------------------------- ------------------------------------------------------------- -----------------------------------------atccatccatccatccaccc -atccatccatccgtccatccattcatccatccatccatcctcccacaaactcaccaagcc -tacaatgcaatcaattctgctgtaacatgaaatatacatttctaaaaattactgtgcaac -gcaaaatcttgctataaaaatcacacagcttatgggaaaatggggtcagtgtcacatcaa -aaacagaaaaaggcaagaatgcagtaaaaatgaaagcatggttttaaatatgttaaatgc -tttagaaatgcacaaatactacaataaaaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9acfddf2b253e2193355eee368ee5233.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_9acfddf2b253e2193355eee368ee5233.msa deleted file mode 100644 index 22d107f8..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9acfddf2b253e2193355eee368ee5233.msa +++ /dev/null @@ -1,60 +0,0 @@ ->syndip_1_chr20:35539120-35539724 -ggattacaggcgtgagccacagcgcccggcctatgttttacatatataacaatttatata -taactacatatataatatatataacagtttatatatatatataacagtttatatatatat -tatatataacagtt--tatatatata---------------------------------- -------------------------------------atatatatgtttatatattatata -taacagtttatatataacagtttatatataatatatataagtttatatataacagtttat -atatataatatatataagtttatatataatatatataagtttatatatg----------- ------------------------------------------tttatatataatatatata -acagtttatatatataatatatataacagtttatatatataatatatataacagtttata -tatataatatatataagtttatatatataatatatataacagtttatatatattatatat -atatatatgcacacacacaaagagagagagagagactcgctctgtcgcccaggctgtagt -gcagt ->syndip_2_chr20:35539120-35539724 -ggattacaggcgtgagccacagcgcccggcctatgttttacatatataacaatttatata -taactacatatataatatatataacagtttatatatatatataacagtttatatatataa -tatatataacagtt--tatatatatatataacagtttatatatataat------------ -------------------------------------atatataagtttatatattatata -taacagtttatatataacagtttatatataatatatataagtttatatataacagtttat -atatataatatatataagtttatatataatatatataagtttatatatatgtttatatat -aatatatataacagtt-------------------------tatatatataatatatata -acagtttatatatataatatatataacagtttatatatataatatatataacagtttata -tatataatatatataagtttatatatataatatatataacagtttatatatattatatat -atatatatgcacacacacaaagagagagagagagactcgctctgtcgcccaggctgtagt -gcagt ->p:HG002_1_chr20:35539120-35539724 -ggattacaggcgtgagccacagcgcccggcctatgttttacatatataacaatttatata -taactacatatataatatatataacagtttatatatatatataacagtttatatatataa -tatatataacagtt--tatatatatatataacagtttatatatataat------------ -------------------------------------atatataagtttatatattatata -taacagtttatatataacagtttatatataatatatataagtttatatataacagtttat -atatataatatatataagtttatatataatatatataagtttatatatatgtttatatat -aatatatataacagtt-------------------------tatatatataatatatata -acagtttatatatataatatatataacagtttatatatataatatatataacagtttata -tatataatatatataagtttatatatataatatatataacagtttatatatattatatat -atatatatgcacacacacaaagagagagagagagactcgctctgtcgcccaggctgtagt -gcagt ->p:HG002_2_chr20:35539120-35539724 -ggattacaggcgtgagccacagcgcccggcctatgttttacatatataacaatttatata -taactacatatataatatatataacagtttatatatatatataacagtttatatatatat -tatatataacagtt--tatatatata---------------------------------- -------------------------------------atatatatgtttatatattatata -taacagtttatatataacagtttatatataatatatataagtttatatataacagtttat -atatataatatatataagtttatatataatatatataagtttatatatg----------- ------------------------------------------tttatatataatatatata -acagtttatatatataatatatataacagtttatatatataatatatataacagtttata -tatataatatatataagtttatatatataatatatataacagtttatatatattatatat -atatatatgcacacacacaaagagagagagagagactcgctctgtcgcccaggctgtagt -gcagt ->ref_chr20:35539120-35539724 -ggattacaggcgtgagccacagcgcccggcctatgttttacatatataacaatttatata -taactacatatataatatatataacagtttatatatatatataacagtttatatatataa -tatatataacagtttatatatatatatataacagtttatatatataatatatataacagt -ttatatatataatatatataacagtttatatatataatatataagtttatatattatata -taacagtttatatataacagtttatatataatatatataagtttatatataacagtttat -atatataatatatataagtttatatataatatatataagtttatatatatgtttatatat -aatatatataacagtttatatatataatatatataacagtttatatatataatatatata -acagtttatatatataatatatataacagtttatatatataaaatatataacagtttata -tatataatatatataagtttatatatataatatatataacagtttatatatattatatat -atatatatgcacacacacaaagagagagagagagactcgctctgtcgcccaggctgtagt -gcagt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9e05dd5ce19d05463716da5776d3ce11.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_9e05dd5ce19d05463716da5776d3ce11.msa deleted file mode 100644 index 579cfee8..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9e05dd5ce19d05463716da5776d3ce11.msa +++ /dev/null @@ -1,85 +0,0 @@ ->syndip_1_chr20:61289625-61290555 -atgtcatggaaaacagcatatgacaccaagatatccccatatccaacgagacttgctggg -tttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctg -ggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgc -tgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagactt -gctgggtttatccccgtatccaacgagacttgctgggtttatccccg------------- -------------------tatccaacgagacttgctgggtttatccccgtatccaacgag -acttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaatg -agacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaa -tgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatcc -aatgagacttgctgggtttatcccgatatccaatgagacttgctggatttatccccgtat -ccaatgagacttgctggg-------------------------------tttatccccgt -atccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatcccg -atatccaatgagacttgctggatttatccccgtatccaatgagacttgctgggtttatcc -ccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctggatttat -ccccgtatccaatgagacttgctggatttatccccatatccaatgagacttgctgggttt -agcaccacagatgccagtcacagaggaaatt ->syndip_2_chr20:61289625-61290555 -atgtcatggaaaacagcatatgacaccaagatatccccatatccaacgagacttgctggg -tttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctg -ggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgc -tgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagactt -gctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaatgagac -ttgctgggtttatccccctatccaatgagacttgctgggtttatccccgtatccaatgag -acttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaatg -agacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaa -tgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatcc -aatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtat -ccaatgagacttgctggg-------------------------------tttatccccgt -atccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatcccg -atatccaatgagacttgctggatttatccccgtatccaatgagacttgctgggtttatcc -ccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctggatttat -ccccgtatccaatgagacttgctggatttatccccatatccaatgagacttgctgggttt -agcaccacagatgccagtcacagaggaaatt ->p:HG002_1_chr20:61289625-61290555 -atgtcatggaaaacagcatatgacaccaagatatccccatatccaacgagacttgctggg -tttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctg -ggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgc -tgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagactt -gctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaatgagac -ttgctgggtttatccccctatccaatgagacttgctgggtttatccccgtatccaatgag -acttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaatg -agacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaa -tgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatcc -aatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtat -ccaatgagacttgctggg-------------------------------tttatccccgt -atccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatcccg -atatccaatgagacttgctggatttatccccgtatccaatgagacttgctgggtttatcc -ccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctggatttat -ccccgtatccaatgagacttgctggatttatccccatatccaatgagacttgctgggttt -agcaccacagatgccagtcacagaggaaatt ->p:HG002_2_chr20:61289625-61290555 -atgtcatggaaaacagcatatgacaccaagatatccccatatccaacgagacttgctggg -tttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctg -ggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgc -tgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagactt -gctgggtttatccccgtatccaacgagacttgctgggtttatccccg------------- -------------------tatccaacgagacttgctgggtttatccccgtatccaacgag -acttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaatg -agacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaa -tgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatcc -aatgagacttgctgggtttatcccgatatccaatgagacttgctggatttatccccgtat -ccaatgagacttgctggg-------------------------------tttatccccgt -atccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatcccg -atatccaatgagacttgctggatttatccccgtatccaatgagacttgctgggtttatcc -ccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctggatttat -ccccgtatccaatgagacttgctggatttatccccatatccaatgagacttgctgggttt -agcaccacagatgccagtcacagaggaaatt ->ref_chr20:61289625-61290555 -atgtcatggaaaacagcatatgacaccaagatatccccatatccaacgagacttgctggg -tttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctg -ggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgc -tgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagactt -gctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagac -ttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgag -acttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaatg -agacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaa -tgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatcc -aatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtat -ccaatgagacttgctgggtttatcccgatatccaatgagacttgctggatttatccccgt -atccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatcccg -atatccaatgagacttgctggatttatccccgtatccaatgagacttgctgggtttatcc -ccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctggatttat -ccccgtatccaatgagacttgctggatttatccccatatccaatgagacttgctgggttt -agcaccacagatgccagtcacagaggaaatt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9e3e6d9da171fc1cf562fdbd868bcc07.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_9e3e6d9da171fc1cf562fdbd868bcc07.msa deleted file mode 100644 index 976e375b..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9e3e6d9da171fc1cf562fdbd868bcc07.msa +++ /dev/null @@ -1,85 +0,0 @@ ->syndip_1_chr20:62875172-62875556 -aggattgtgaggagtgaattcatcggggagccccgcaccctcacctgcaccctcaccccc -acccccacccccacccccacccccacccccacccgcacccccacccccacccgcaccccc -acccccacccccacccgcacccccacccccacccccacccgcacccccacccccacccgc -acccccacccccacccccacccgcacccccacccccacccccacccgcacccgcaccccc -acccccacccgcacccgcacccccacccccacccccacccgcacccccacccccaccccc -acccccacccgcacccgcacccgcacccccacccccaccctcacccgcacccgcaccccc -acccccacccccacccgcacccgcacccccacccccacccc------------caccccc -acccccacccgcacccgcacccgcacccccaccctcaccctcacccgcacccgcaccccc -acccccacccgcacccccacccgcacccccacccccacccccacccccacccgcacccgc -acccccacccccacccccacccccacccccacccccacccccaccccca------ccctc -acccgcacccccaccctcacccccaccctcacccccaccctcacccgcaccctcacccgc -acccgcacccccaccctcacccacaccctcacccccaccctcacccccacccccaccctc -acccgcacccgcacccccaccctcacccccacccccacccccaccctcaccctcaccctc -acccgcacccgcacccccacccgcacccccaccctcacccccaccctcacccccaccctc -acccccacccccaccctcacccgcaccctcactcgcaccgcaccctcactggcaccctca -cccacaccgcacccacacccacatcggggaagagctccatgatcattct ->syndip_2_chr20:62875172-62875556 -aggattgtgaggagtgaattcatcggggagccccgcaccctcacctgcaccctcaccccc -acccccacccccacccccacccccacccgcacccgcacccccacccccacccgcaccccc -acccccacccccacccgcacccccacccccacccccacccgcacccccacccccaccccc -acccgcacccgcacccgcacccccacccccacccgcacccccacccccacccgcacccgc -acccccacccgcacccccacccccacccccaccctcacccccacccgcacccccaccccc -acccccacccgcacccgcacccccacccccacccccacccgcacccccacccccaccccc -acccgcacccgcacccccacccgcacccccacccccacccccacccgcacccgcaccccc -acccgcacccgcacccccacccgcacccccacccccacctccacccccacccgcacccgc -acccccacccccacccgcacccccacccccacccgcacccccacccccaccctcacccgc -acccccacccccacccgcacccccacccccaccctcacccccaccctcacccgcacccgc -acccccaccctcacccccaccctcacccccaccctcacccgcacccccacccccaccccc -acccccaccctcccccccacccgcacccgcacccccaccctcacccgcacccccaccctc -acccccaccctcacccccaccctcacccccacccccaccctcacccgcacccccactcgc -acccgcacccccaccctcacccgcacccccaccctcacccccaccctcacccccaccctc -acccccacccccaccctcacccgcaccctcactcgcaccgcaccctcactggcaccctca -cccacaccgcacccacacccacatcggggaagagctccatgatcattct ->p:HG002_1_chr20:62875172-62875556 -aggattgtgaggagtgaattcatcggggagccccgcaccctcacctgcaccctcaccccc -acccccacccccacccccacccccacccgcacccgcacccccacccccacccgcaccccc -acccccacccccacccgcacccccacccccacccccacccgcacccccacccccaccccc -acccgcacccgcacccgcacccccacccccacccgcacccccacccccacccgcacccgc -acccccacccgcacccccacccccacccccaccctcacccccacccgcacccccaccccc -acccccacccgcacccgcacccccacccccacccccacccgcacccccacccccaccccc -acccgcacccgcacccccacccgcacccccacccccacccccacccgcacccgcaccccc -acccgcacccgcacccccacccgcacccccacccccacctccacccccacccgcacccgc -acccccacccccacccgcacccccacccccacccgcacccccacccccaccctcacccgc -acccccacccccacccgcacccccacccccaccctcacccccaccctcacccgcacccgc -acccccaccctcacccccaccctcacccccaccctcacccgcacccccacccccaccccc -acccccaccctcccccccacccgcacccgcacccccaccctcacccgcacccccaccctc -acccccaccctcacccccaccctcacccccacccccaccctcacccgcacccccactcgc -acccgcacccccaccctcacccgcacccccaccctcacccccaccctcacccccaccctc -acccccacccccaccctcacccgcaccctcactcgcaccgcaccctcactggcaccctca -cccacaccgcacccacacccacatcggggaagagctccatgatcattct ->p:HG002_2_chr20:62875172-62875556 -aggattgtgaggagtgaattcatcggggagccccgcaccctcacctgcaccctcaccccc -acccccacccccacccccacccccacccccacccgcacccccacccccacccgcaccccc -acccccacccccacccgcacccccacccccacccccacccgcacccccacccccacccgc -acccccacccccacccccacccgcacccccacccccacccccacccgcacccgcaccccc -acccccacccgcacccgcacccccacccccacccccacccgcacccccacccccaccccc -acccccacccgcacccgcacccgcacccccacccccaccctcacccgcacccgcaccccc -acccccacccccacccgcacccgcacccccacccccacccc------------caccccc -acccccacccgcacccgcacccgcacccccaccctcaccctcacccgcacccgcaccccc -acccccacccgcacccccacccgcacccccacccccacccccacccccacccgcacccgc -acccccacccccacccccacccccacccccacccccacccccaccccca------ccctc -acccgcacccccaccctcacccccaccctcacccccaccctcacccgcaccctcacccgc -acccgcacccccaccctcacccacaccctcacccccaccctcacccccacccccaccctc -acccgcacccgcacccccaccctcacccccacccccacccccaccctcaccctcaccctc -acccgcacccgcacccccacccgcacccccaccctcacccccaccctcacccccaccctc -acccccacccccaccctcacccgcaccctcactcgcaccgcaccctcactggcaccctca -cccacaccgcacccacacccacatcggggaagagctccatgatcattct ->ref_chr20:62875172-62875556 -aggattgtgaggagtgaattcatcggggagc----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------cccgc -accctcacctgcaccctcacccccacccccacccccacccccacccccacccgcaccccc -acccccaccctcccccccacccgcacccgcacccccaccctcacccgcacccccaccctc -acccccaccctcacccccaccctcacccccacccccaccctcacccgcacccccactcgc -acccgcacccccaccctcacccgcacccccaccctcacccccaccctcacccccaccctc -acccccacccccaccctcacccgcaccctcactcgcaccgcaccctcactggcaccctca -cccacaccgcacccacacccacatcggggaagagctccatgatcattct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9e6357b521dd55e8882c9daece46c6c4.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_9e6357b521dd55e8882c9daece46c6c4.msa deleted file mode 100644 index 7d0782b4..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9e6357b521dd55e8882c9daece46c6c4.msa +++ /dev/null @@ -1,90 +0,0 @@ ->syndip_1_chr20:41196010-41196848 -cggtttatcctggagagtattccatgtgaatttgagaagactgtgtattctgctgttgtt -gggtggtattctgcttatgtctatttggtctaatttgcttagagtgttgttgaaatcctc -tatttcctgattgatcttctgtctggtttctatatccattatcggacatggaatattaaa -gtctccaactatttttgtctttctccctttaattctgtcatttctgtttcatatgttttg -gagctctgttaggggtatatatatatataatatatataaataaatatataaaaataaata -tatatttataataaatatatttttatttcatatataaatatatatcttataaatatatat -atttatataacataaatatatatttatatatattata----------------------- --aatatatattatatataatatatatttatataaatatatatattatatataatatattt -atatataatatatatttatatattataaatatatattatatataatatatatttatataa -atatatattatatataaatatatattatatataatatatatttatataaatatatattat -atattatataaatattatatataatatatatttatataaatatatattatatattataaa -tatatattatatattatatattatataaatattatatataatatatattatatataatat -atataaaaatatatatatttatatatataaatattttatcaatataatatccttgtctct -tgtaacctttcttgatttaacatttattttgtgtgcctttttcaaaagaggacactggag -gtgaagaaggaagctcttgactctcctaaagctgatcccaaagtgaaggctttgaaggcc -aagaaggcagtgctgaaaggcatccacacagccaccaagaaaaaaaaaaaaaagattcac -acatcacccaccttcctgtggcccaagacattatgactct ->syndip_2_chr20:41196010-41196848 -cggtttatcctggagagtattccatgtgaatttgagaagactgtgtattctgctgttgtt -gggtggtattctgcttatgtctatttggtctaatttgcttagagtgttgttgaaatcctc -tatttcctgattgatcttctgtctggtttctatatccattatcggacatggaatattaaa -gtctccaactatttttgtctttctccctttaattctgtcatttctgtttcatatgttttg -gagctctgttaggggtatatatatatataatatatataaataaatatataaaaataaata -tatatttataataaatatatttttatttcatatataaatatatatcttataaatatatat -atttatataacataaatatatatttatatatattatataacataaatatatatttatata -tattatatattatatataatatatatttatataaatatatatattatatataatatattt -atatataatatatatttatatattataaatatatattatatataatatatatttatataa -atatatattatatat-----------------------------tataaatatatattat -atattatataaatattatatataatatatatttatataaatatataatatatattataaa -tatatattatatattatatattatataaatattatatataatatatattatatataatat -atataaaaatatatatatttatatatataaatattttatcaatataatatccttgtctct -tgtaacctttcttgatttaacatttattttgtgtgcctttttcaaaagaggacactggag -gtgaagaaggaagctcttgactctcctaaagctgatcccaaagtgaaggctttgaaggcc -aagaaggcagtgctgaaaggcatccacacagccaccaagaaaaaaaaaaaaaagattcac -acatcacccaccttcctgtggcccaagacattatgactct ->p:HG002_1_chr20:41196010-41196848 -cggtttatcctggagagtattccatgtgaatttgagaagactgtgtattctgctgttgtt -gggtggtattctgcttatgtctatttggtctaatttgcttagagtgttgttgaaatcctc -tatttcctgattgatcttctgtctggtttctatatccattatcggacatggaatattaaa -gtctccaactatttttgtctttctccctttaattctgtcatttctgtttcatatgttttg -gagctctgttaggggtatatatatatataatatatataaataaatatataaaaataaata -tatatttataataaatatatttttatttcatatataaatatatatcttataaatatatat -atttatataacataaatatatatttatatatattatataacataaatatatatttatata -tattatatattatatataatatatatttatataaatatatatattatatataatatattt -atatataatatatatttatatattataaatatatattatatataatatatatttatataa -atatatattatatat-----------------------------tataaatatatattat -atattatataaatattatatataatatatatttatataaatatataatatatattataaa -tatatattatatattatatattatataaatattatatataatatatattatatataatat -atataaaaatatatatatttatatatataaatattttatcaatataatatccttgtctct -tgtaacctttcttgatttaacatttattttgtgtgcctttttcaaaagaggacactggag -gtgaagaaggaagctcttgactctcctaaagctgatcccaaagtgaaggctttgaaggcc -aagaaggcagtgctgaaaggcatccacacagccaccaagaaaaaaaaaaaaaagattcac -acatcacccaccttcctgtggcccaagacattatgactct ->p:HG002_2_chr20:41196010-41196848 -cggtttatcctggagagtattccatgtgaatttgagaagactgtgtattctgctgttgtt -gggtggtattctgcttatgtctatttggtctaatttgcttagagtgttgttgaaatcctc -tatttcctgattgatcttctgtctggtttctatatccattatcggacatggaatattaaa -gtctccaactatttttgtctttctccctttaattctgtcatttctgtttcatatgttttg -gagctctgttaggggtatatatatatataatatatataaataaatatataaaaataaata -tatatttataataaatatatttttatttcatatataaatatatatcttataaatatatat -atttatataacataaatatatatttatatatattata----------------------- --aatatatattatatataatatatatttatataaatatatatattatatataatatattt -atatataatatatatttatatattataaatatatattatatataatatatatttatataa -atatatattatatataaatatatattatatataatatatatttatataaatatatattat -atattatataaatattatatataatatatatttatataaatatatattatatattataaa -tatatattatatattatatattatataaatattatatataatatatattatatataatat -atataaaaatatatatatttatatatataaatattttatcaatataatatccttgtctct -tgtaacctttcttgatttaacatttattttgtgtgcctttttcaaaagaggacactggag -gtgaagaaggaagctcttgactctcctaaagctgatcccaaagtgaaggctttgaaggcc -aagaaggcagtgctgaaaggcatccacacagccaccaagaaaaaaaaaaaaaagattcac -acatcacccaccttcctgtggcccaagacattatgactct ->ref_chr20:41196010-41196848 -cggtttatcctggagagtattccatgtgaatttgagaagactgtgtattctgctgttgtt -gggtggtattctgcttatgtctatttggtctaatttgcttagagtgttgttgaaatcctc -tatttcctgattgatcttctgtctggtttctatatccattatcggacatggaatattaaa -gtctccaactatttttgtctttctccctttaattctgtcatttctgtttcatatgttttg -gagctctgttaggggtatatatatatataatatatataaataaatatataaaaataaata -tatatttataataaatatatttttatttcatatataaatatatatcttataaatatatat -atttatataacataaatatatatttatatat----------------------------- --attatatattatatataatatatatttatataaatatatatattatatataatatattt -atatataatatatatttatatattataaatatatat------------------------ ------------------------------------------------------------- ------------------------------------------------tatatattataaa -tatatattatatattatatattatataaatattatatataatatatattatatataatat -atataaaaatatatatatttatatatataaatattttatcaatataatatccttgtctct -tgtaacctttcttgatttaacatttattttgtgtgcctttttcaaaagaggacactggag -gtgaagaaggaagctcttgactctcctaaagctgatcccaaagtgaaggctttgaaggcc -aagaaggcagtgctgaaaggcatccacacagccaccaagaaaaaaaaaaaaaagattcac -acatcacccaccttcctgtggcccaagacattatgactct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9ea51c545a39a6fd69abe2ddc42e9ece.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_9ea51c545a39a6fd69abe2ddc42e9ece.msa deleted file mode 100644 index 269a0494..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9ea51c545a39a6fd69abe2ddc42e9ece.msa +++ /dev/null @@ -1,95 +0,0 @@ ->syndip_1_chr20:21721174-21721735 -atcgtgttttaaccttgtagaccacattggctattacatatatatatataatatatatgt -aatatatatatgtaatgtatattatatatgtaatgtatataatatatgtaatgtatataa -tatatatgtaatacatatatattatatatgtatataatacatatatatgtatatatatgt -atgtatatatatatgtatatatgtatatatatatgtatataatacatatatatacatata -tattatatatgtaatacatatataatatatatgtaatgtatatatatgtaatgtatataa -tatatatgtaatacatatataatatatatgtaatgtatataatatatatgtaatacatat -ataatatatatgtaatgtatattatatatgtaatgtatataatatgtatgtaatacatat -attatatatgtaatgtatattatatatgtattacatatatgtattacatatataacatat -atgtattacatatatgtattacatatataacatatatgtattacatatatgtattacata -tataacatatatgtattacatatatgtattacatatataacatatatgtaatacatatat -gtattacatatataacatatatgtattacatatatgtattacatatataacatatatgta -ttacatatatgtattacatatataacatatatgtattacatatatgtattacatatataa -catatatgtattacatatatgtattacatatataacatatatgtattacatatatgtaat -acatatataacatatatgtattacatatatgtaatacatatataacatatatgtattaca -tatatgtaatacatatataacatatatgtattacatatatgtaatacatatataac---- -atgtattacatatatgtaatacatatataac--------------------------atg -tattacatatatgtaatacatatataacatgtattacatatatgtaatacacatataata -tatatgttatatatatatatatatataaaattttttaaaaaattgtttcttgagata ->syndip_2_chr20:21721174-21721735 -atcgtgttttaaccttgtagaccacattggctattacatatatatatataatatatatgt -aatatatatatgtaatgtatattatatatgtaatgtatataatatatgtaatgtatataa -tacatatgtaatacatatatattatatatgtatataatacatatatatgtatatatatgt -atgtatatatatatgtatatatgtatatatatatgtatataatacatatatatacatata -tattatatatgtaatacatatataatatatatgtaatgtatatatatgtaatgtatataa -tatatatgtaatacatatataatatatatgtaatgtatataatatatatgtaatacatat -ataatatatatgtaatgtatattatatatgtaatgtatataatatgtatgtaatacatat -attatatatgtaatgtatattatatatgtattacatatatgtattacatatataacatat -atgtattacatatatgtattacatatataacatatatgtattacatatatgtattacata -tataacatatatgtattacatatatgtattacatatataacatatatgtattacatatat -gtattacatatataacatatatgtattacatatatgtattacatatataacatatatgta -ttacatatatgtattacatatataacatatatgtattacatatatgtattacatatataa -catatatgtattacatatatgtattacatatataacatatatgtattacatatatgtatt -acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca -tatatgtattacatatataacatatatgtattacatatatgtaatacatatataacatat -atgtattacatatatgtaatacatatataacatatatgtaatacatatataacatatatg -tattacatatatgtaatacatatataacatgtattacatatatgtaatacacatataata -tatatgttatatatatatatatatataaaattttttaaaaaattgtttcttgagata ->p:HG002_1_chr20:21721174-21721735 -atcgtgttttaaccttgtagaccacattggctattacatatatatatataatatatatgt -aatatatatatgtaatgtatattatatatgtaatgtatataatatatgtaatgtatataa -tacatatgtaatacatatatattatatatgtatataatacatatatatgtatatatatgt -atgtatatatatatgtatatatgtatatatatatgtatataatacatatatatacatata -tattatatatgtaatacatatataatatatatgtaatgtatatatatgtaatgtatataa -tatatatgtaatacatatataatatatatgtaatgtatataatatatatgtaatacatat -ataatatatatgtaatgtatattatatatgtaatgtatataatatgtatgtaatacatat -attatatatgtaatgtatattatatatgtattacatatatgtattacatatataacatat -atgtattacatatatgtattacatatataacatatatgtattacatatatgtattacata -tataacatatatgtattacatatatgtattacatatataacatatatgtattacatatat -gtattacatatataacatatatgtattacatatatgtattacatatataacatatatgta -ttacatatatgtattacatatataacatatatgtattacatatatgtattacatatataa -catatatgtattacatatatgtattacatatataacatatatgtattacatatatgtatt -acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca -tatatgtattacatatataacatatatgtattacatatatgtaatacatatataacatat -atgtattacatatatgtaatacatatataacatatatgtaatacatatataacatatatg -tattacatatatgtaatacatatataacatgtattacatatatgtaatacacatataata -tatatgttatatatatatatatatataaaattttttaaaaaattgtttcttgagata ->p:HG002_2_chr20:21721174-21721735 -atcgtgttttaaccttgtagaccacattggctattacatatatatatataatatatatgt -aatatatatatgtaatgtatattatatatgtaatgtatataatatatgtaatgtatataa -tatatatgtaatacatatatattatatatgtatataatacatatatatgtatatatatgt -atgtatatatatatgtatatatgtatatatatatgtatataatacatatatatacatata -tattatatatgtaatacatatataatatatatgtaatgtatatatatgtaatgtatataa -tatatatgtaatacatatataatatatatgtaatgtatataatatatatgtaatacatat -ataatatatatgtaatgtatattatatatgtaatgtatataatatgtatgtaatacatat -attatatatgtaatgtatattatatatgtattacatatatgtattacatatataacatat -atgtattacatatatgtattacatatataacatatatgtattacatatatgtattacata -tataacatatatgtattacatatatgtattacatatataacatatatgtaatacatatat -gtattacatatataacatatatgtattacatatatgtattacatatataacatatatgta -ttacatatatgtattacatatataacatatatgtattacatatatgtattacatatataa -catatatgtattacatatatgtattacatatataacatatatgtattacatatatgtaat -acatatataacatatatgtattacatatatgtaatacatatataacatatatgtattaca -tatatgtaatacatatataacatatatgtattacatatatgtaatacatatataac---- -atgtattacatatatgtaatacatatataac--------------------------atg -tattacatatatgtaatacatatataacatgtattacatatatgtaatacacatataata -tatatgttatatatatatatatatataaaattttttaaaaaattgtttcttgagata ->ref_chr20:21721174-21721735 -atcgtgttttaaccttgtagaccacattggctattacatatatatatataatatatatgt -aatatatatatgtaatgtatattatatatgtaatgtatataatatatgtaatgtatataa -tatatatgtaatacatatatattatatatgtatataatacatatatatgtatatatatgt -atgtatatatatatgtatatatgtatatatatatgtatataatacatatatatacatata -tattatatatgtaatacatatataatatatatgtaatgt--------------------- ----------------------atatatatgtaatgtatataatatatatgtaatacatat -ataatatatatgtaatgtatattatatatgtaatgtatataatatgtatgtaatacatat -attatatatgtaatgtatattatatatgtattacatatatgtattacatatataacatat -atgtattacatatatgtattacatatataacatatatgtattacatatatgtaatacaca -tataatatatatgttatatatatatatat------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------atataaaattttttaaaaaattgtttcttgagata diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9ef1d89bb5eb70baea85637a4d38ca23.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_9ef1d89bb5eb70baea85637a4d38ca23.msa deleted file mode 100644 index 3fa86d1b..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9ef1d89bb5eb70baea85637a4d38ca23.msa +++ /dev/null @@ -1,195 +0,0 @@ ->syndip_1_chr20:20337075-20337834 -gacagagaagagagggagaaaagtttacgtggaagcatagggaaggaagggatgtttgtt -gaggggtggtgtgatgcagcagaggaagaggaccagaggaaagcagccactggaaataag -gaaacagggtttaggaaggcctcactagacctgttaggatggatgcatggatggatggat -ggatggacagaatgggtgggtggatggatggatggatggatggatggatggatagatggg -tgggtggatggatggatggatagatgggtggatggatagatgggtggatggataaatgga -tggatggatggatggatagatgggtgggtagatggatggatggatggatggatggatgga -tggatggatggatggatagatgggtgggtgggtggatggatggatggatggatggatgga -tggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtgga -tggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatggg -tgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgga -tggataaatggatggatggatggatggatagatgggtgggtggatggatggatggatgga -tggatggatggatggatagatagatggatagatgggtgggtggatggatggatggatgga -tggatggatggatggatggatagatgggtggatggatggatagatgggtgggtggatgga -tggatggatagatggatagatgggtgggtggatggatggatggatagatggatagatggg -tgggtggatggatggatggatagatgggtgggtggatggatggatggatagatggataga -tgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgga -tagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggataga -tgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgga -tagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatgga -tggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatgga -tggatggatggatggatggatggatggatggatagatggatagatgggtgggtggatgga -tggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatgga -tggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggatggatggatagatggatagatgggtgggtggatggatggatggataga -tgggtgggtggatggatggatggatggatggatggatggatggatggatagatggataga -tgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgga -tagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatgga -tagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatgga -tggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatgga -tggatggatagatgggtgggtgggtggatggatggatggatggatagaataaaaaagaaa -gctaggacatggttctagtgttcttagcagacgtcccaccatggaagaggtcatggagca -caggggctttgggaaaggtgtttacaatcctgcctgcctctcacccagacctcttgccag -ggttggcacacccagatgcctg ->syndip_2_chr20:20337075-20337834 -gacagagaagagagggagaaaagtttacgtggaagcatagggaaggaagggatgtttgtt -gaggggtggtgtgatgcagcagaggaagaggaccagaggaaagcagccactggaaataag -gaaacagggtttaggaaggcctcactagacctgttaggatggatgcatggatggatggat -ggatggacagaatgggtgggtggatggatggatggatggatggatggatg----gatgga -tagatgggtgggtggatggatggatggatagatgggtggatggataaatggatggatgga -tggatggatagatgggtgggtagatggatggatggatggatggatggatggatggatgga -tggatggatagatgggtgggtgggtggatggatggatggatggatggatggatggatgga -tggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtgga -tggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatggg -tgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgga -tggataaatggatggatggatggatggatagatgggtgggtggatggatggatggatgga -tggatggatggatggataga----------------tgggtgggtggatggatggatgga -tggatggatggatggatggatagatgggtggatggatggatagatgggtgggtggatgga -tggatggatagatggatagatgggtgggtggatggatggatggatagatggatagatggg -tgggtggatggatggatggatagatgggtgggtggatggatggatggatagatggataga -tgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgga -tagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggataga -tgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgga -tagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatgga -tggatagatggatagatgggtgggtggatggatggatggatagatgggtggg----tgga -tggatggatggatggatggatggatggatggatagatggatagatgggtgggtggatgga -tggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggata-------------- -------gatggatagatgggtgggtggatggatggatggatagatgggtgggtggatgga -tggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggataga-------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------tgggtgggtgggtgga -tggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatgga -tggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatgga -tggatggatagatgggtgggtgggtggatggatggatggatggatagaataaaaaagaaa -gctaggacatggttctagtgttcttagcagacgtcccaccatggaagaggtcatggagca -caggggctttgggaaaggtgtttacaatcctgcctgcctctcacccagacctcttgccag -ggttggcacacccagatgcctg ->p:HG002_1_chr20:20337075-20337834 -gacagagaagagagggagaaaagtttacgtggaagcatagggaaggaagggatgtttgtt -gaggggtggtgtgatgcagcagaggaagaggaccagaggaaagcagccactggaaataag -gaaacagggtttaggaaggcctcactagacctgttaggatggatgcatggatggatggat -ggatggacagaatgggtgggtggatggatggatggatagatggatggatg----gatgga -tggatggatggatggatggatggatggatagatgggtgggtgggtggatggatggatgga -tggatggatggatggatggatggatggatagatgggtgggtggatggatggatggataga -tggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatgga -tagatgggtggatggataaatggatggatggatggatggatagatgggtgggtggatgga -tggatggatggatggatggatggatggatagatggatggatagatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatggg -tgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgga -tggataaatggatggatggatggatggatagatgggtgggtggatggatggatggatgga -tggatggatagatggataga----------------tgggtgggtggatggatggatgga -tggatggatggatggatggatagatgggtggatggatggatagatgggtgggtggatgga -tggatggatagatggatagatgggtgggtggatggatggatggatagatggatagatggg -tgggtggatggatggatggatagatgggtgggtggatggatggatggatagatggataga -tgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgga -tagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggataga -tgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgga -tagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatgga -tggatagatggatagatgggtgggtggatggatggatggatagatgggtggg----tgga -tggatggatggatggatggatggatggatggatagatggatagatgggtgggtggatgga -tggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggata-------------- -------gatggatagatgggtgggtggatggatggatggatagatgggtgggtggatgga -tggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggataga-------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------tgggtgggtgggtgga -tggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatgga -tggatagatggatgggtggatggatggatggatagatgggtgggtgggtggatggatgga -tggatggatagatgggtgggtgggtggatggatggatggatggatagaataaaaaagaaa -gctaggacatggttctagtgttcttagcagacgtcccaccatggaagaggtcatggagca -caggggctttgggaaaggtgtttacaatcctgcctgcctctcacccagacctcttgccag -ggttggcacacccagatgcctg ->p:HG002_2_chr20:20337075-20337834 -gacagagaagagagggagaaaagtttacgtggaagcatagggaaggaagggatgtttgtt -gaggggtggtgtgatgcagcagaggaagaggaccagaggaaagcagccactggaaataag -gaaacagggtttaggaaggcctcactagacctgttaggatggatgcatggatggatggat -ggatggacagaatgggtgggtggatggatggatggatggatggatggatggatagatggg -tgggtggatggatggatggatagatgggtggatggatagatgggtggatggataaatgga -tggatggatggatggatagatgggtgggtggatggatggatggatggatggatggatgga -tggatggatagatggatagatgggtgggtggatggatggatggatggatggatggatgga -tggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtgga -tggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatggg -tgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgga -tggataaatggatggatggatggatggatagatgtgtgggtggatggatggatggatgga -tggatggatggatggatggatagatggatagatgggtgggtggatggatggatggatgga -tggatggatggatggatggatagatgggtggatggatggatagatgggtgggtggatgga -tggatggatagatggatagatgggtgggtggatggatggatggatagatggatagatggg -tgggtggatggatggatggatagatgggtgggtggatggatggatggatagatggataga -tgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgga -tagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggataga -tgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgga -tagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatgga -tggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatgga -tggatggatggatggatggatggatggatggatagatggatagatgggtgggtggatgga -tggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatgga -tggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggatggatggatagatggatagatgggtgggtggatggatggatggataga -tgggtgggtggatagatggatggatggatggatggatggatggatggatggatggatgga -tagatgggtgggtgggtggatggatggatggatggatggatggatggatggatggatgga -tagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatagatgggtgggtggatggatggatggatagatgggtggatggataaatggatgga -tggatggatggatagatgggtgggtggatggatggatggatggatggatggatggatgga -tagatagatgggtgggtggatggatggatggatagatgggtgggtgggtggatggatgga -tggatggatagatgggtgggtgggtggatggatggatggatggatagaataaaaaagaaa -gctaggacatggttctagtgttcttagcagacgtcccaccatggaagaggtcatggagca -caggggctttgggaaaggtgtttacaatcctgcctgcctctcacccagacctcttgccag -ggttggcacacccagatgcctg ->ref_chr20:20337075-20337834 -gacagagaagagagggagaaaagtttacgtggaagcatagggaaggaagggatgtttgtt -gaggggtggtgtgatgcagcagaggaagaggaccagaggaaagcagccactggaaataag -gaaacagggtttaggaaggcctcactagacctgttaggatggatgcatggatggatggat -ggatggacagaatgggtgggtggatggatggatggatagatggatggatg----gatgga -tggatggatggatggatggatggatggatagatgggtgggtgggtggatggatggatgga -tggatggatggatggatggatggatggatagatgggtgggtggatggatggatggataga -tggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatgga -tagatgggtgga------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------tggataaatggatgga -tggatggatggatagatgggtgggtggatggatggatggatggatggatggatggatgga -tagat------gtgggtggatggatggatggatagatgggtgggtgggtggatggatgga -tggatggatagatgggtgggtgggtggatggatggatggatggatagaataaaaaagaaa -gctaggacatggttctagtgttcttagcagacgtcccaccatggaagaggtcatggagca -caggggctttgggaaaggtgtttacaatcctgcctgcctctcacccagacctcttgccag -ggttggcacacccagatgcctg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9f39fd42a919221900df58119fa5b451.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_9f39fd42a919221900df58119fa5b451.msa deleted file mode 100644 index b807fb61..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9f39fd42a919221900df58119fa5b451.msa +++ /dev/null @@ -1,675 +0,0 @@ ->syndip_1_chr20:63693125-63694084 -acgccccttcctctacaggcttctaccagtttgtgcggccccaccataagcagcagtttg -aggaggtctgtatccagctgacaggacgaggctgtggctatcggcctgagcacagcattc -cccgaaggcagcgggcacagccggtcctggaccccactggtaaatggggccccaggtggg -accctcagactcctgcgtggaaggcagtgtgggccagagtcctgggctgcttggggtggg -catcctcgggccctgcttggccccgcctctctgttcccctatgggagtgatgggggcctc -cacctccaccaccagcaccagcagcaccacctccaccttcaccaccaccacctccaccac -cacctccaccacctccacctccaccacctccaccacctccaccaccaccacctccaccac -caccacctccaccaccaccaccaccaccacctccaccaccaccaccaccaccaccacctc -cacctccaccacctccaccaccacctccacctccaccaccacctccacctccacctccac 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-caccaccaccaccacctccacctccacctccaccacctccacctccaccacctccaccac -cacctccacctccaccacctccacctccacctccaccacctccacctccaccacctccac -ctccacctccaccacctccaccaccaccacctccaccaccacctccaccacctccaccac -cacctccacctccaccacctccaccaccacctccaccaccacctccaccaccaccacctc -caccaccacctccaccacctccaccaccacctccacctccaccacctccacctccacctc -caccacctccaccaccaccaccaccaccaccaccaccaccaccacctccaccaccaccac -ctccaccaccacctccaccaccaccaccaccacctccaccaccaccaccaccacctccac -caccacctccaccacctccaccaccaccaccaccaccaccaccacctccaccaccacctc -caccaccaccaccaccaccaccaccacctccaccacctccacctccaccaccaccaccac -ctccaccaccaccaccaccaccacctccacctccaccaccaccacctccaccaccaccac -cacctccaccaccacctccaccaccaccaccaccaccaccaccaccacctccaccacctc -caccacctccaccaccacctccaccacctccaccaccaccaccaccacctccaccaccac -ctccaccaccaccaccaccaccaccacctccacctccacctccaccacctccacctccac -cacctccacctccaccacctccacctccacctccaccacctccaccaccacctccacctc -caccaccacctcctccaccaccaccacctccaccaccacctccaccaccaccacctccac -ctccaccacctccacctccaccaccaccacctccacctccaccaccaccacctccaccac -ctccaccaccacctccaccacctccacctccaccaccaccacctccaccaccaccacctc -cacctccaccaccaccaccaccaccacctccacctccaccaccacctccaccaccacctc -cacctccacctccaccacctccaccaccacctccaccacctccaccacctccacctccac -caccaccaccacctccaccaccaccaccaccacctctaccacctctaccaccaccaccac -cacctccaccaccaccaccaccacctccaccaccaccaccaccaccacctccaccaccac -ctccaccacctccaccaccaccaccaccacctctaccacctccacctccaccaccaccac -cacctctaccaccaccaccaccacctccaccaccaccaccacctccaccaccaccaccac -ctccaccaccacctccaccaccacctccaccacctccaccaccaccaccacctccacctc -caccacctccaccaccacctccaccaccaccaccaccaccacctccaccaccacctccac -cacctccaccaccaccaccaccacctctaccacctccacctccaccaccaccaccacctc -cacctccaccaccaccaccaccaccaccaccaccaccacctccaccaccaccaccaccac -cacctctaccaccaccaccaccacctccaccaccaccaccacctccaccaccaccaccac -ctccaccaccacctccaccaccaccaccaccaccaccaccacctctaccaccaccaccac -cacctccaccaccaccaccacctccaccaccaccaccacctccaccaccacctccaccac -caccaccacctccaccaccacctccaccaccacctccaccacctccaccaccaccaccac -cacctccaccaccacctccacctccaccaccaccaccaccacctccaccaccaccaccac -caccaccacctccaccaccacctccaccaccacctccaccacctccaccaccaccaccac -cacctccaccaccacctccacctccaccaccaccaccaccacctccaccaccacctccac -caccaccaccaccaccacctccaccaccacctccaccacctccaccaccaccaccaccac -ctctaccacctctaccaccaccaccaccacctccaccaccaccaccacctccaccaccac -caccacctccaccaccaccacctccacctccaccaccaccacctccaccacctccaccac -cacctccaccaccaccacctccacctccaccaccaccacctccaccacctccaccaccac -caccaccaccaccaccacctccaccaccaccaccaccaccacctccaccaccacctccac -cacctccaccaccaccaccaccacctctaccacctctaccaccaccaccaccacctccac -caccaccaccacctccaccaccaccaccacctccaccaccacctccaccaccaccacctc -cacctccaccaccaccacctccaccaccaccacctccacctccaccaccaccacctccac -cacctccaccaccacctccaccaccaccacctccacctccaccaccaccacctccaccac -ctccaccaccaccacctccaccaccaccacctccaccacctccaccaccaccaccaccac -ctccaccacctccaccacctccaccaccaccaccaccacctccacctccacctccaccac -ctccaccaccaccacctccaccaccaccaccaccaccaccaccacctccacctccacctc -caccacctccacctccaccaccaccaccaccaccaccaccaccaccaccacctccacctc -cacctccaccacctccaccaccaccacctccaccaccaccacctccacctccaccacctc -caccaccacctccaccaccaccacctccacctccaccaccaccacctccaccaccaccac -ctccacctccaccaccaccacctccaccacctccaccaccacctccaccaccaccacctc -cacctccaccaccaccacctccaccacctccaccaccaccacctccaccaccaccacctc -caccacctccaccaccaccaccaccacctccaccacctccaccacctccaccaccaccac -caccacctccacctccacctccaccacctccaccaccaccacctccaccaccaccaccac -caccacctccaccacctccaccaccaccaccaccacctccacctccacctccaccacctc -caccaccaccacctccaccaccaccaccaccaccaccaccaccacctccacctccacctc -caccacctccacctccaccaccaccaccaccaccaccacctccaccaccacctccacctc -cacctccaccacctccacctccaccaccaccaccaccaccaccaccaccaccaccacctc -cacctccacctccaccaccaccacctctaccaccacctccaccaccaccaccaccaccac -caccaccacctccaccacctccaccaccaccacctccaccaccaccacctccacctccac -caccaccaccacctccaccacctccaccaccacctccacctccacctccaccacctccac -caccaccacctccaccaccaccaccaccaccaccacctccaccacctccaccaccaccac -ctccaccaccaccacctccacctccaccacctccaccacctccaccaccaccaccacctc -caccaccaccaccaccaccacctccacctccaccacctctaccaccacctccaccaccac -caccaccaccacctccacctccaccacctccacctccaccacctctaccaccacctccac -caccaccacctccacctccacctccaccaccaccacctccacctccacctccaccaccac -caccaccaccaccacctccaccaccaccaccaccaccaccaccaccacctccacctccac -caccaccacctccaccaccaccacctccaccacctccaccaccacctccacctccaccac -caccacctccacctccacctccaccaccaccaccaccacctccaccaccaccacctccac -caccaacacctccacctccacctccaccaccaccaccaccacctccacctccaccaccac -ctccaccaccaccacctccacctccaccaccaccacctccaccaccacctccaccacctc -caccaccaccacctccaccaccacctccaccaccaccaccaccaccacctccacctccac -ctccaccaccaccacctctaccaccacctccaccaccaccaccaccaccaccaccaccac -ctccacctccacctccaccacctccacctccaccaccaccaccaccaccaccacctccac -caccacctccacctccacctccaccacctccacctccaccaccaccaccaccaccaccac -caccaccaccacctccacctccacctccaccaccaccacctctaccaccacctccaccac -caccaccaccaccaccaccaccacctccaccaccaccacctccacctccaccaccaccac -ctccacctccaccaccaccacctccacctccaccaccaccaccaccaccaccacctccac -caccaccacctccaccacctccaccaccacctccaccaccaccacctccaccacctccac -caccacctccacctccaccaccaccacctccaccaccaccacctccacctccaccaccac -cacctccacctccacctccaccacctccacctccaccacctccaccaccaccacctccac -cacctccaccaccacctccacctccaccaccaccacctccaccaccaccacctccaccac -ctccaccaccacctccacctccaccaccaccacctccacctccacctccaccaccaccac -caccacctccactaccaccacctccacctccaccaccaccacctccaccaccaacacctc -cacctccacctccacctccaccaccaccacctccacctccaccaccaccacctccaccac -caccacctccaccacctccacctccaccaccaccacctccaccaccacctccaccaccac -caccacctccaccaccaccacctccaccaccacctccaccaccaccacctccaccaccac -ctccaccaccacctccacctccaccaccaccacctgcaccaccacctccacctccaccac -caccaccacctccacctccaccagcagcagcatcacttgttggggagaccctgtgcaact -ccatgcacagccctgtccctgccatagccccgacccctaagcacagccctgtccaactgc -cacacgtcccctgcctcccatgcatggtcctggggggtcaactgcacacgccagggtcct -agggtcctagacccctgtcctccctgtttctgcctctgtttggggtggagtccaagtctc -cagaggcggaagcatctgtgttcgtgtgttaatgaacagcccctacagagttcccctagt -tcacccaggggggaacctagcctgttgggacgaccccag ->syndip_2_chr20:63693125-63694084 -acgccccttcctctacaggcttctaccagtttgtgcggccccaccataagcagcagtttg -aggaggtctgtatccagctgacaggacgaggctgtggctatcggcctgagcacagcattc -cccgaaggcagcgggcacagccggtcctggaccccactggtaaatggggccccaggtggg -accctcagactcctgcgtggaaggcagtgtgggccagagtcctgggctgcttggggtggg -catcctcgggccctgcttggccccgcctctctgttcccctatgggagtgatgggggcctc -cacctccaccaccagcaccagcagcaccacctccacc----------------------- -----------acctccacctccaccacct---------------------------ccac -ctccacctccaccaccacctccacctccacctccacctccacctccaccaccaccaccac -cacctccaccacctccacctccacctccacctccacctccacctccacctccacctccac -cacgtcca---------------------ccacctccaccaccacctccaccaccacctc -cacctccacctccacctccaccaccacctccaccaccacctccaccaccacct------- ------------ccaccaccacctccaccaccaccaccaccaccaccacctccaccacctc -caccacctccacctccacctccaccaccaccacctccaccacctccaccacctccaccac -caccaccaccaccacctccacctccaccacct---------------------------- ---------------------ccacctccacctccaccacctccacctccacctccaccac -cacctccaccacct---ccaccacctccaccacctccacctccaccacctcca------- ------------------------------ccacctccaccaccaccaccaccaccacctc -caccaccacctccaccaccacctcca---------------------------------- ------------------ccaccacctccaccaccacctccaccacctccacctccacctc -caccacctccaccacctccaccaccaccaccaccaccaccacctccaccaccacctccac -caccaccacctccacctccaccaccaccacctcca------------------ccacctc -caccacctccaccaccaccaccaccaccacctccacctccaccacctccacctccacctc -caccacctccacct---------------------------------------------- ------------------------------------------------------------- ------------------------------------ccacctccaccaccacctccaccac -ctccaccacctccaccacctccacctccaccacctccaccacctccaccaccaccaccac -caccacctccaccaccacctccaccacc-------------------------------- -----------------------------acctccaccaccacctccaccaccacctccac -cacctccacctccacctccaccacctccacctccacctccaccaccaccacct------- ------------------------------------------------------------c -cacctccaccaccacctccaccaccaccacctccacct---------------------- ------------------------------------------------------------- ---------------------------------------------------ccaccacctc -caccaccagcaccacctccaccaccaccacctccacctccacctccacctccacctccac -ctccacctccaccaccacctccacct---------------------------------- ------------------------ccaccacctccacctccaccaccaccaccaccaccac -caccaccaccacctccacctccaccaccacctcca------------------ccacctc -caccacctccaccaccaccacctccaccacctccacctccaccacctccaccaccacctc -ca------ccaccaccacctccacctccaccaccacctccaccacctccaccacctccac -caccaccaccaccacctccaccacctccaccaccaccacctccacctccacctccaccac -caccaccaccacctccaccacctccaccaccaccacctccacctccaccaccacctccac -cacctccaccacca---ccaccaccacctccaccacctccaccaccaccacctccaccac -cacctccaccaccaccacctccacctccaccaccacctccaccacctcca------ccac -ctccaccacctccacctccacctccaccacctccaccaccacctccaccacctccaccac -cacctccaccacctccacctccacctccacct---------------------ccacctc -caccaccacctccaccacctccaccaccacctccacctccaccacctccacctccacctc -caccacctccaccacca------------------------------------------- ---------------------------------------------------------cctc -caccacctccaccacctccaccaccaccaccaccacctccaccacctccaccaccacctc -caccacctccacctccacctcca------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------cctccacctccaccaccacctccaccacctccaccaccac -ctccaccaccacctccaccacctccacctccacctccacct------------------- ---------------ccacctccaccaccacctccaccacctccaccaccacctccacctc -caccacctccacctccacctccaccacctccaccaccacctccaccacctcca------- ---------------------------------------ccaccacctccacctccaccac -ctccaccaccacctccaccacct------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------ccaccacctccaccaccac -caccaccacctccaccacctccaccaccacctccaccacctccacctccacctccacctc -cacctccaccaccacctccaccacct---------------------------------- ------------------------------------------ccaccaccacctccacctc -caccacctccacctccacctccaccacctccaccaccaccacctccaccaccacct---- 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-----------------------------acctccaccaccacctccaccaccacctccac -cacctccacctccacctccaccacctccacctccacctccaccaccaccacct------- ------------------------------------------------------------c -cacctccaccaccacctccaccaccaccacctccacct---------------------- ------------------------------------------------------------- ---------------------------------------------------ccaccacctc -caccaccagcaccacctccaccaccaccacctccacctccacctccacctccacctccac -ctccacctccaccaccacctccacct---------------------------------- ------------------------ccaccacctccacctccaccaccaccaccaccaccac -caccaccaccacctccacctccaccaccacctcca------------------ccacctc -caccacctccaccaccaccacctccaccacctccacctccaccacctccaccaccacctc -ca------ccaccaccacctccacctccaccaccacctccaccacctccaccacctccac -caccaccaccaccacctccaccacctccaccaccaccacctccacctccacctccaccac -caccaccaccacctccaccacctccaccaccaccacctccacctccaccaccacctccac -cacctccaccacca---ccaccaccacctccaccacctccaccaccaccacctccaccac -cacctccaccaccaccacctccacctccaccaccacctccaccacctcca------ccac 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------------------------------------------------------------- ---------------------------------cctccaccacctccacctccacctccac -ctccacctccaccacctccacctccacctccaccacctccacctccacctccacctccac -cacgtccaccaccaccacctccaccaccaccaccaccacct------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---ccaccaccacctccacctccaccaccacctccaccaccacctccaccaccaccacct- ---------------ccacctccaccaccaccacctccacctccaccaccaccaccaccac -cacctccaccaccacctccacctcca---------------------------ccaccac -ctccacctccaccacctccaccaccagcaccaccaccacctccaccaccaccacctccac -ctcca------------------------------------------------------- ------------------------------------------------------------- ---------------ccaccaccaccaccaccacctccaccaccacctccacctccacctc -cacctccaccaccacctccaccaccacctccacca------------------------- ------------cctccaccaccacctccacctccaccacctccacctccacctccaccac -ctccacctccacctccaccacct---ccacctccacctccacctccaccaccaccacctc 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------------------------------------------ccaccaccacctccaccac -ctccacctccacctccacctccaccaccacctccaccacctccaccacca---------- ------------------------cctccaccacctccaccacctccacctccaccaccac -ctccacctccacctccaccacctccaccacca---------------------------c -caccaccaccacctccaccaccacctccacca------------------ccacctccac -ctccacctccaccacctccaccaccacctccaccaccaccaccacctccacctccaccac -ctccacctccacctccacca---------------------------------------- ------------------------------ccacctccaccacctccaccaccaccaccac -cacctccaccacctccacctccacct---------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------ccacctccacctccaccacctccacctccacctccaccaccaccaccacctccac -cacctccacca------------------------------------------------- ---------------ccacctccaccacctccacctccacctccacctccaccaccacctc -caccacctccaccaccacctccaccacctccaccacctccacct---------------- ---------------------ccaccaccacctccacctccacctccaccacctccaccac -caccaccaccaccacctccaccttcaccaccaccaccacctccaccacctccaccaccac -ctcca------------------------------------------------------- ---------------ccaccacctccaccaccacctcctccacctccaccacctccaccac -caccaccacctccacctccaccagcagcagcatcacttgttggggagaccctgtgcaact -ccatgcacagccctgtccctgccatagccccgacccctaagcacagccctgtccaactgc -cacacgtcccctgcctcccatgcatggtcctggggggtcaactgcacacgccagggtcct -agggtcctagacccctgtcctccctgtttctgcctctgtttggggtggagtccaagtctc -cagaggcggaagcatctgtgttcgtgtgttaatgaacagcccctacagagttcccctagt -tcacccaggggggaacctagcctgttgggacgaccccag ->p:HG002_2_chr20:63693125-63694084 -acgccccttcctctacaggcttctaccagtttgtgcggccccaccataagcagcagtttg -aggaggtctgtatccagctgacaggacgaggctgtggctatcggcctgagcacagcattc -cccgaaggcagcgggcacagccggtcctggaccccactggtaaatggggccccaggtggg -accctcagactcctgcgtggaaggcagtgtgggccagagtcctgggctgcttggggtggg 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-cacctctaccaccaccaccaccacctccaccaccaccaccacctccaccaccaccaccac -ctccaccaccacctccaccaccaccaccaccaccaccaccacctctaccaccaccaccac -cacctccaccaccaccaccacctccaccaccaccaccacctccaccaccacctccaccac -caccaccacctccaccaccacctccaccaccacctccaccacctccaccaccaccaccac -cacctccaccaccacctccacctccaccaccaccaccaccacctccaccaccaccaccac -caccaccacctccaccaccacctccaccaccacctccaccacctccaccaccaccaccac -cacctccaccaccacctccacctccaccaccaccaccaccacctccaccaccacctccac -caccaccaccaccaccacctccaccaccacctccaccacctccaccaccaccaccaccac -ctctaccacctctaccaccaccaccaccacctccaccaccaccaccacctccaccaccac -caccacctccaccaccaccacctccacctccaccaccaccacctccaccacctccaccac -cacctccaccaccaccacctccacctccaccaccaccacctccaccacctccaccaccac -caccaccaccaccaccacctccaccaccaccaccaccaccacctccaccaccacctccac -cacctccaccaccaccaccaccacctctaccacctctaccaccaccaccaccacctccac -caccaccaccacctccaccaccaccaccacctccaccaccacctccaccaccaccacctc -cacctccaccaccaccacctccaccaccaccacctccacctccaccaccaccacctccac -cacctccaccaccacctccaccaccaccacctccacctccaccaccaccacctccaccac -ctccaccaccaccacctccaccaccaccacctccaccacctccaccaccaccaccaccac -ctccaccacctccaccacctccaccaccaccaccaccacctccacctccacctccaccac -ctccaccaccaccacctccaccaccaccaccaccaccaccaccacctccacctccacctc -caccacctccacctccaccaccaccaccaccaccaccaccaccaccaccacctccacctc -cacctccaccacctccaccaccaccacctccaccaccaccacctccacctccaccacctc -caccaccacctccaccaccaccacctccacctccaccaccaccacctccaccaccaccac -ctccacctccaccaccaccacctccaccacctccaccaccacctccaccaccaccacctc -cacctccaccaccaccacctccaccacctccaccaccaccacctccaccaccaccacctc -caccacctccaccaccaccaccaccacctccaccacctccaccacctccaccaccaccac -caccacctccacctccacctccaccacctccaccaccaccacctccaccaccaccaccac -caccacctccaccacctccaccaccaccaccaccacctccacctccacctccaccacctc -caccaccaccacctccaccaccaccaccaccaccaccaccaccacctccacctccacctc -caccacctccacctccaccaccaccaccaccaccaccacctccaccaccacctccacctc -cacctccaccacctccacctccaccaccaccaccaccaccaccaccaccaccaccacctc -cacctccacctccaccaccaccacctctaccaccacctccaccaccaccaccaccaccac -caccaccacctccaccacctccaccaccaccacctccaccaccaccacctccacctccac -caccaccaccacctccaccacctccaccaccacctccacctccacctccaccacctccac -caccaccacctccaccaccaccaccaccaccaccacctccaccacctccaccaccaccac -ctccaccaccaccacctccacctccaccacctccaccacctccaccaccaccaccacctc -caccaccaccaccaccaccacctccacctccaccacctctaccaccacctccaccaccac -caccaccaccacctccacctccaccacctccacctccaccacctctaccaccacctccac -caccaccacctccacctccacctccaccaccaccacctccacctccacctccaccaccac -caccaccaccaccacctccaccaccaccaccaccaccaccaccaccacctccacctccac -caccaccacctccaccaccaccacctccaccacctccaccaccacctccacctccaccac -caccacctccacctccacctccaccaccaccaccaccacctccaccaccaccacctccac -caccaacacctccacctccacctccaccaccaccaccaccacctccacctccaccaccac -ctccaccaccaccacctccacctccaccaccaccacctccaccaccacctccaccacctc -caccaccaccacctccaccaccacctccaccaccaccaccaccaccacctccacctccac -ctccaccaccaccacctctaccaccacctccaccaccaccaccaccaccaccaccaccac -ctccacctccacctccaccacctccacctccaccaccaccaccaccaccaccacctccac -caccacctccacctccacctccaccacctccacctccaccaccaccaccaccaccaccac -caccaccaccacctccacctccacctccaccaccaccacctctaccaccacctccaccac -caccaccaccaccaccaccaccacctccaccaccaccacctccacctccaccaccaccac -ctccacctccaccaccaccacctccacctccaccaccaccaccaccaccaccacctccac -caccaccacctccaccacctccaccaccacctccaccaccaccacctccaccacctccac -caccacctccacctccaccaccaccacctccaccaccaccacctccacctccaccaccac -cacctccacctccacctccaccacctccacctccaccacctccaccaccaccacctccac -cacctccaccaccacctccacctccaccaccaccacctccaccaccaccacctccaccac -ctccaccaccacctccacctccaccaccaccacctccacctccacctccaccaccaccac -caccacctccactaccaccacctccacctccaccaccaccacctccaccaccaacacctc -cacctccacctccacctccaccaccaccacctccacctccaccaccaccacctccaccac -caccacctccaccacctccacctccaccaccaccacctccaccaccacctccaccaccac -caccacctccaccaccaccacctccaccaccacctccaccaccaccacctccaccaccac -ctccaccaccacctccacctccaccaccaccacctgcaccaccacctccacctccaccac -caccaccacctccacctccaccagcagcagcatcacttgttggggagaccctgtgcaact -ccatgcacagccctgtccctgccatagccccgacccctaagcacagccctgtccaactgc -cacacgtcccctgcctcccatgcatggtcctggggggtcaactgcacacgccagggtcct -agggtcctagacccctgtcctccctgtttctgcctctgtttggggtggagtccaagtctc -cagaggcggaagcatctgtgttcgtgtgttaatgaacagcccctacagagttcccctagt -tcacccaggggggaacctagcctgttgggacgaccccag ->ref_chr20:63693125-63694084 -acgccccttcctctacaggcttctaccagtttgtgcggccccaccataagcagcagtttg -aggaggtctgtatccagctgacaggacgaggctgtggctatcggcctgagcacagcattc -cccgaaggcagcgggcacagccggtcctggaccccactggtaaatggggccccaggtggg -accctcagactcctgcgtggaaggcagtgtgggccagagtcctgggctgcttggggtggg -catcctcgggccctgcttggccccgcctctctgttcccctatgggagtgatgggggcctc -cacctccaccaccagcaccagcagcaccacctccacct---------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---ccacctccacct---------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------ccacctccaccaccacctccacctc -caccaccacctcctccaccaccaccacctccaccacca---------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------ccaccaccaccaccac -ct---------------------ccacctccaccacctccacctccaccaccaccacctc -cacctccacca------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------ccaccacctccacctccaccaccac -ctccaccaccaccacctccacctccacca------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------ccacctccaccaccaccaccaccaccaccac -caccaccacca------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------ccacctccaccaccaccacctgcaccaccacctccacctccaccac -caccaccacctccacctccaccagcagcagcatcacttgttggggagaccctgtgcaact -ccatgcacagccctgtccctgccatagccccgacccctaagcacagccctgtccaactgc -cacacgtcccctgcctcccatgcatggtcctggggggtcaactgcacacgccagggtcct -agggtcctagacccctgtcctccctgtttctgcctctgtttggggtggagtccaagtctc -cagaggcggaagcatctgtgttcgtgtgttaatgaacagcccctacagagttcccctagt -tcacccaggggggaacctagcctgttgggacgaccccag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9f893fa5fa2e1b0492f5953369db9454.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_9f893fa5fa2e1b0492f5953369db9454.msa deleted file mode 100644 index 1f6310f9..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9f893fa5fa2e1b0492f5953369db9454.msa +++ /dev/null @@ -1,120 +0,0 @@ ->syndip_1_chr20:62874972-62875756 -ggaacggctgggagtgacccaccccccacccccattttcttcatcagtcaccgaaacttt -cgccccacaggtagctgaccctaaattcagtgaaatccagaactttcctggcacactgga -gaggacggcagaacgctgggatggatttatcgtgcaagaccagcttgatgtccttagggc -ttggaggtcaccccttcacgaggattgtgaggagtgaattcatcggggagccccgcaccc -tcacctgcaccctcacccccacccccacccccacccccacccccacccccacccgcaccc -ccacccccacccgcacccccacccccacccccacccgcacccccacccccacccccaccc -gcacccccacccccacccgcacccccacccccacccccacccgcacccccacccccaccc -ccacccgcacccgcacccccacccccacccgcacccgcacccccacccccacccccaccc -gcacccccacccccacccccacccccacccgcacccgcacccgcacccccacccccaccc -tcacccgcacccgcacccccacccccacccccacccgcacccgcacccccacccccaccc -c------------cacccccacccccacccgcacccgcacccgcacccccaccctcaccc -tcacccgcacccgcacccccacccccacccgcacccccacccgcacccccacccccaccc -ccacccccacccgcacccgcacccccacccccacccccacccccacccccacccccaccc -ccacccccaccctcacccgcacccccaccctcacccccaccctcacccccaccctcaccc -gcaccctcacccgcacccgcacccccaccct------cacccacaccctcacccccaccc -tcacccccacccccaccctcacccgcacccgcacccccaccctcacccccacccccaccc -ccaccctcaccctcaccctcacccgcacccgcacccccacccgcacccccaccctcaccc -ccaccctcacccccaccctcacccccacccccaccctcacccgcaccctcactcgcaccg -caccctcactggcaccctcacccacaccgcacccacacccacatcggggaagagctccat -gatcattcttttctgtaggcgaaaaactgcggcgggaactgctgccatgcagctgggctc -ccaatgcagtggggatggtggcgctctgggctggcgggagctatcctgccggacgtgatt -cccagcacagccgtgagcggcagcagaggcgcagtcatctgacccacatagttcctgcgt -tgcctgatgggcgcagcttccctagaact ->syndip_2_chr20:62874972-62875756 -ggaacggctgggagtgacccaccccccacccccattttcttcatcagtcaccgaaacttt -cgccccacaggtagctgaccctaaattcagtgaaatccagaactttcctggcacactgga -gaggacggcagaacgctgggatggatttatcgtgcaagaccagcttgatgtccttagggc -ttggaggtcaccccttcacgaggattgtgaggagtgaattcatcggggagccccgcaccc -tcacctgcaccctcacccccacccccacccccacccccacccccacccgcacccgcaccc -ccacccccacccgcacccccacccccacccccacccgcacccccacccccacccccaccc -gcacccccacccccacccccacccgcacccgcacccgcacccccacccccacccgcaccc -ccacccccacccgcacccgcacccccacccgcacccccacccccacccccaccctcaccc -ccacccgcacccccacccccacccccacccgcacccgcacccccacccccacccccaccc -gcacccccacccccacccccacccgcacccgcacccccacccgcacccccacccccaccc -ccacccgcacccgcacccccacccgcacccgcacccccacccgcacccccacccccacct -ccacccccacccgcacccgcacccccacccccacccgcacccccacccccacccgcaccc -ccacccccaccctcacccgcacccccacccccacccgcacccccacccccaccctcaccc -ccaccctcacccgcacccgcacccccaccctcacccccaccctcacccccaccctcaccc -gcacccccacccccacccccacccccaccctcccccccacccgcacccgcacccccaccc -tcacccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccc -tcacccgcacccccactcgcacccgcacccccaccctcacccgcacccccaccctcaccc -ccaccctcacccccaccctcacccccacccccaccctcacccgcaccctcactcgcaccg -caccctcactggcaccctcacccacaccgcacccacacccacatcggggaagagctccat -gatcattcttttctgtaggcgaaaaactgcggcgggaactgctgccatgcagctgggctc -ccaatgcagtggggatggtggcgctctgggctggcgggagctatcctgccggacgtgatt -cccagcacagccgtgagcggcagcagaggcgcagtcatctgacccacatagttcctgcgt -tgcctgatgggcgcagcttccctagaact ->p:HG002_1_chr20:62874972-62875756 -ggaacggctgggagtgacccaccccccacccccattttcttcatcagtcaccgaaacttt -cgccccacaggtagctgaccctaaattcagtgaaatccagaactttcctggcacactgga -gaggacggcagaacgctgggatggatttatcgtgcaagaccagcttgatgtccttagggc -ttggaggtcaccccttcacgaggattgtgaggagtgaattcatcggggagccccgcaccc -tcacctgcaccctcacccccacccccacccccacccccacccccacccgcacccgcaccc -ccacccccacccgcacccccacccccacccccacccgcacccccacccccacccccaccc -gcacccccacccccacccccacccgcacccgcacccgcacccccacccccacccgcaccc -ccacccccacccgcacccgcacccccacccgcacccccacccccacccccaccctcaccc -ccacccgcacccccacccccacccccacccgcacccgcacccccacccccacccccaccc -gcacccccacccccacccccacccgcacccgcacccccacccgcacccccacccccaccc -ccacccgcacccgcacccccacccgcacccgcacccccacccgcacccccacccccacct -ccacccccacccgcacccgcacccccacccccacccgcacccccacccccacccgcaccc -ccacccccaccctcacccgcacccccacccccacccgcacccccacccccaccctcaccc -ccaccctcacccgcacccgcacccccaccctcacccccaccctcacccccaccctcaccc -gcacccccacccccacccccacccccaccctcccccccacccgcacccgcacccccaccc -tcacccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccc -tcacccgcacccccactcgcacccgcacccccaccctcacccgcacccccaccctcaccc -ccaccctcacccccaccctcacccccacccccaccctcacccgcaccctcactcgcaccg -caccctcactggcaccctcacccacaccgcacccacacccacatcggggaagagctccat -gatcattcttttctgtaggcgaaaaactgcggcgggaactgctgccatgcagctgggctc -ccaatgcagtggggatggtggcgctctgggctggcgggagctatcctgccggacgtgatt -cccagcacagccgtgagcggcagcagaggcgcagtcatctgacccacatagttcctgcgt -tgcctgatgggcgcagcttccctagaact ->p:HG002_2_chr20:62874972-62875756 -ggaacggctgggagtgacccaccccccacccccattttcttcatcagtcaccgaaacttt -cgccccacaggtagctgaccctaaattcagtgaaatccagaactttcctggcacactgga -gaggacggcagaacgctggaatggatttatcgtgcaagaccagcttgatgtccttagggc -ttggaggtcaccccttcacgaggattgtgaggagtgaattcatcggggagccccgcaccc -tcacctgcaccctcacccccacccccacccccacccccacccccacccccacccgcaccc -ccacccccacccgcacccccacccccacccccacccgcacccccacccccacccccaccc -gcacccccacccccacccgcacccccacccccacccccacccgcacccccacccccaccc -ccacccgcacccgcacccccacccccacccgcacccgcacccccacccccacccccaccc -gcacccccacccccacccccacccccacccgcacccgcacccgcacccccacccccaccc -tcacccgcacccgcacccccacccccacccccacccgcacccgcacccccacccccaccc -c------------cacccccacccccacccgcacccgcacccgcacccccaccctcaccc -tcacccgcacccgcacccccacccccacccgcacccccacccgcacccccacccccaccc -ccacccccacccgcacccgcacccccacccccacccccacccccacccccacccccaccc -ccacccccaccctcacccgcacccccaccctcacccccaccctcacccccaccctcaccc -gcaccctcacccgcacccgcacccccaccct------cacccacaccctcacccccaccc -tcacccccacccccaccctcacccgcacccgcacccccaccctcacccccacccccaccc -ccaccctcaccctcaccctcacccgcacccgcacccccacccgcacccccaccctcaccc -ccaccctcacccccaccctcacccccacccccaccctcacccgcaccctcactcgcaccg -caccctcactggcaccctcacccacaccgcacccacacccacatcggggaagagctccat -gatcattcttttctgtaggcgaaaaactgcggcgggaactgctgccatgcagctgggctc -ccaatgcagtggggatggtggcgctctgggctggcgggagctatcctgccggacgtgatt -cccagcacagccgtgagcggcagcagaggcgcagtcatctgacccacatagttcctgcgt -tgcctgatgggcgcagcttccctagaact ->ref_chr20:62874972-62875756 -ggaacggctgggagtgacccaccccccacccccattttcttcatcagtcaccgaaacttt -cgccccacaggtagctgaccctaaattcagtgaaatccagaactttcctggcacactgga -gaggacggcagaacgctgggatggatttatcgtgcaagaccagcttgatgtccttagggc -ttggaggtcaccccttcacgaggattgtgaggagtgaattcatcggggagccccgcaccc -tcacctgcaccctcacccccacccccacccccacccccacccccacccg----------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------cacccccacccccaccctcccccccacccgcacccgcacccccaccc -tcacccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccc -tcacccgcacccccactcgcacccgcacccccaccctcacccgcacccccaccctcaccc -ccaccctcacccccaccctcacccccacccccaccctcacccgcaccctcactcgcaccg -caccctcactggcaccctcacccacaccgcacccacacccacatcggggaagagctccat -gatcattcttttctgtaggcgaaaaactgcggcgggaactgctgccatgcagctgggctc -ccaatgcagtggggatggtggcgctctgggctggcgggagctatcctgccggacgtgatt -cccagcacagccgtgagcggcagcagaggcgcagtcatctgacccacatagttcctgcgt -tgcctgatgggcgcagcttccctagaact diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a0dd4d0153a1b9ee5df03250bab1b338.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a0dd4d0153a1b9ee5df03250bab1b338.msa deleted file mode 100644 index f36eea14..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a0dd4d0153a1b9ee5df03250bab1b338.msa +++ /dev/null @@ -1,105 +0,0 @@ ->syndip_1_chr20:35580013-35580886 -ttggagcctacaaagtgctgtcagaagctgggcatggtggctcatgcctgtaaccccagc -actttgggaggctgaggcaggcagactgctcaaactcaggagttcgagaccagcctgggc -aacatggcaagacaccatctgtaccaaaaatacaaaaaaatagccgggcatagtggtgcg -cacctgtggtcccagctactcaggaggttgaggtgggaggatcacttgagcccagggggc -ggaggttacagtgagccaagatttgcactccagccttggtgacagagcaagagaccctgt -ctaaaatatatatgtgtatatacacacacacacacacaaatatattttttggctgggcat -ggtggctgacacctgtaatcccagcactttgggaggccaaggcaggcagatcacttgagg -tcaggagtttgagaccagcctggccaagatgatgaaatcctgtctctactaaaaatacaa -aaaaattagctgggtgtggtaacgggtggctgtaatcccagctacttgggaagctgaggc -agaagaatagcttgaacctgggaggcacaggttgcagtgagccgagatcgcgccactgca -gcctaggcagcagagtgagactctgtcttaaaatatatattatggtttattttattttat -ggttaaaggccatatatatatatatat-atatatatataatatatatatatataaaatat -atatatataaaatatatatatatataaaatatatatatataaaatatatatatatatata -aaatatatatatataaaatatatatatataaaatatatatatatataaaatatatatata -tataaaatatatatatataaaatatatatatatataaaatatatatatataaaatatata -tatataaaatatatatatatataaaatatatatatataaaatatatatatataaaatata -tatatatataatatatatatataaaatatatatatataaaatatatatataaaatatata -tatataaaatatatatatataaaatatatatatataaaatatatatatataaaatatata -tataaaatatatatatataaaatatatatatataaaatatatatatataaaatatatata -tggaattccatatctatcaatggatcctaag ->syndip_2_chr20:35580013-35580886 -ttggagcctacaaagtgctgtcagaagctgggcatggtggctcatgcctgtaaccccagc -actttgggaggctgaggcaggcagactgctcaaactcaggagttcgagaccagcctgggc -aacatggcaagacaccatctgtaccaaaaatacaaaaaaatagccgggcatagtggtgcg -cacctgtggtcccagctactcaggaggttgaggtgggaggatcacttgagcccagggggc -ggaggttacagtgagccaagatttgcactccagccttggtgacagagcaagagaccctgt -ctaaaatatatatgtgtatatacacacacacacacacaaatatattttttggctgggcat -ggtggctgacacctgtaatcccagcactttgggaggccaaggcaggcagatcacttgagg -tcaggagtttgagaccagcctggccaagatgatgaaatcctgtctctactaaaaatacaa -aaaaattagctgggtgtggtaacgggtggctgtaatcccagctacttgggaagctgaggc -agaagaatagcttgaacctgggaggcacaggttgcagtgagccgagatcgcgccactgca -gcctaggcagcagagtgagactctgtcttaaaatatatattatggtttattttattttat -ggttaaaggccatatatatat---------atatatatatataaaatatatataatatat -atatatata-----------------------atatatatataaaatatatataa----- --aatatatatatataaaatatatatatataaaatatatatatataaaatatatatatata -tataaaatatatatatggaa---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------ttccatatctatcaatggatcctaag ->p:HG002_1_chr20:35580013-35580886 -ttggagcctacaaagtgctgtcagaagctgggcatggtggctcatgcctgtaaccccagc -actttgggaggctgaggcaggcagactgctcaaactcaggagttcgagaccagcctgggc -aacatggcaagacaccatctgtaccaaaaatacaaaaaaatagccgggcatagtggtgcg -cacctgtggtcccagctactcaggaggttgaggtgggaggatcacttgagcccagggggc -ggaggttacagtgagccaagatttgcactccagccttggtgacagagcaagagaccctgt -ctaaaatatatatgtgtatatacacacacacacacacaaatatattttttggctgggcat -ggtggctgacacctgtaatcccagcactttgggaggccaaggcaggcagatcacttgagg -tcaggagtttgagaccagcctggccaagatgatgaaatcctgtctctactaaaaatacaa -aaaaattagctgggtgtggtaacgggtggctgtaatcccagctacttgggaagctgaggc -agaagaatagcttgaacctgggaggcacaggttgcagtgagccgagatcgcgccactgca -gcctaggcagcagagtgagactctgtcttaaaatatatattatggtttattttattttat -ggttaaaggccatatatatat---------atatatatatataaaatatatataatatat -atatatata-----------------------atatatatataaaatatatataa----- --aatatatatatataaaatatatatatataaaatatatatatataaaatatatatatata -tataaaatatatatatggaa---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------ttccatatctatcaatggatcctaag ->p:HG002_2_chr20:35580013-35580886 -ttggagcctacaaagtgctgtcagaagctgggcatggtggctcatgcctgtaaccccagc -actttgggaggctgaggcaggcagactgctcaaactcaggagttcgagaccagcctgggc -aacatggcaagacaccatctgtaccaaaaatacaaaaaaatagccgggcatagtggtgcg -cacctgtggtcccagctactcaggaggttgaggtgggaggatcacttgagcccagggggc -ggaggttacagtgagccaagatttgcactccagccttggtgacagagcaagagaccctgt -ctaaaatatatatgtgtatatacacacacacacacacaaatatattttttggctgggcat -ggtggctgacacctgtaatcccagcactttgggaggccaaggcaggcagatcacttgagg -tcaggagtttgagaccagcctggccaagatgatgaaatcctgtctctactaaaaatacaa -aaaaattagctgggtgtggtaacgggtggctgtaatcccagctacttgggaagctgaggc -agaagaatagcttgaacctgggaggcacaggttgcagtgagccgagatcgtgccactgca -gcctaggcagcagagtgagactctgtcttaaaatatatattatggtttattttattttat -ggttaaaggccatatatatatatatat-atatatatataataaatatatatataaaatat -atatatataaaatatatatatatataaaatatatatatataaaatatatatatatatata -aaatatatatatataaaatatatatatataaaatatatatatatataaaatatatatata -tataaaatatatatatataaaatatatatatatataaaatatatatatataaaatatata -tatataaaatatatatatatataaaatatatatatataaaatatatatatataaaatata -tatatatataatatatatatataaaatatatatatataaaatatatatataaaatatata -tatataaaatatatatatataaaatatatatatataaaatatatatatataaaatatata -tataaaatatatatatataaaatatatatatataaaatatatatatataaaatatatata -tggaattccatatctatcaatggatcctaag ->ref_chr20:35580013-35580886 -ttggagcctacaaagtgctgtcagaagctgggcatggtggctcatgcctgtaaccccagc -actttgggaggctgaggcaggcagactgctcaaactcaggagttcgagaccagcctgggc -aacatggcaagacaccatctgtaccaaaaatacaaaaaaatagccgggcatagtggtgcg -cacctgtggtcccagctactcaggaggttgaggtgggaggatcacttgagcccagggggc -ggaggttacagtgagccaagatttgcactccagccttggtgacagagcaagagaccctgt -ctaaaatatatatgtgtatatacacacacacacacacaaatatattttttggctgggcat -ggtggctgacacctgtaatcccagcactttgggaggccaaggcaggcagatcacttgagg -tcaggagtttgagaccagcctggccaagatgatgaaatcctgtctctactaaaaatacaa -aaaaattagctgggtgtggtaacgggtggctgtaatcccagctacttgggaagctgaggc -agaagaatagcttgaacctgggaggcacaggttgcagtgagccgagatcgcgccactgca -gcctaggcagcagagtgagactctgtcttaaaatatatattatggtttattttattttat -ggttaaaggccatatatatatatatataaaatatatatatataaaatatatataaaatat -atatatataaaatatatatat------aatatatatatataaaatatatatatat----- --aatatatatatataaaatatatatatataaaatatatatatatataaaatatatatata -tataaaatatatatatggaa---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------ttccatatctatcaatggatcctaag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a2808b205fb6e4ff2a694b9b59fe99d7.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a2808b205fb6e4ff2a694b9b59fe99d7.msa deleted file mode 100644 index c5bff334..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a2808b205fb6e4ff2a694b9b59fe99d7.msa +++ /dev/null @@ -1,75 +0,0 @@ ->syndip_1_chr20:61289562-61290373 -tgaccacaggccagtggcagtccctgcctttggattaaagagccctttgaggcttgcttg -gtgatgtcatggaaaacagcatatgacaccaagatatccccatatccaacgagacttgct -gggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttg -ctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagact -tgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgaga -cttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacga -gacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaac -gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca -atgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatc -caatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgta -tccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccg -tatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc -gatatccaatgagacttgctggatttatcc------------------------------ --------------------------------- ->syndip_2_chr20:61289562-61290373 -tgaccacaggccagtggcagtccctgcctttggattaaagagccctttgaggcttgcttg -gtgatgtcatggaaaacagcatatgacaccaagatatccccatatccaacgagacttgct -gggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttg -ctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagact -tgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgaga -cttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacga -gacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaac -gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca -atgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatc -caatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgta -tccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccg -tatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc -cgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctggatttatc -c------------------------------- ->p:HG002_1_chr20:61289562-61290373 -tgaccacaggccagtggcagtccctgcctttggattaaagagccctttgaggcttgcttg -gtgatgtcatggaaaacagcatatgacaccaagatatccccatatccaacgagacttgct -gggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttg -ctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagact -tgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgaga -cttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacga -gacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaac -gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca -atgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatc -caatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgta -tccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccg -tatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc -cgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctggatttatc -c------------------------------- ->p:HG002_2_chr20:61289562-61290373 -tgaccacaggccagtggcagtccctgcctttggattaaagagccctttgaggcttgcttg -gtgatgtcatggaaaacagcatatgacaccaagatatccccatatccaacgagacttgct -gggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttg -ctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagact -tgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgaga -cttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacga -gacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaac -gagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatcca -atgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatc -caatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgta -tccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccg -tatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc -gatatccaatgagacttgctggatttatcc------------------------------ --------------------------------- ->ref_chr20:61289562-61290373 -tgaccacaggccagtggcagtccctgcctttggattaaagagccctttgaggcttgcttg -gtgatgtcatggaaaacagcatatgacaccaagatatccccatatccaacgagacttgct -gggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttg -ctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagact -tgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgaga -cttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacga -gacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaac -gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca -atgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatc -caatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgta -tccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccg -tatccaatgagacttgctgggtttatcccgatatccaatgagacttgctggatttatccc -cgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatc -ccgatatccaatgagacttgctggatttatcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a39c892a8f6b6200a6027f804af32ba7.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a39c892a8f6b6200a6027f804af32ba7.msa deleted file mode 100644 index 0b1260fe..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a39c892a8f6b6200a6027f804af32ba7.msa +++ /dev/null @@ -1,130 +0,0 @@ ->syndip_1_chr20:55944062-55945385 -atacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggaggctg -aggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcaccac -tgcattccagctgggcaacagagagagactctttcttaaatatatatattttatatatat -atagatacacacacacacacacacacacacac---------------------------- -------atatatatatatatatatatatatatatatatatgcatgcatgccagatgcagt -ggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgaggtca -ggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaaaat -tagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcaggaga -atcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactccag -cctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatctatag -atatatatctagatatagatctatgagtatatatctatagatatctagatatatatttat -agatagatatatctatagatatctatatatttctatcgatagagatatctatagatatct -atcaatatatctatagatttctagagatatgtatctagatataaatctatagacatagat -atagatatatagatatttaactgccaatgtcctaaacactttatactcaacacatttttt -ataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatagtat -ctatctagatatctgtgtagatgtctagatatctatctagatat-----tatctatctag -atatctgtcgctatctagatatctatctagatatctgtcgctatctagatatctatctag -atatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatc -tagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagata -tctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatc -tagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtc -gctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagta -tctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctag -atagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatct -atctagatagtatctgtcgcta ->syndip_2_chr20:55944062-55945385 -atacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggaggctg -aggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcaccac -tgcattccagctgggcaacagagagagactctttcttaaatatatatattttatatatat -atagatacacacacacacacacacacacacacacacacacacacacacacacatatatat -atatatatatatatatatatatatatatatatatatatatgcatgcatgccagatgcagt -ggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgaggtca -ggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaaaat -tagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcaggaga -atcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactccag -cctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatctatag -atatatatctagatatagatctatgagtatatatctatagatatctagatatatatttat -agatagatatatctatagatatctatatatttctatcgatagagatatctatagatatct -atcaatatatctatagatttctagagatatgtatctagatataaatctatagacatagat -atagatatatagatatttaactgccaatgtcctaaacactttatactcaacacatttttt -ataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatagtat -ctatctagatatcggtctagat-----agtatctatctagatatctgtgtagatgtctag -atatctatctagatat---tatctatctagatatctgtcgctatctagatatctatctag -atatctgtcgctatctagatatctatctaga---tatctgtcgctatctagatatctatc -tagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagata -tctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatc -tagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtc -gcta-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------- ->p:HG002_1_chr20:55944062-55945385 -atacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggaggctg -aggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcaccac -tgcattccagctgggcaacagagagagactctttcttaaatatatatattttatatatat -atagatacacacacacacacacacacacacacacacacacacacacacacacatatatat -atatatatatatatatatatatatatatatatatatatatgcatgcatgccagatgcagt -ggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgaggtca -ggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaaaat -tagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcaggaga -atcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactccag -cctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatctatag -atatatatctagatatagatctatgagtatatatctatagatatctagatatatatttat -agatagatatatctatagatatctatatatttctatcgatagagatatctatagatatct -atcaatatatctatagatttctagagatatgtatctagatataaatctatagacatagat -atagatatatagatatttaactgccaatgtcctaaacactttatactcaacacatttttt -ataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatagtat -ctatctagatatctgtgtagatgtctagatatctatctagatat-----tatctatctag -atatctgtcgctatctagatatctatctagatatctgtcgctatctagatatctatctag -atatctgtcgctatctagatatctatctaga---tatctgtcgctatctagatatctatc -tagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagata -tctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatc -tagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtc -gcta-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------- ->p:HG002_2_chr20:55944062-55945385 -atacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggaggctg -aggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcaccac -tgcattccagctgggcaacagagagagactctttcttaaatatatatattttatatatat -atagatacacacacacacacacacacacacac---------------------------- -------atatatatatatatatatatatatatatatatatgcatgcatgccagatgcagt -ggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgaggtca -ggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaaaat -tagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcaggaga -atcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactccag -cctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatctatag -atatatatctagatatagatctatgagtatatatctatagatatctagatatatatttat -agatagatatatctatagatatctatatatttctatcgatagagatatctatagatatct -atcaatatatctatagatttctagagatatgtatctagatataaatctatagacatagat -atagatatatagatatttaactgccaatgtcctaaacactttatactcaacacatttttt -ataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatagtat -ctatctagatatctgtgtagatgtctagatatctatctagatat-----tatctatctag -atatctgtcgctatctagatatctatctagatatctgtcgctatctagatatctatctag -atatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatc -tagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagata -tctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatc -tagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtc -gctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagta -tctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctag -atagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatct -atctagatagtatctgtcgcta ->ref_chr20:55944062-55945385 -atacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggaggctg -aggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcaccac -tgcattccagctgggcaacagagagagactctttcttaaatatatatattttatatatat -atagatacacacacacacacacacacacacac---------------------------- -------atatatatatatatatatatatatatatatatatgcatgcatgccagatgcagt -ggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgaggtca -ggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaaaat -tagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcaggaga -atcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactccag -cctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatctatag -atatatatctagatatagatctatgagtatatatctatagatatctagatatatatttat -agatagatatatctatagatatctatatatttctatcgatagagatatctatagatatct -atcaatatatctatagatttctagagatatgtatctagatataaatctatagacatagat -atagatatatagatatttaactgccaatgtcctaaacactttatactcaacacatttttt -ataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatagtat -ctatctagatatctgtgtagatgtctagatatctatctagatat-----tatctatctag -atatctgtcgctatctagatatctatctagatatctgtcgctatctagatatctatctag -atatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatc -tagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagata -tctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatc -tagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtc -gctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagta -tctgtcgctatctagatatctatctagatagtatctgtcgcta----------------- ------------------------------------------------------------- ----------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a482ea03632d092e1e2b08a17721ef54.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a482ea03632d092e1e2b08a17721ef54.msa deleted file mode 100644 index 8e000e6a..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a482ea03632d092e1e2b08a17721ef54.msa +++ /dev/null @@ -1,75 +0,0 @@ ->syndip_1_chr20:5039949-5040499 -ggcagaaagagttagacaggtattgggttagccagcctacagtgtctaacacaccaacaa -aatcaagcattggagagcatttggatatggaagagtgctgagaaggtgtggtggctcatg -cctataatcctagtactttgggaggctgaggcaggaggatcacttaagtccaggagtttg -agagcagcctgggcaacaaagtgagaccttgtctctacaaaaaataaacaaaattagctg -gtggtggcacctgcctgttgtcccagctactcagggggctgaggtgggaggatggcttga -gcctgggagattgaagcttcagttagccatgatcatgccactgcgctccagcctgggtga -cagagagagatcctgcctcaaaaaaaaaaataaaaataaaaaagaggggccgggtgtggt -ggctcaggcctgtaatcttagcactctttgggaggctgagactggaggatcctttgagcc -caggggtttgagaccagcctgggcaacatagggagaacttgtctctatttaaaaaaaaaa -at---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------gctcatacgt ->syndip_2_chr20:5039949-5040499 -ggcagaaagagttagacaggtattgggttagccagcctacagtgtctaacacaccaacaa -aatcaagcattggagagcatttggatatggaagagtgctgagaaggtgtggtggctcatg -cctataatcctagtactttgggaggctgaggcaggaggatcacttaagtccaggagtttg -agagcagcctgggcaacaaagtgagaccttgtctctacaaaaaataaacaaaattagctg -gtggtggcacctgcctgttgtcccagctactcagggggctgaggtgggaggatggcttga -gcctgggagattgaagcttcagttagccatgatcatgccactgcgctccagcctgggtga -cagagagagatcctgcctc-aaaaaaaaaataaaaataaaaaagaggggccgggtgtggt -ggctcaggcctgtaatcttagcactctttgggaggctgagactggaggatcctttgagcc -caggggtttgagaccagcctgggcaacatagggagaacttgtctctatttaaaaaaaaaa -at---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------gctcatacgt ->p:HG002_1_chr20:5039949-5040499 -ggcagaaagagttagacaggtattgggttagccagcctacagtgtctaacacaccaacaa -aatcaagcattggagagcatttggatatggaagagtgctgagaaggtgtggtggctcatg -cctataatcctagtactttgggaggctgaggcaggaggatcacttaagtccaggagtttg -agagcagcctgggcaacaaagtgagaccttgtctctacaaaaaataaacaaaattagctg -gtggtggcacctgcctgttgtcccagctactcagggggctgaggtgggaggatggcttga -gcctgggagattgaagcttcagttagccatgatcatgccactgcgctccagcctgggtga -cagagagagatcctgcctc-aaaaaaaaaataaaaataaaaaagaggggccgggtgtggt -ggctcaggcctgtaatcttagcactctttgggaggctgagactggaggatcttttgagcc -caggggtttgagaccagcctgggcaacatagggagaacttgtctctatttaaaaaaaaag -gccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggtggat -catgaggtcaggagatcgagaccatcctggctaaaacggtgaaaccccgtctctactaaa -aatacaaaaaattagccgggcgcggtggcgggcgcctaggcaggagaatggcgtgaaccc -gggaagcggagcttgcagtgagccgagattgcgccactgcagtccgcagtccgacctggg -cgacagagagagactccgtctcaaaaaaaaaaaaaaaaaaaaaaatgctcatacgt ->p:HG002_2_chr20:5039949-5040499 -ggcagaaagagttagacaggtattgggttagccagcctacagtgtctaacacaccaacaa -aatcaagcattggagagcatttggatatggaagagtgctgagaaggtgtggtggctcatg -cctataatcctagtactttgggaggctgaggcaggaggatcacttaagtccaggagtttg -agagcagcctgggcaacaaagtgagaccttgtctctacaaaaaataaacaaaattagctg -gtggtggcacctgcctgttgtcccagctactcagggggctgaggtgggaggatggcttga -gcctgggagattgaagcttcagttagccatgatcatgccactgcgctccagcctgggtga -cagagagagatcctgcctcaaaaaaaaaaataaaaataaaaaagaggggccgggtgtggt -ggctcaggcctgtaatcttagcactctttgggaggctgagactggaggatcttttgagcc -caggggtttgagaccagcctgggcaacatagggagaacttgtctctattttaaaaaaaag -gccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggtggat -catgaggtcaggagatcgagaccatcctggctaaaacggtgaaaccccgtctctactaaa -aatacaaaaaattagccgggcgcggtggcgggcgcctaggcaggagaatggcgtgaaccc -gggaagcggagcttgcagtgagccgagattgcgccactgcagtccgcagtccgacctggg -cgacagagagagactccgtctc---aaaaaaaaaaaaaaaaaaaatgctcatacgt ->ref_chr20:5039949-5040499 -ggcagaaagagttagacaggtattgggttagccagcctacagtgtctaacacaccaacaa -aatcaagcattggagagcatttggatatggaagagtgctgagaaggtgtggtggctcatg -cctataatcctagtactttgggaggctgaggcaggaggatcacttaagtccaggagtttg -agagcagcctgggcaacaaagtgagaccttgtctctacaaaaaataaacaaaattagctg -gtggtggcacctgcctgttgtcccagctactcagggggctgaggtgggaggatggcttga -gcctgggagattgaagcttcagttagccatgatcatgccactgcgctccagcctgggtga -cagagagagatcctgcctc-aaaaaaaaaataaaaataaaaaagaggggccgggtgtggt -ggctcaggcctgtaatcttagcactctttgggaggctgagactggaggatcctttgagcc -caggggtttgagaccagcctgggcaacatagggagaacttgtctctatttaaaaaaaaaa -at---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------gctcatacgt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a581badea33e501a16d0fa1f334b802a.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a581badea33e501a16d0fa1f334b802a.msa deleted file mode 100644 index 79b1101e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a581badea33e501a16d0fa1f334b802a.msa +++ /dev/null @@ -1,185 +0,0 @@ ->syndip_1_chr20:8661711-8662857 -atggcctaaattgttattaacactgtttaaagcaggccaaatagtactagaggaagcaca -cagtctctggtgttctagtcttacaaactcaaacttacaagccaacctacgttaagtaat -tcataacttcagtatttaataaatcttcagtgaaaggcaagaggctacacacagtgacag -acccagagataaaccctgtgcccctagagatttgcactcctcttaaaagtgtatatatat -ataattatataattatttattatataattatatataattatataattatttattatataa -ttatatataattatataattatttattatataattatatataa-tatacaattatttatt -atataattatatataattatatatttattatatttat-----tatacagttatataataa -ataattatataattatatataattatata---------tatataattatatataattata -ta-----taattatataattatatataattg----------------------------- ---tatataattatttattatataattatat-----------attatttattatataatta -tata----------------attatat------------------attatttattatata ------------------------------------------------------------- -ttatataattatataattatatattatttattatata-----atatataattatatat-- ------tatttattatataattatatattatttatta---------tatatattatttatt -atata----------------------attatatattatgtattatataattatataatt -atatattatgtattatataat----------------tatatattatgtattatataatt -atataattatatattatgtattatataattatatattatttattatataattatataatt -atatattatttattatataattatataattatatattatttattatataat--------- -------------tatataattatatattatttattatataattatataattatatattat -tt--------attatataattatatattatttattatataattatatattatttattaca -taaatatatattatttattacataagtatatatcacttattatataattgcatataatta -tttattatataattgcatataa----ttattatataattgtatatagttatttattatat -aattgtatatagttatttattatataattctatataattatttattatctaattctatat -taaatataattatttattatc--------------------------------taattct -atattatatataattatttattatataattctatattatatataattattatataattct -atatataattatttattatataattctatacataagtatttattatataattatgtatat -aattatttattatataattatgtataatatgtaattatttattatataattatgtataat -atgtaattatttattatataattatgtataatatataattatttattatataattatgta -taatatataattatttattatataattatgtgttatgtataa----ttattatataatta -tgtataatatatatataattttttattatataattatgtataatatataattttttataa -ttatgtgtaatatataattatttatcatataattacaatatatattattaacataatatc -taaatatattaataatctaatatctataattaatataatatataaatattacttcttgaa -atccaacgtgcacctgaatcacctgagccgttgttaaaatgcagattcgagatcctgcat -ttctaacaagttactgggtgaggcagaagatgcttagcaaaggcccacaccgagtagcaa -agctctaagaagtaaagagaaggcgcattaagcatgaagataatgagatttcttcctgta -ggggacagttcatggaagagataacatttg ->syndip_2_chr20:8661711-8662857 -atggcctaaattgttattaacactgtttaaagcaggccaaatagtactagaggaagcaca -cagtctctggtgttctagtcttacaaactcaaacttacaagccaacctacgttaagtaat -tcataacttcagtatttaataaatcttcagtgaaaggcaagaggctacacacagtgacag -acccagagataaaccctgtgcccctagagatttgcactcctcttaaaagtgtatatatat -ataattatataattatttattatataatgatatataattatataattatttattatataa -tgatatataattatataattatttattatataattatatataattatataattatttatt -atataattatatataattatataattatttattatataattatatataattatataatta -tttattatataattatatataattatataattatttattatataattatatataattata -taattatttattatataattatatataattatataattatttattatataattatatata -attatataattatttattatataattatatataattatataattatttattatataatta -tatataatatacaattatttattatataattatatataatatacaattatttattatata -attatatataattatatatttattatatttattatacagttatataataaatatataatt -atatataaatatataattatatataattatatatatataattatatgtaattatatataa -ttatataattattatataattgtatataatatataattatataattatatattatttatt -atataatatataattatataattatatattatttattatataatatataattatataatt -atatattatttattatataattatatattatttattatatatattatttattatataatt -atataattatatattatttattatataattatatattatttattatataa-tatataatt -atatattatttattatataa-tatataattatatattatttattatataattatatatta -tgtattatataatatataattatatattatgtattatataattatataattatatattat -ttattatataattatataattatatattatttattacataattatatattatttattaca -taagtatatattatttattacataagtatatatcacttattatataattgtatataatta -tttattatataattgcatataattatttattatataattgtatatagttatttattatat -aattctatatagttatttattatataattctatataattatttattatctaattctatat -tatatataattatttattatctaattctatattatatataattatttattatataattct -atattatatataattatttattatataattctatattatatataattattatataattct -atatataattatttattatataattctatacataagtatttattatataattatgtatat -aattatttattatataattatgtataatatgtaattatttattatataattatgtataat -atataattgtttattatataattatgtataatatataattatttattatataattatgta -taatatataattatttattatataattatgtgttatgtataattatttattatataatta -tgtataatatatatataattttttattatataattatgtataatatataattttttataa -ttatgtgtaatatataattatttatcatataattacaatatatattattaacataatatc -taaatatattaataatctaatatctataattaatataatatataaatattacttcttgaa -atccaacgtgcacctgaatcacctgagccgttgttaaaatgcagattcgagatcctgcat -ttctaacaagttactgggtgaggcagaagatgcttagcaaaggcccacaccgagtagcaa -agctctaagaagtaaagagaaggcgcattaagcatgaagataatgagatttcttcctgta -ggggacagttcatggaagagataacatttg ->p:HG002_1_chr20:8661711-8662857 -atggcctaaattgttattatcactgtttaaagcaggccaaatagtactagaggaagcaca -cagtctctggtattctagtcttacaaactcaaacttacaagccaacctacgttaagtaat -tcataacttcagtattcaataaatcttcagtgaaaggcaagaggctacacacagtgacag -acccagagataaaccctgtgcccctagagatttgcactcctcttaaaagtgtatatatat -ataattatataattatttattatataatgatatataattatataattatttattatataa -tgatatataattatataattatttattatataattatatataattatataattatttatt -atataattatatataattatataattatttattatataattatatataattatataatta -tttattatataattatatataattatataattatttattatataattatatataattata -taattatttattatataattatatataattatataattatttattatataattatatata -attatataattatttattatataattatatataattatataattatttattatataatta -tatataatatacaattatttattatataattatatataatatacaattatttattatata -attatatataattatatatttattatatttattatacagttatataataaatatataatt -atatataaatatataattatatataattatatatatataattatatgtaattatatataa -ttatataattattatataattgtatataatatataattatataattatatattatttatt -atataatatataattatataattatatattatttattatataatatataattatataatt -atatattatttattatataattatatattatttattatatatattatttattatataatt -atataattatatattatttattatataattatatattatttattatataa-tatataatt -atatattatttattatataa-tatataattatatattatttattatataattatatatta -tgtattatataatatataattatatattatgtattatataattatataattatatattat -ttattatataattatataattatatattatttattacataattatatattatttattaca -taagtatatattatttattacataagtatatatcacttattatataattgtatataatta -tttattatataattgcatataattatttattatataattgtatatagttatttattatat -aattctatatagttatttattatataattctatataattatttattatctaattctatat -tatatataattatttattatctaattctatattatatataattatttattatataattct -atattatatataattatttattatataattctatattatatataattattatataattct -atatataattatttattatataattctatacataagtatttattatataattatgtatat -aattatttattatataattatgtataatatgtaattatttattatataattatgtataat -atataattgtttattatataattatgtataatatataattatttattatataattatgta -taatatataattatttattatataattatgtgttatgtataattatttattatataatta -tgtataatatatatataattttttattatataattatgtataatatataattttttataa -ttatgtgtaatatataattatttatcatataattacaatatatattattaacataatatc -taaatatattaataatctaatatctataattaatataatatataaatattacttcttgaa -atccaacgtgcacctgaatcacctgagccgttgttaaaatgcagattcgagatcctgcat -ttctaacaagttactgggtgaggcagaagatgcttagcaaaggcccacaccgagtagcaa -agctctaagaagtaaagagaaggcgcattaagcatgaagataatgagatttcttcctgta -ggggacagttcatggaagagataacatttg ->p:HG002_2_chr20:8661711-8662857 -atggcctaaattgttattaacactgtttaaagcaggccaaatagtactagaggaagcaca -cagtctctggtgttctagtcttacaaactcaaacttacaagccaacctacgttaagtaat -tcataacttcagtatttaataaatcttcagtgaaaggcaagaggctacacacagtgacag -acccagagataaaccctgtgcccctagagatttgcactcctcttaaaagtgtatatatat -ataattatataattatttattatataattatatataattatataattatttattatataa -ttatatataattatataattatttattatataattatatataa-tatacaattatttatt -atataattatatataattatatatttattatatttat-----tatacagttatataataa -ataattatataattatatataattatata---------tatataattatatataattata -ta-----taattatataattatatataattg----------------------------- ---tatataattatttattatataattatat-----------attatttattatataatta -tata----------------attatat------------------attatttattatata ------------------------------------------------------------- -ttatataattatataattatatattatttattatata-----atatataattatatat-- ------tatttattatataattatatattatttatta---------tatatattatttatt -atata----------------------attatatattatgtattatataattatataatt -atatattatgtattatataat----------------tatatattatgtattatataatt -atataattatatattatgtattatataattatatattatttattatataattatataatt -atatattatttattatataattatataattatatattatttattatataat--------- -------------tatataattatatattatttattatataattatataattatatattat -tt--------attatataattatatattatttattatataattatatattatttattaca -taaatatatattatttattacataagtatatatcacttattatataattgcatataatta -tttattatataattgcatataa----ttattatataattgtatatagttatttattatat -aattgtatatagttatttattatataattctatataattatttattatctaattctatat -taaatataattatttattatc--------------------------------taattct -atattatatataattatttattatataattctatattatatataattattatataattct -atatataattatttattatataattctatacataagtatttattatataattatgtatat -aattatttattatataattatgtataatatgtaattatttattatataattatgtataat -atgtaattatttattatataattatgtataatatataattatttattatataattatgta -taatatataattatttattatataattatgtgttatgtataa----ttattatataatta -tgtataatatatatataattttttattatataattatgtataatatataattttttataa -ttatgtgtaatatataattatttatcatataattacaatatatattattaacataatatc -taaatatattaataatctaatatctataattaatataatatataaatattacttcttgaa -atccaacgtgcacctgaatcacctgagccgttgttaaaatgcagattcgagatcctgcat -ttctaacaagttactgggtgaggcagaagatgcttagcaaaggcccacaccgagtagcaa -agctctaagaagtaaagagaaggcgcattaagcatgaagataatgagatttcttcctgta -ggggacagttcatggaagagataacatttg ->ref_chr20:8661711-8662857 -atggcctaaattgttattaacactgtttaaagcaggccaaatagtactagaggaagcaca -cagtctctggtgttctagtcttacaaactcaaacttacaagccaacctacgttaagtaat -tcataacttcagtatttaataaatcttcagtgaaaggcaagaggctacacacagtgacag -acccagagataaaccctgtgcccctagagatttgcactcctcttaaaagtgtata----- -----------------------------tatatataattatataattatttattatataa -ttatatataattatataattatttattatataattatatataa-tatacaattatttatt -atataattatatataattatatatttattatatttat-----tatacagttatataataa -ataattatataattatatataattatata------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------ttatttattatctaattctatat -taaatataattatttattatc--------------------------------taattct -atattatatataattatttattatataattctatattatatataattattatataattct -atatataattatttattatataattctatacataagtatttattatataattatgtatat -aattatttattatataattatgtataatatgtaattatttattatataattatgtataat -atgtaattatttattatataattatgtataatatataattatttattatataattatgta -taatatataattatttattatataattatgtgttatgtataa----ttattatataatta -tgtataatatatatataattttttattatataattatgtataatatataattttttataa -ttatgtgtaatatataattatttatcatataattacaatatatattattaacataatatc -taaatatattaataatctaatatctataattaatataatatataaatattacttcttgaa -atccaacgtgcacctgaatcacctgagccgttgttaaaatgcagattcgagatcctgcat -ttctaacaagttactgggtgaggcagaagatgcttagcaaaggcccacaccgagtagcaa -agctctaagaagtaaagagaaggcgcattaagcatgaagataatgagatttcttcctgta -ggggacagttcatggaagagataacatttg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a5ec7e2b87aea7347111c17d3c5a7eee.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a5ec7e2b87aea7347111c17d3c5a7eee.msa deleted file mode 100644 index 8c650d91..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a5ec7e2b87aea7347111c17d3c5a7eee.msa +++ /dev/null @@ -1,95 +0,0 @@ ->syndip_1_chr20:63559088-63560163 -gttcctcctccaagtccacccacttcctgccccagggagatcctgaggccaggaggcagg -ctggcccaggcaggctgatggcggagggtggtggggagggtgggggggccctggactttc -cctcccagtcctggcaccttgcaggtggagagggctcttcaggaaggcatagttggcctc -ctgcagacgcgcacctggccggcaggcacgagggtctgctgagcctcgcagaagtccagg -aggctacgccagagggggcagcagcgcagaaggaggtggtctcctgtgagggtgggagtc -agatgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgggag---------- -------------------------------tcagtcagggtcaggtgggaggagtcaggg -tcagatgggagtcagtcagagtcaggtgggaggagtcagggtcaggtgggaggagtcagg -gtcaggt---cggagtcagggtcaggtgggaggagtcagggtcaggtgggagtcagtcag -ggtcaggtgggagg---------------------------------------------- ---------------------------------agtcagggtcaggtgggaggagtcaggg -tcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcagg -gtcaggtgggaggagtcagggtcaggtcggagtcagggtcaggcaggagtcggcagctcc -ctagcccagccctggcctcacctgtgttcccaccctggaagagcccagccccgccctcac -cgatcaggcagagcccctcctgggcccgcgtgacagccacattcacttggttggggtcca -caacgaagcccagaaacttcttgagccagctcttggtgggccgctggtccaggtcgctct -tggcacaggtgcggacggtgctcaccagcacatagcgccactcgctccctgcgggatggg -aggtgaggccctgctgccgctgcgcccaccctcccggccccacccacgagccccca ->syndip_2_chr20:63559088-63560163 -gttcctcctccaagtccacccacttcctgccccagggagatcctgaggccaggaggcagg -ctggcccaggcaggctgatggcggagggtggtggggagggtgggggggccctggactttc -cctcccagtcctggcaccttgcaggtggagagggctcttcaggaaggcatagttggcctc -ctgcagacgcgcacctggccggcaggcacgagggtctgctgagcctcgcagaagtccagg -aggctacgccagagggggcagcagcgcagaaggaggtggtctcctgtgagggtgggagtc -agatgggagtcagtcagggtcaggtggga------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------ggagtcagggtcaggtgggaggagtcagggtcaggtgggagtc------ ------------------------------------------------------------- ---------------------------------agtcagggtcaggtgggaggagtcaggg -tcaggtgggaggagtcagggtcagatgggagtcagtcagggtcaggtgggaggagtcagg -gtcaggtgggaggagtcagggtcaggtcggagtcagggtcaggcaggagtcggcagctcc -ctagcccagccctggcctcacctgtgttcccaccctggaagagcccagccccgccctcac -cgatcaggcagagcccctcctgggcccgcgtgacagccacattcacttggttggggtcca -caacgaagcccagaaacttcttgagccagctcttggtgggccgctggtccaggtcgctct -tggcacaggtgcggacggtgctcaccagcacatagcgccactcgctccctgcgggatggg -aggtgaggccctgctgccgctgcgcccaccctcccggccccacccacgagccccca ->p:HG002_1_chr20:63559088-63560163 -gttcctcctccaagtccacccacttcctgccccagggagatcctgaggccaggaggcagg -ctggcccaggcaggctgatggcggagggtggtggggagggtgggggggccctggactttc -cctcccagtcctggcaccttgcaggtggagagggctcttcaggaaggcatagttggcctc -ctgcagacgcgcacctggccggcaggcacgagggtctgctgagcctcgcagaagtccagg -aggctacgccagagggggcagcagcgcagaaggaggtggtctcctgtgagggtgggagtc -agatgggagtcagtcagggtcaggtggga------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------ggagtcagggtcaggtgggaggagtcagggtcaggtgggagtc------ ------------------------------------------------------------- ---------------------------------agtcagggtcaggtgggaggagtcaggg -tcaggtgggaggagtcagggtcagatgggagtcagtcagggtcaggtgggaggagtcagg -gtcaggtgggaggagtcagggtcaggtcggagtcagggtcaggcaggagtcggcagctcc -ctagcccagccctggcctcacctgtgttcccaccctggaagagcccagccccgccctcac -cgatcaggcagagcccctcctgggcccgcgtgacagccacgttcacttggttggggtcca -caacgaagcccagaaacttcttgagccagctcttggtgggccgctggtccaggtcgctct -tggcacaggtgcggacggtgctcaccagcacatagcgccactcgctccctgcgggatggg -aggtgaggccctgcggccgctgcgcccaccctcccggccccacccacgagccccca ->p:HG002_2_chr20:63559088-63560163 -gttcctcctccaagtccacccacttcctgccccagggagatcctgaggccaggaggcagg -ctggcccaggcaggctgatggcggagggtggtggggagggtgggggggccctggactttc -cctcccagtcctggcaccttgcaggtggagagggctcttcaggaaggcatagttggcctc -ctgcagacgcgcacctggccggcaggcacgagggtctgctgagcctcgcagaagtccagg -aggctacgccagagggggcagcagcgcagaaggaggtggtctcctgtgagggtgggagtc -agatgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgggag---------- -------------------------------tcagtcagggtcaggtgggaggagtcaggg -tcagatgggagtcagtcagagtcaggtgggaggagtcagggtcaggtgggaggagtcagg -gtcaggt---cggagtcagggtcaggtgggaggagtcagggtcaggtgggagtcagtcag -ggtcaggtgggagg---------------------------------------------- ---------------------------------agtcagggtcaggtgggaggagtcaggg -tcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcagg -gtcaggtgggaggagtcagggtcaggtcggagtcagggtcaggcaggagtcggcagctcc -ctagcccagccctggcctcacctgtgttcccaccctggaagagcccagccccgccctcac -cgatcaggcagagcccctcctgggcccgcgtgacagccacgttcacttggttggggtcca -caacgaagcccagaaacttcttgagccagctcttggtgggccgctggtccaggtcgctct -tggcacaggtgcggacggtgctcaccagcacatagcgccactcgctccctgcgggatggg -aggtgaggccctgcggccgctgcgcccaccctcccggccccacccacgagccccca ->ref_chr20:63559088-63560163 -gttcctcctccaagtccacccacttcctgccccagggagatcctgaggccaggaggcagg -ctggcccaggcaggctgatggcggagggtggtggggagggtgggggggccctggactttc -cctcccagtcctggcaccttgcaggtggagagggctcttcaggaaggcatagttggcctc -ctgcagacgcgcacctggccggcaggcacgagggtctgctgagcctcgcagaagtccagg -aggctacgccagagggggcagcagcgcagaaggaggtggtctcctgtgagggtgggagtc -agatgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgggaggagtcagggt -caggtgggagtcagtcagggtcaggtgggaggagtcagggtcaggtgggaggagtcaggg -tcagatgggagtcagtcagagtcaggtgggaggagtcagggtcaggtgggaggagtcagg -gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcag -agtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggt -caggtgggaggagtcagggtcaggtgggagtcagtcagggtcaggtgggaggagtcaggg -tcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcagg -gtcaggtgggaggagtcagggtcaggtcggagtcagggtcaggcaggagtcggcagctcc -ctagcccagccctggcctcacctgtgttcccaccctggaagagcccagccccgccctcac -cgatcaggcagagcccctcctgggcccgcgtgacagccacattcacttggttggggtcca -caacgaagcccagaaacttcttgagccagctcttggtgggccgctggtccaggtcgctct -tggcacaggtgcggacggtgctcaccagcacatagcgccactcgctccctgcgggatggg -aggtgaggccctgctgccgctgcgcccaccctcccggccccacccacgagccccca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a6346927c0c5fbdaadc9421ed1c6ae1a.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a6346927c0c5fbdaadc9421ed1c6ae1a.msa deleted file mode 100644 index 494766e3..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a6346927c0c5fbdaadc9421ed1c6ae1a.msa +++ /dev/null @@ -1,100 +0,0 @@ ->syndip_1_chr20:55627344-55628450 -gtcaagtatttatcactagtatgtgttaatataaatagcttaataaaaatagggcattta -tatgtatatatgtgggtgttcatgtatatatttttatatgtatatatgtgggtgtgcatg -tatacattaaatgatgaatttatatgtatatattaaatgtatatattatatgtatatatt -acatatatacatattgtatattacatatacataatacataaaatgtttaatacatacata -atatatacataatataatattgtatattattaaattatacatgtatatatgtatactata -tgtatatatgtatacaaaatatgtatataatatatacaaaaatatgtgtatttttgtaca -tatattgtacaaaaatatgtatattatatatacaaaatatgtatataatatatacatata -ttatgtaatataatatatacataatgtgtattacatacattatatgtaatatatacatat -attatata---atatatatgtatatattatatacatatatattatatacatatatgtata -tattatata-----------------catatatgtatacattatatattatgtatacata -tatgtatatatgtatacattatatattatgtatacatatatgtatatatgtatacattat -atattatgtatacatatatgtatatatgtatacattatatattatgtatacatatatgta -tatatgtatacattatatattatgtatacatatatgtatatatgtatacattatatatta -tgtatacatatatgtatatatgtatacattatatattatgtatacatatatgtata---- ------------------------------------------------------------- -------------------------------tatgtatacatgtatatacatatatacgta -tacacatatatacgtg--------tatatacgtatatacacgtatatattaaatgataaa -tttatatgtatatatgcgtgtgtgcacacacacacgagatatgttggttttgtgtaatgc -aaccaaataaattaagtatacataggagagagtcactgccctgactctt ->syndip_2_chr20:55627344-55628450 -gtcaagtatttatcactagtatgtgttaatataaatagcttaataaaaatagggcattta -tatgtatatatgtgggtgttcatgtatatatttttatatgtatatatgtgggtgtgcatg -tatacattaaatgatgaatttatatgtatatattaaatgtatatattatatgtatatatt -acatatatacatattgtatattacatatacataatacataaaatgtttaatacatacata -atatatacataatataatattgtatattattaaattatacatgtatatatgtatac---- --------atgtatacaaaatatgtatataatatatacaaaaa-atgtgtatttttgtaca -tatattgtacaaaaatatgtatattatatatacaaaatatgtatataatatatacatata -ttatgtaatataatatatacgtaatgtgtattacatacattatatgtaatatatacatat -atattatatacatatatatgtatatattatatacatatatattatatacatatatgtata -tattatatattatgtatacacatatgtatatatgtatatattatatattatgtatacaca -tatgtatatatgtatatattatatattatgtatacac--------atatgtatatattat -atattatgtatacacatatgtatatatgtatatattatatattatgtatac--------a -catatgtatatattatatattatgtatacacatatgtatatatgtatatattatatatta -tgtatacacatatgtatat--------attatatattatgtatacacatatgtatatatt -atatat------------------------------------------------------ -------------------------------tatgtatacacgtatatacatatatacgta -tacacgtatatacgta--tatacgtatatacgtatatacacgtatatattaaatgataaa -tttatatgtatatatgcgtgtgtgcacacacacacgagatatgttggttttgtgtaatgc -aaccaaataaattaagtatacataggagagagtcactgccctgactctt ->p:HG002_1_chr20:55627344-55628450 -gtcaagtatttatcactagtatgtgttaatataaatagcttaataaaaatagggcattta -tatgtatatatgtgggtgttcatgtatatatttttatatgtatatatgtgggtgtgcatg -tatacattaaatgatgaatttatatgtatatattaaatgtatatattatatgtatatatt -acatatatacatattgtatattacatatacataatacataaaatgtttaatacatacata -atatatacataatataatattgtatattattaaattatacatgtatatatgtatac---- --------atgtatacaaaatatgtatataatatatacaaaaa-atgtgtatttttgtaca -tatattgtacaaaaatatgtatattatatatacaaaatatgtatataatatatacatata -ttatgtaatataatatatacgtaatgtgtattacatacattatatgtaatatatacatat -atattatatacatatatatgtatatattatatacatatatattatatacatatatgtata -tattatatattatgtatacacatatgtatatatgtatatattatatattatgtatacaca -tatgtatatatgtatatattatatattatgtatacac--------atatgtatatattat -atattatgtatacacatatgtatatatgtatatattatatattatgtatac--------a -catatgtatatattatatattatgtatacacatatgtatatatgtatatattatatatta -tgtatacacatatgtatat--------attatatattatgtatacacatatgtatatatt -atatat------------------------------------------------------ -------------------------------tatgtatacacgtatatacatatatacgta -tacacgtatatacgta--tatacgtatatacgtatatacacgtatatattaaatgataaa -tttatatgtatatatgcgtgtgtgcacacacacacgagatatgttggttttgtgtaatgc -aaccaaataaattaagtatacataggagagagtcactgccctgactctt ->p:HG002_2_chr20:55627344-55628450 -gtcaagtatttatcactagtatgtgttaatataaatagcttaataaaaatagggcattta -tatgtatatatgtgggtgttcatgtatatatttttatatgtatatatgtgggtgtgcatg -tatacattaaatgatgaatttatatgtatatattaaatgtatatattatatgtatatatt -acatatatacatattgtatattacatatacataatacataaaatgtttaatacatacata -atatatacataatataatattgtatattattaaattatacatgtatatatgtatactata -tgtatatatgtatacaaaatatgtatataatatatacaaaaatatgtgtatttttgtaca -tatattgtacaaaaatatgtatattatatatacaaaatatgtatataatatatacatata -ttatgtaatataatatatacataatgtgtattacatacattatatgtaatatatacatat -attatata---atatatatgtatatattatatacatatatattatatacatatatgtata -tattatata-----------------catatatgtatacattatatattatgtatacata -tatgtatatatgtatacattatatattatgtatacatatatgtatatatgtatacattat -atattatgtatacatatatgtatatatgtatacattatatattatgtatacatatatgta -tatatgtatacattatatattatgtatacatatatgtatatatgtatacattatatatta -tgtatacatatatgtatatatgtatacattatatattatgtatacatatatgtata---- ------------------------------------------------------------- -------------------------------tatgtatacatgtatatacatatatacgta -tacacatatatacgtg--------tatatacgtatatacacgtatatattaaatgataaa -tttatatgtatatatgcgtgtgtgcacacacacacgagatatgttggttttgtgtaatgc -aaccaaataaattaagtatacataggagagagtcactgccctgagtctt ->ref_chr20:55627344-55628450 -gtcaagtatttatcactagtatgtgttaatataaatagcttaataaaaatagggcattta -tatgtatatatgtgggtgttcatgtatatatttttatatgtatatatgtgggtgtgcatg -tatacattaaatgatgaatttatatgtatatattaaatgtatatattatatgtatatatt -acatatatacatattgtatattacatatacataatacataaaatgtttaatacatacata -atatatacataatataatattgtatattattaaattatacatgtatatatgtatac---- --------atgtatacaaaatatgtatataatatatacaaaaa-atgtgtatttttgtaca -tatattgtacaaaaatatgtatattatatatacaaaatatgtatataatatatacatata -ttatgtaatataatatatacataatgtgtattacatacattatatgtaatatatacatat -atattatatacatatatat-tatata-catatatgtatatattatatacatatatgtata -tattatatattatgtatacacatatgtatatatgtatatattatatattatgtatacaca -tatgtatatatgtatatattatatattatgtatacacatatgtatatatgtatatattat -atattatgtatacacatatgtatatatgtatatattatatattatgtatacatatatgta -tatatgtatatattatatattatgtatacatatatgtatatatgtatatattatatatta -tgtatacatatatgtatat--------attatatattatgtatacatatatgtatatatt -atatattatgtatacatatatgtatatattatatattatgtatacatatatgtatatatt -atatattatgtatacatatatgtatatatgtatgtatacatgtatatacatatatacgta -tacacatatatacgtgtatatacatatatacgtatatacacgtatatattaaatgataaa -tttatatgtatatatgcgtgtgtgcacacacacacgagatatgttggttttgtgtaatgc -aaccaaataaattaagtatacataggagagagtcactgccctgactctt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a6f3026f51a93a438dcacef4d22f4901.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a6f3026f51a93a438dcacef4d22f4901.msa deleted file mode 100644 index 77ba8084..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a6f3026f51a93a438dcacef4d22f4901.msa +++ /dev/null @@ -1,50 +0,0 @@ ->syndip_1_chr20:62830612-62830838 -gctcccctgcaccccctctacccatgtaccacagtcccccaccccccaccgtgctccacc -------------------------------------------ccccaccacagtccccca -ccccccaccccagtccccaaacccctaccacagtcccccaa-ccccaccacagtccccca -ccccctaccacagtcccccaccccctaccacagtcccccaacccccaccacagtccccca -cccccaccacagtccgccaacccccatgacagtccctcaaccc--ccaccacagtccccc -aacccccatgacagtcccccaaccccc--------------------accacagtccccc -aacccccaccacagtccccaccccctaccacagtcccccaacccccaccacagtccccca -ccccctaccacaatccccca-cccccaccacagtcccctgggacgcagacagggagaggc -ccttgcag ->syndip_2_chr20:62830612-62830838 -gctcccctgcaccccctctacccatgtaccacagtcccccaccccccaccacagtccccc -accccccaccccagtccccaaacccctaccacagtcccccaaccccaccacagtccccca -ccccctaccacagtcccccaacccctaccacagtcccccaacccccaccacagtccccca -ccccc-accacagtccgccaacccccatgacagtcccccaacccccaccacagtccccca -cccccaccacagtccgccaacccccatgacagtcccccaaccc--ccaccacagtccccc -aacccccatgacagtcccccaacccccaccacagtcccccaacccctaccacagtccccc -aacccccaccacagtccccaccccctaccacagtcccccaacccccaccacagtccccca -ccccctaccacaatcccccaccccccaccacagtcccctgggacgcagacagggagaggc -ccttgcag ->p:HG002_1_chr20:62830612-62830838 -gctcccctgcaccccctctacccatgtaccacagtcccccaccccccaccacagtccccc -accccccaccccagtccccaaacccctaccacagtcccccaaccccaccacagtccccca -ccccctaccacagtcccccaacccctaccacagtcccccaacccccaccacagtccccca -ccccc-accacagtccgccaacccccatgacagtcccccaacccccaccacagtccccca -cccccaccacagtccgccaacccccatgacagtcccccaaccc--ccaccacagtccccc -aacccccatgacagtcccccaacccccaccacagtcccccaacccctaccacagtccccc -aacccccaccacagtccccaccccctaccacagtcccccaacccccaccacagtccccca -ccccctaccacaatcccccaccccccaccacagtcccctgggacgcagacagggagaggc -ccttgcag ->p:HG002_2_chr20:62830612-62830838 -gctcccctgcaccccctctacccatgtaccacagtcccccaccccccaccgtgctccacc -------------------------------------------ccccaccacagtccccca -ccccccaccccagtccccaaacccctaccacagtcccccaa-ccccaccacagtccccca -ccccctaccacagtcccccaccccctaccacagtcccccaacccccaccacagtccccca -cccccaccacagtccgccaacccccatgacagtccctcaaccc--ccaccacagtccccc -aacccccatgacagtcccccaaccccc--------------------accacagtccccc -aacccccaccacagtccccaccccctaccacagtcccccaacccccaccacagtccccca -ccccctaccacaatccccca-cccccaccacagtcccctgggacgcagacagggagaggc -ccttgcag ->ref_chr20:62830612-62830838 -g----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------ctcccctgcaccccctctacccatgtaccacagtccccc --acccccatgacagtcccccaacccccaccacagtcccccaacccctaccacagtccccc -aacccccaccacagtccccaccccctaccacagtcccccaacccccaccacagtccccca -ccccctaccacaatcccccaccccccaccacagtcccctgggacgcagacagggagaggc -ccttgcag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a7fa4251fe52e4107a6839e111b1195d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a7fa4251fe52e4107a6839e111b1195d.msa deleted file mode 100644 index b72c2aff..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a7fa4251fe52e4107a6839e111b1195d.msa +++ /dev/null @@ -1,85 +0,0 @@ ->syndip_1_chr20:63027797-63028366 -ggccagggcgggtgaattcccggggacccagcccttgcctgcaccaggagagtaagcgac -ttattaatagggtaatttatgcgggtgcctgcgcaccgggacggaccagcatctatcatg -gctgttttgcgtttcttgatttcacgatgtctgttgtgtgctcaggcccctcctctccaa -ggtcccagctgtccttgccctgttccctgtgaagagtgaagaaccaacgcgggcggggag -tggaccggtggggagagggccggtggggagagggccggtggggagaggaccggtggggag -ggggccggtggagagggggccggtggggagggggccggtggggagaggaccggtggggag -gggccggtggggagggggccggtggggagaggaccggtggggaggggccggtggggaggg -ggccggtggggagaggaccggtggggaggggccggtggggagggggccggcggggagggg -gccggcggggagggtgccggtggggagtggtctggtggggagggggccggtggggagggg -gcccgcggggaggggccggtggggagggggcctgcggggagggggccggcggggaggggc -cggtggggaggggccggtggggtggggccggtggggagggggccggtgggggggggcctg -cagggagggggccggtggggaggaggctggtgaagtagcgtcaggtgcgggcctggcgtc -ggcgagtcaagtcgagctgatccagggccttctttctgcagcttcatcaggttctcaatt -agcggagggcgctggcggtggaggagggcattagccgtgcctgctctcgggctctgcctg -ccagagtgccctcatgtggcatgagattaaggctcagcctctttcctgacagcaggtttt -ccattttt ->syndip_2_chr20:63027797-63028366 -ggccagggcgggtgaattcccggggacccagcccttgcctgcaccaggagagtaagcgac -ttattaatagggtaatttatgcgggtgcctgcgcaccgggacggaccagcatctatcatg -gctgttttgcgtttcttgatttcacgatgtctgttgtgtgctcaggcccctcctctccaa -ggtcccagctgtccttgccctgttccctgtgaagagtgaagaaccaacgcgggcggggag -tggaccggtggggagagggccggtggggagaggaccggtgggga---------------- -ggggccggtggagagggggccggtggggagggggccggcggggag--------------t -ggtttggtggggagggggccggtggggagggggcctgcggggaggggccggtggggag-- ----------------------------ggggccggtggggagggggccggcggggagggg -gccggcggggagggggccggcggggagtggtctggtggggag------------------ ------------ggggccggtggggagggggccggcggggagggggccggcggggaggggc -cggtggggagtggtctg------------------------------------------g -tggggagggggccggtggggaggaggctggtgaagtagcgtcaggtgcgggcctggcgtc -ggcgagtcaagtcgagctgatccagggccttctttctgcagcttcatcaggttctcaatt -agcggagggcgctggcggtggaggagggcattagccgtgcctgctctcgggctctgcctg -ccagagtgccctcatgtggcatgagattaaggctcagcctctttcctgacagcaggtttt -ccattttt ->p:HG002_1_chr20:63027797-63028366 -ggccagggcgggtgaattcccggggacccagcccttgcctgcaccaggagagtaagcgac -ttattaatagggtaatttatgcgggtgcctgcgcaccgggacggaccagcatctatcatg -gctgttttgcgtttcttgatttcacgatgtctgttgtgtgctcaggcccctcctctccaa -ggtcccagctgtccttgccctgttccctgtgaagagtgaagaaccaacgcgggcggggag -tggaccggtggggagagggccggtggggagaggaccggtgggga---------------- -ggggccggtggagagggggccggtggggagggggccggcggggag--------------t -ggtttggtggggagggggccggtggggagggggcctgcggggaggggccggtggggag-- ----------------------------ggggccggtggggagggggccggcggggagggg -gccggcggggagggggccggcggggagtggtctggtggggag------------------ ------------ggggccggtggggagggggccggcggggagggggccggcggggaggggc -cggtggggagtggtctg------------------------------------------g -tggggagggggccggtggggaggaggctggtgaagtagcgtcaggtgcgggcctggcgtc -ggcgagtcaagtcgagctgatccagggccttctttctgcagcttcatcaggttctcaatt -agcggagggcgctggcggtggaggagggcattagccgtgcctgctctcgggctctgcctg -ccagagtgccctcatgtggcatgagattaaggctcagcctctttcctgacagcaggtttt -ccattttt ->p:HG002_2_chr20:63027797-63028366 -ggccagggcgggtgaattcccggggacccagcccttgcctgcaccaggagagtaagcggc -ttattaatagggtaatttatgcgggtgcctgcgcaccgggacggaccagcatctatcatg -gctgttttgcgtttcttgatttcacgatgtctgttgtgtgctcaggcccctcctctccaa -ggtcccagctgtccttgccctgttccctgtgaagagtgaagaaccaacgcgggcggggag -tggaccggtggggagagggccggtggggagagggccggtggggagaggaccggtggggag -ggggccggtggagagggggccggtggggagggggccggtggggagaggaccggtggggag -gggccggtggggagggggccggtggggagaggaccggtggggaggggccggtggggaggg -ggccggtggggagaggaccggtggggaggggccggtggggagggggccggcggggagggg -gccggcggggagggtgccggtggggagtggtctggtggggagggggccggtggggagggg -gcccgcggggaggggccggtggggagggggcctgcggggagggggccggcggggaggggc -cggtggggaggggccggtggggtggggccggtggggagggggccggtgggggggggcctg -cagggagggggccggtggggaggaggctggtgaagtagcgtcaggtgcgggcctggcgtc -ggcgagtcaagtcgagctgatccagggccttctttctgcagcttcatcaggttctcaatt -agcggagggcgctggcggtggaggagggcattagccgtgcctgctctcgggctctgcctg -ccagagtgccctcatgtggcatgagattaaggctcagcctctttcctgacagcaggtttt -ccattttt ->ref_chr20:63027797-63028366 -ggccagggcgggtgaattcccggggacccagcccttgcctgcaccaggagagtaagcgac -ttattaatagggtaatttatgcgggtgcctgcgcaccgggacggaccagcatctatcatg -gctgttttgcgtttcttgatttcacgatgtctgttgtgtgctcaggcccctcctctccaa -ggtcccagctgtccttgccctgttccctgtgaagagtgaagaaccaacgcgggcggggag -tggaccggtggggagagggccggtggggagaggaccggtgggga---------------- -ggggccggtggagagggggccggtggggagggggccggcggggag--------------t -ggttt------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------ggtggggaggaggctggtgaagtagcgtcaggtgcgggcctggcgtc -ggcgagtcaagtcgagctgatccagggccttctttctgcagcttcatcaggttctcaatt -agcggagggcgctggcggtggaggagggcattagccgtgcctgctctcgggctctgcctg -ccagagtgccctcatgtggcatgagattaaggctcagcctctttcctgacagcaggtttt -ccattttt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a8ef332758ccf7a4733475f49a087d68.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a8ef332758ccf7a4733475f49a087d68.msa deleted file mode 100644 index 67d453fb..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a8ef332758ccf7a4733475f49a087d68.msa +++ /dev/null @@ -1,110 +0,0 @@ ->syndip_1_chr20:5039749-5040699 -aaatgatataactcccacatgtgtacctatgatcgattctgaacaaacactgatgttttg -ccaattgtgcttctattttttttccttaataaaacacgagagacacagtgtccaggattg -cattatgtggccaccccagatgaaggggagatgagaatgtgagtgttccgttttctaata -tgtataatacaggtaggctgggcagaaagagttagacaggtattgggttagccagcctac -agtgtctaacacaccaacaaaatcaagcattggagagcatttggatatggaagagtgctg -agaaggtgtggtggctcatgcctataatcctagtactttgggaggctgaggcaggaggat -cacttaagtccaggagtttgagagcagcctgggcaacaaagtgagaccttgtctctacaa -aaaataaacaaaattagctggtggtggcacctgcctgttgtcccagctactcagggggct -gaggtgggaggatggcttgagcctgggagattgaagcttcagttagccatgatcatgcca -ctgcgctccagcctgggtgacagagagagatcctgcctcaaaaaaaaaaataaaaataaa -aaagaggggccgggtgtggtggctcaggcctgtaatcttagcactctttgggaggctgag -actggaggatcctttgagcccaggggtttgagaccagcctgggcaacatagggagaactt -gtctctattt-------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------aaaaaa -aaaaatgctcatacgtggttggcaggagtgtaaatagcctcaaccaatttggaaagcaat -ttgccaatactagttaatataacgatctagatagtgggcaacccggattagccttttcca -gatatttgcagctgggaagctctcatacatgttcacagagatacctgcaaatgttcattt -cagc-tttttttttctcaatggcaaaaaactggaaat ->syndip_2_chr20:5039749-5040699 -aaatgatataactcccacatgtgtacctatgatcgattctgaacaaacactgatgttttg -ccaattgtgcttctattttttttccttaataaaacacgagagacacagtgtccaggattg -cattatgtggccaccccagatgaaggggagatgagaatgtgagtgttccgttttctaata -tgtataatacaggtaggctgggcagaaagagttagacaggtattgggttagccagcctac -agtgtctaacacaccaacaaaatcaagcattggagagcatttggatatggaagagtgctg -agaaggtgtggtggctcatgcctataatcctagtactttgggaggctgaggcaggaggat -cacttaagtccaggagtttgagagcagcctgggcaacaaagtgagaccttgtctctacaa -aaaataaacaaaattagctggtggtggcacctgcctgttgtcccagctactcagggggct -gaggtgggaggatggcttgagcctgggagattgaagcttcagttagccatgatcatgcca -ctgcgctccagcctgggtgacagagagagatcctgcctc-aaaaaaaaaataaaaataaa -aaagaggggccgggtgtggtggctcaggcctgtaatcttagcactctttgggaggctgag -actggaggatcctttgagcccaggggtttgagaccagcctgggcaacatagggagaactt -gtctctattt-------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------aaaaaa -aaaaatgctcatacgtggttggcaggagtgtaaatagcctcaaccaatttggaaagcaat -ttgccaatactagttaatataacgatctagatagtgggcaacccggattagccttttcca -gatatttgcagctgggaagctctcatacatgttcacagagatacctgcaaatgttcattt -cagcttttttttttctcaatggcaaaaaactggaaat ->p:HG002_1_chr20:5039749-5040699 -aaatgatataactcccacatgtgtacctatgatcgattctgaacaaacactgatgttttg -ccaattgtgcttctattttttttccttaataaaacacgagagacacagtgtccaggattg -cattatgtggccaccccagatgaaggggagatgagaatgtgagtgttccgttttctaata -tgtataatacaggtaggctgggcagaaagagttagacaggtattgggttagccagcctac -agtgtctaacacaccaacaaaatcaagcattggagagcatttggatatggaagagtgctg -agaaggtgtggtggctcatgcctataatcctagtactttgggaggctgaggcaggaggat -cacttaagtccaggagtttgagagcagcctgggcaacaaagtgagaccttgtctctacaa -aaaataaacaaaattagctggtggtggcacctgcctgttgtcccagctactcagggggct -gaggtgggaggatggcttgagcctgggagattgaagcttcagttagccatgatcatgcca -ctgcgctccagcctgggtgacagagagagatcctgcctc-aaaaaaaaaataaaaataaa -aaagaggggccgggtgtggtggctcaggcctgtaatcttagcactctttgggaggctgag -actggaggatcttttgagcccaggggtttgagaccagcctgggcaacatagggagaactt -gtctctatttaaaaaaaaaggccgggcgcggtggctcacgcctgtaatcccagcactttg -ggaggccgaggcgggtggatcatgaggtcaggagatcgagaccatcctggctaaaacggt -gaaaccccgtctctactaaaaatacaaaaaattagccgggcgcggtggcgggcgcctagg -caggagaatggcgtgaacccgggaagcggagcttgcagtgagccgagattgcgccactgc -agtccgcagtccgacctgggcgacagagagagactccgtctcaaaaaaaaaaaaaaaaaa -aaaaatgctcatacgtggttggcaggagtgtaaatagcctcaaccaatttggaaagcaat -ttgccaatactagttaatataacgatctagatagtgggcaacccggattagccttttcca -gatatttgcagctgggaagctctcatacatgttcacagagatacctgcaaatgttcattt -cagcttttttttttctcaatggcaaaaaactggaaat ->p:HG002_2_chr20:5039749-5040699 -aaatgatataactcccacatgtgtacctatgatcgattctgaacaaacactgatgttttg -ccaattgtgcttctattttttttccttaataaaacacgagagacacagtgtccaggattg -cattatgtggccaccccagatgaaggggagatgagaatgtgagtgttccgttttctaata -tgtataatacaggtaggctgggcagaaagagttagacaggtattgggttagccagcctac -agtgtctaacacaccaacaaaatcaagcattggagagcatttggatatggaagagtgctg -agaaggtgtggtggctcatgcctataatcctagtactttgggaggctgaggcaggaggat -cacttaagtccaggagtttgagagcagcctgggcaacaaagtgagaccttgtctctacaa -aaaataaacaaaattagctggtggtggcacctgcctgttgtcccagctactcagggggct -gaggtgggaggatggcttgagcctgggagattgaagcttcagttagccatgatcatgcca -ctgcgctccagcctgggtgacagagagagatcctgcctcaaaaaaaaaaataaaaataaa -aaagaggggccgggtgtggtggctcaggcctgtaatcttagcactctttgggaggctgag -actggaggatcttttgagcccaggggtttgagaccagcctgggcaacatagggagaactt -gtctctattttaaaaaaaaggccgggcgcggtggctcacgcctgtaatcccagcactttg -ggaggccgaggcgggtggatcatgaggtcaggagatcgagaccatcctggctaaaacggt -gaaaccccgtctctactaaaaatacaaaaaattagccgggcgcggtggcgggcgcctagg -caggagaatggcgtgaacccgggaagcggagcttgcagtgagccgagattgcgccactgc -agtccgcagtccgacctgggcgacagagagagactccgtctc---aaaaaaaaaaaaaaa -aaaaatgctcatacgtggttggcaggagtgtaaatagcctcaaccaatttggaaagcaat -ttgccaatactagttaatataacgatctagatagtgggcaacccggattagccttttcca -gatatttgcagccgggaagctctcatacatgttcacagagatacctgcaaatgttcattt -cagc-tttttttttctcaatggcaaaaaactggaaat ->ref_chr20:5039749-5040699 -aaatgatataactcccacatgtgtacctatgatcgattctgaacaaacactgatgttttg -ccaattgtgcttctattttttttccttaataaaacacgagagacacagtgtccaggattg -cattatgtggccaccccagatgaaggggagatgagaatgtgagtgttccgttttctaata -tgtataatacaggtaggctgggcagaaagagttagacaggtattgggttagccagcctac -agtgtctaacacaccaacaaaatcaagcattggagagcatttggatatggaagagtgctg -agaaggtgtggtggctcatgcctataatcctagtactttgggaggctgaggcaggaggat -cacttaagtccaggagtttgagagcagcctgggcaacaaagtgagaccttgtctctacaa -aaaataaacaaaattagctggtggtggcacctgcctgttgtcccagctactcagggggct -gaggtgggaggatggcttgagcctgggagattgaagcttcagttagccatgatcatgcca -ctgcgctccagcctgggtgacagagagagatcctgcctc-aaaaaaaaaataaaaataaa -aaagaggggccgggtgtggtggctcaggcctgtaatcttagcactctttgggaggctgag -actggaggatcctttgagcccaggggtttgagaccagcctgggcaacatagggagaactt -gtctctattt-------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------aaaaaa -aaaaatgctcatacgtggttggcaggagtgtaaatagcctcaaccaatttggaaagcaat -ttgccaatactagttaatataacgatctagatagtgggcaacccggattagccttttcca -gatatttgcagctgggaagctctcatacatgttcacagagatacctgcaaatgttcattt -cagc-tttttttttttcaatggcaaaaaactggaaat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ab25a3b3912003fe18c90ad0cc944954.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ab25a3b3912003fe18c90ad0cc944954.msa deleted file mode 100644 index 0cd8f02c..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ab25a3b3912003fe18c90ad0cc944954.msa +++ /dev/null @@ -1,155 +0,0 @@ ->syndip_1_chr20:8661911-8662657 -cccctagagatttgcactcctcttaaaa-------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------gtgtatatatatataattatataattatttattat -ataattatatataattatataattatttattatataattatatataattatataattatt -tattatataattatatataatatacaattatttattatataattatatataattatatat -ttattatatttattatacagttatataataaataattatataattatatataattatata -tatataattatatataattatatataattatataattatatataattgtatataattat- ----ttattatataattatatattatttattatataattatataattatatattatttatt -atatattatataattatataattatatattatttattatataa--------tatataatt -atatattatttattatataattatatattatttattatatatattatttattatataatt -atatattatgtattatataattatataattatatattatgtattatataattatatatta -tgtattatataattatataattatatattatgtattatataattatatattatttattat -ataattatataattatatattatttattatataattatataattatatattatttattat -ataattatataattatatattatttattatataattatataattatat-attatttatta -tataattatatattatttattatataattatatattatttattacataaatatatattat -ttattacataagtata---tatcacttattatataattgcatataattatttattatata -attgcatataa----ttattatataattgtatatagttatttattatataattgtatata -gttatttattatataattc-------tatataattatttattatctaattctatattaaa -tataattatttattatctaattctatattatatataattatttattatataattctatat -tatatataattattatataattctatatataattatttattatataattctatacataag -tatttattatataattatgtatataattatttattatataattatgtataatatgtaatt -atttattatataattatgtataatatgtaattatttattatataattatgtataatatat -aattatttattatataattatgtataatatataattatttattatataattatgtgttat -gtataa----ttattatataattatgtataatatatatataattttttattatataatta -tgtataatatataattttttataattatgtgtaatatataattatttatcatataattac -aatatatattattaacataatatctaaatatattaataatctaatatctataattaatat -aatatataaatattacttcttgaaatccaacgtg ->syndip_2_chr20:8661911-8662657 -cccctagagatttgcactcctcttaaaagtgtatatatatataattatataattatttat -tatataatgatatataattatataattatttattatataatgatatataattatataatt -atttattatataattatatataattatataattatttattatataattatatataattat -ataattatttattatataattatatataattatataattatttattatataattatatat -aattatataattatttattatataattatatataattatataattatttattatataatt -atatataattatataattatttattatataattatatataattatataattatttattat -ataattatatataattatataattatttattatataattatatataa-tatacaattatt -tattatataattatatataatatacaattatttattatataattatatataattatatat -ttattatatttattatacagttatataataaa----tatataattatatataa------a -tatataattatatataattatata----tatataattatatgtaattatatataattata -taattattatataattgtata-----taatatataattatataattatatattatttatt -atataatatataattatataattatatattatttattatataatatataattatataatt -atatattatttattatataattatatattatttattatatatattatt------------ -----------tattatataattatataattatatattatttattatataattatatatta -tttattatataa-tatataattatatattatttattatataatatataattatatattat --ttattatataattatatattatgtattatataa-tatataattatatattatgtattat -ataattatataattatatattatttattatataattatataattatat-attatttatta -cataattatatattatttattacataagtatatattatttattacataagtatatatcac -ttattatataattgtatataattatttattatataattgcatataattatttattatata -attgtatatagttatttattatataattctatatagttatttattatataattctatata -attatttattatctaattctatattatatataattatttattatctaattctatattata -tataattatttattatataattctatattatatataattatttattatataattctatat -tatatataattattatataattctatatataattatttattatataattctatacataag -tatttattatataattatgtatataattatttattatataattatgtataatatgtaatt -atttattatataattatgtataatatataattgtttattatataattatgtataatatat -aattatttattatataattatgtataatatataattatttattatataattatgtgttat -gtataattatttattatataattatgtataatatatatataattttttattatataatta -tgtataatatataattttttataattatgtgtaatatataattatttatcatataattac -aatatatattattaacataatatctaaatatattaataatctaatatctataattaatat -aatatataaatattacttcttgaaatccaacgtg ->p:HG002_1_chr20:8661911-8662657 -cccctagagatttgcactcctcttaaaagtgtatatatatataattatataattatttat -tatataatgatatataattatataattatttattatataatgatatataattatataatt -atttattatataattatatataattatataattatttattatataattatatataattat -ataattatttattatataattatatataattatataattatttattatataattatatat -aattatataattatttattatataattatatataattatataattatttattatataatt -atatataattatataattatttattatataattatatataattatataattatttattat -ataattatatataattatataattatttattatataattatatataa-tatacaattatt -tattatataattatatataatatacaattatttattatataattatatataattatatat -ttattatatttattatacagttatataataaa----tatataattatatataa------a -tatataattatatataattatata----tatataattatatgtaattatatataattata -taattattatataattgtata-----taatatataattatataattatatattatttatt -atataatatataattatataattatatattatttattatataatatataattatataatt -atatattatttattatataattatatattatttattatatatattatt------------ -----------tattatataattatataattatatattatttattatataattatatatta -tttattatataa-tatataattatatattatttattatataatatataattatatattat --ttattatataattatatattatgtattatataa-tatataattatatattatgtattat -ataattatataattatatattatttattatataattatataattatat-attatttatta -cataattatatattatttattacataagtatatattatttattacataagtatatatcac -ttattatataattgtatataattatttattatataattgcatataattatttattatata -attgtatatagttatttattatataattctatatagttatttattatataattctatata -attatttattatctaattctatattatatataattatttattatctaattctatattata -tataattatttattatataattctatattatatataattatttattatataattctatat -tatatataattattatataattctatatataattatttattatataattctatacataag -tatttattatataattatgtatataattatttattatataattatgtataatatgtaatt -atttattatataattatgtataatatataattgtttattatataattatgtataatatat -aattatttattatataattatgtataatatataattatttattatataattatgtgttat -gtataattatttattatataattatgtataatatatatataattttttattatataatta -tgtataatatataattttttataattatgtgtaatatataattatttatcatataattac -aatatatattattaacataatatctaaatatattaataatctaatatctataattaatat -aatatataaatattacttcttgaaatccaacgtg ->p:HG002_2_chr20:8661911-8662657 -cccctagagatttgcactcctcttaaaa-------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------gtgtatatatatataattatataattatttattat -ataattatatataattatataattatttattatataattatatataattatataattatt -tattatataattatatataatatacaattatttattatataattatatataattatatat -ttattatatttattatacagttatataataaataattatataattatatataattatata -tatataattatatataattatatataattatataattatatataattgtatataattat- ----ttattatataattatatattatttattatataattatataattatatattatttatt -atatattatataattatataattatatattatttattatataa--------tatataatt -atatattatttattatataattatatattatttattatatatattatttattatataatt -atatattatgtattatataattatataattatatattatgtattatataattatatatta -tgtattatataattatataattatatattatgtattatataattatatattatttattat -ataattatataattatatattatttattatataattatataattatatattatttattat -ataattatataattatatattatttattatataattatataattatat-attatttatta -tataattatatattatttattatataattatatattatttattacataaatatatattat -ttattacataagtata---tatcacttattatataattgcatataattatttattatata -attgcatataa----ttattatataattgtatatagttatttattatataattgtatata -gttatttattatataattc-------tatataattatttattatctaattctatattaaa -tataattatttattatctaattctatattatatataattatttattatataattctatat -tatatataattattatataattctatatataattatttattatataattctatacataag -tatttattatataattatgtatataattatttattatataattatgtataatatgtaatt -atttattatataattatgtataatatgtaattatttattatataattatgtataatatat -aattatttattatataattatgtataatatataattatttattatataattatgtgttat -gtataa----ttattatataattatgtataatatatatataattttttattatataatta -tgtataatatataattttttataattatgtgtaatatataattatttatcatataattac -aatatatattattaacataatatctaaatatattaataatctaatatctataattaatat -aatatataaatattacttcttgaaatccaacgtg ->ref_chr20:8661911-8662657 -cccctagagatttgcactcctcttaaa--------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------agtgtatatatatataattatataattatttatta -tataattatatataattatata-----------attatttattatataattatatataat -atac---------------aattatttattatataattatatataattatat-------- -atttattatat----ttattatacagt--tatataataaataattatataattatatata -attatat-------------------------attatttattatctaattctatattaaa -tataattatttattatctaattctatattatatataattatttattatataattctatat -tatatataattattatataattctatatataattatttattatataattctatacataag -tatttattatataattatgtatataattatttattatataattatgtataatatgtaatt -atttattatataattatgtataatatgtaattatttattatataattatgtataatatat -aattatttattatataattatgtataatatataattatttattatataattatgtgttat -gtataa----ttattatataattatgtataatatatatataattttttattatataatta -tgtataatatataattttttataattatgtgtaatatataattatttatcatataattac -aatatatattattaacataatatctaaatatattaataatctaatatctataattaatat -aatatataaatattacttcttgaaatccaacgtg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_abdba6c7928c969dac93be53f6bf0a92.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_abdba6c7928c969dac93be53f6bf0a92.msa deleted file mode 100644 index e94f6f5e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_abdba6c7928c969dac93be53f6bf0a92.msa +++ /dev/null @@ -1,90 +0,0 @@ ->syndip_1_chr20:57110012-57110985 -gttgtgtcgccaggctctgagcacttaggctacaaacggagcacagactctgagggctgg -ggtcgctgctgctcctgcaaacagcccatgctcccagtctagaaaaatcctccagaagat -gacagttccagttgatgggactgacaagccccccacaggaaggcagtctccagctgacca -ctgttccgtgaggctgtctgagcaggcttcgctatgcacgcataatagcgacagcgcaaa -cagcagcagcagcagcagcctcagctggctcggcggggcttggctcagcgtgtgcggggt -gctgagctaagtcttcccaaacggcgtgtgcggggtgctgcgctgtcttccagatccgct -tgtgcagggcgctgtgctgtcttctggttcggcgtgtgcggggcgctgtgctaagtcttc -cggctgggcgtgtgcggggcgctgtgctaagtcttccggctgggcgtgtgcggggc---- ------------------------------------------------------------- -------------------------------------------gctgtgctaagtcttccg -gctgggcgtgtgcggggcgctgtgctgtcttccggttcggcgtgtgcggggcgttatgct -aagtcttccggctgggcgtgtgcggggcgctgtgctgtcttccggttcggcgtgtgcggg -gcgctgtgctaagtcttccggctgcattcgcactctttccctccgactcaaccatggcag -tgaggcactgttttgttttgctttgcttctcaattttcctgtggtaaaatacacctaata -ttcaccatcttaaccgtttttaagtgtacagttcagtggcattaagtaccttcataatat -tatacaaccatcaccatctccagaaccctttcattttcccaaactgaaactctgtccctg -ttaaacactaactc ->syndip_2_chr20:57110012-57110985 -gttgtgtcgccaggctctgagcacttaggctacaaacggagcacagactctgagggctgg -ggtcgctgctgctcctgcaaacagcccatgctcccagtctagaaaaatcctccagaagat -gacagttccagttgatgggactgacaagccccccacaggaaggcagtctccagctgacca -ctgttccgtgaggctgtctgagcaggcttcgctatgcacgcataatagcgacagcgcaaa -cagcagcagcagcagcagcctcagctggctcggcggggcttggctcagcgtgtgcggggt -gctgagctaagtcttcccaaacggcgtgtgcggggtgctgcgctgtcttccagatccgct -tgtgcagggcgctgtgctgtcttctggttc------------------------------ -------ggcgtgtgcggggcgctgtgctaagtcttccggctgggcgtgtgcggggc---- ------------------------------------------------------------- -------------------------------------------gctgtgctaagtcttccg -gctgggcgtgtgcggggcgctgtgctgtcttccggttcggcgtgtgcggggcgttatgct -aagtcttccggctgggcgtgtgcggggcgctgtgctgtcttccggttcggcgtgtgcggg -gcgctgtgctaagtcttccggctgcattcgcactctttccctccgactcaaccatggcag -tgaggcactgttttgttttgctttgcttctcaattttcctgtggtaaaatacacctaata -ttcaccatcttaaccgtttttaagtgtacagttcagtggcattaagtaccttcataatat -tatacaaccatcaccatctccagaaccctttcattttcccaaactgaaactctgtccctg -ttaaacactaactc ->p:HG002_1_chr20:57110012-57110985 -gttgtgtcgccaggctctgagcacttaggctacaaacggagcacagactctgagggctgg -ggtcgctgctgctcctgcaaacagcccatgctcccagtctagaaaaatcctccagaagat -gacagttccagttgatgggactgacaagccccccacaggaaggcagtctccagctgacca -ctgttccgtgaggctgtctgagcaggcttcgctatgcacgcataatagcgacagcgcaaa -cagcagcagcagcagcagcctcagctggctcggcggggcttggctcagcgtgtgcggggt -gctgagctaagtcttcccaaacggcgtgtgcggggtgctgcgctgtcttccagatccgct -tgtgcagggcgctgtgctgtcttctggttc------------------------------ -------ggcgtgtgcggggcgctgtgctaagtcttccggctgggcgtgtgcggggc---- ------------------------------------------------------------- -------------------------------------------gctgtgctaagtcttccg -gctgggcgtgtgcggggcgctgtgctgtcttccggttcggcgtgtgcggggcgttatgct -aagtcttccggctgggcgtgtgcggggcgctgtgctgtcttccggttcggcgtgtgcggg -gcgctgtgctaagtcttccggctgcattcgcactctttccctccgactcaaccatggcag -tgaggcactgttttgttttgctttgcttctcaattttcctgtggtaaaatacacctaata -ttcaccatcttaaccgtttttaagtgtacagttcagtggcattaagtaccttcataatat -tatacaaccatcaccatctccagaaccctttcattttcccaaactgaaactctgtccctg -ttaaacactaactc ->p:HG002_2_chr20:57110012-57110985 -gttgtgtcgccaggctctgagcacttaggctacaaacggagcacagactctgagggctgg -ggtcgctgctgctcctgcaaacagcccatgctcccagtctagaaaaatcctccagaagat -gacagttccagttgatgggactgacaagccccccacaggaaggcagtctccagctgacca -ctgttccgtgaggctgtctgagcaggcttcgctatgcacgcataatagcgacagcgcaaa -cagcagcagcagcagcagcctcagctggctcggcggggcttggctcagcgtgtgcggggt -gctgagctaagtcttcccaaacggcgtgtgcggggtgctgcgctgtcttccagatccgct -tgtgcagggcgctgtgctgtcttctggttcggcgtgtgcggggcgctgtgctaagtcttc -cggctgggcgtgtgcggggcgctgtgctaagtcttccggctgggcgtgtgcggggc---- ------------------------------------------------------------- -------------------------------------------gctgtgctaagtcttccg -gctgggcgtgtgcggggcgctgtgctgtcttccggttcggcgtgtgcggggcgttatgct -aagtcttccggctgggcgtgtgcggggcgctgtgctgtcttccggttcggcgtgtgcggg -gcgctgtgctaagtcttccggctgcattcgcactctttccctccgactcaaccatggcag -tgaggcactgttttgttttgctttgcttctcaattttcctgtggtaaaatacacctaata -ttcaccatcttaaccgtttttaagtgtacagttcagtggcattaagtaccttcataatat -tatacaaccatcaccatctccagaaccctttcattttcccaaactgaaactctgtccctg -ttaaacactaactc ->ref_chr20:57110012-57110985 -gttgtgtcgccaggctctgagcacttaggctacaaacggagcacagactctgagggctgg -ggtcgctgctgctcctgcaaacagcccatgctcccagtctagaaaaatcctccagaagat -gacagttccagttgatgggactgacaagccccccacaggaaggcagtctccagctgacca -ctgttccgtgaggctgtctgagcaggcttcgctatgcacgcataatagcgacagcgcaaa -cagcagcagcagcagcagcctcagctggctcggcggggcttggctcagcgtgtgcggggt -gctgagctaagtcttcccaaacggcgtgtgcggggtgctgcgctgtcttccagatccgct -tgtgcagggcgctgtgctgtcttctggttcggcgtgtgcggggcgctgtgctaagtcttc -cggctgggcgtgtgcggggcgctgtgctaagtcttccggctgggcgtgtgcggggcgctg -tgctaagtcttccggctgggcgtgtgcggggcgctgtgctgtcttccggttcggcgtgtg -cggggcgctgtgctaagtcttccggctgggcgtgtgcggggtgctgtgctaagtcttccg -gctgggcgtgtgcggggcgctgtgctgtcttccggttcggcgtgtgcggggcgttatgct -aagtcttccggctgggcgtgtgcggggcgctgtgctgtcttccggttcggcgtgtgcggg -gcgctgtgctaagtcttccggctgcattcgcactctttccctccgactcaaccatggcag -tgaggcactgttttgttttgctttgcttctcaattttcctgtggtaaaatacacctaata -ttcaccatcttaaccgtttttaagtgtacagttcagtggcattaagtaccttcataatat -tatacaaccatcaccatctccagaaccctttcattttcccaaactgaaactctgtccctg -ttaaacactaactc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ad9413a98dbfef4e588d42dda31a3447.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ad9413a98dbfef4e588d42dda31a3447.msa deleted file mode 100644 index 55d97bfb..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ad9413a98dbfef4e588d42dda31a3447.msa +++ /dev/null @@ -1,35 +0,0 @@ ->syndip_1_chr20:23560883-23561191 -ttattccctaatgttcttcagcattcctttctctctctttctttctttctttctttcttt -ccttccttccttccttccttccttccttccttccttccttccttccttcct---ttcttt -ctttctttctttctttctttctttctttctttttttctttctttctttctttctttttct -ttt--------------------------------------------------------- -----------------------------------------------------------ac -agagtcttactcttgttgccc ->syndip_2_chr20:23560883-23561191 -ttattccctaatgttcttcagcattcctttctctctctttctttctttctttctttcttt -ctttctttctttctttctttctttctttccttccttccttccttccttccttccttcctt -ccttccttccttctttccttctttccttctttccttctttccttctttccttctttcctt -ctttccttctttccttctttctttctttctttctttctttctttctttctttctttcttt -ctttctttctttctttctttctttctttctttctttcttctttctttctttttcttttac -agagtcttactcttgttgccc ->p:HG002_1_chr20:23560883-23561191 -ttattccctaatgttcttcagcattcctttctctctctttctttctttctttctttcttt -ctttctttctttctttctttctttctttccttccttccttccttccttccttccttcctt -ccttccttccttctttccttctttccttctttccttctttccttctttccttctttcctt -ctttccttctttccttctttctttctttctttctttctttctttctttctttctttcttt -ctttctttctttctttctttctttctttctttctttcttctttctttctttttcttttac -agagtcttactcttgttgccc ->p:HG002_2_chr20:23560883-23561191 -ttattccctaatgttcttcagcattcctttctctctctttctttctttctttctttcttt -ccttccttccttccttccttccttccttccttccttccttccttccttcct---ttcttt -ctttctttctttctttctttctttctttctttttttctttctttctttctttctttttct -ttt--------------------------------------------------------- -----------------------------------------------------------ac -agagtcttactcttgttgccc ->ref_chr20:23560883-23561191 -ttattccctaatgttcttcagcattcctttctctttctttctttctttctttctttcttt -ctttctttctttctttccttctttccttccttccttccttccttccttccttccttcctt -ccttccttccttccttccttctttccttctttccttctttccttctttccttctttcctt -ctttccttctttcc------------ttctttccttctttccttctttctttctttcttt -ctttctttctttctttctttctttctttctttctttcttctttctttctttttcttttac -agagtcttactcttgttgccc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ae169973544e2359dc86d68707dc0299.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ae169973544e2359dc86d68707dc0299.msa deleted file mode 100644 index db2f4fc4..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ae169973544e2359dc86d68707dc0299.msa +++ /dev/null @@ -1,35 +0,0 @@ ->syndip_1_chr20:37361752-37362058 -ctgagcaggggcagggcaggagtgctgctgagggc------------------------- ------------------------------------------------------------- ----------------ctctgtgtgcaggtagagatgccggggtctctgtgtgcaggtaga -gatgccggggtctctgtgtgcaggtagagatgtagagatgctggggtctctgtgtgcagg -tagagatgctggggtctctgtgtgcaggcagagatgctgaagcccaggttagctcttatt -tatgtct ->syndip_2_chr20:37361752-37362058 -ctgagcaggggcagggcaggagtgctgctgagggcctctgtgtgcaggtagagatgccgg -ggtctctgtgtgcag--------------------------------------------g -tagagatgccggggtctctgtgtgcaggtagagatgccggggtctctgtgtgcaggtaga -gatgccggggtctctgtgtgcaggtagagatgtagagatgctggggtctctgtgtgcagg -tagagatgctggggtctctgtgtgcaggcagagatgctgaagcccaggttagctcttatt -tatgtct ->p:HG002_1_chr20:37361752-37362058 -ctgagcaggggcagggcaggagtgctgctgagggcctctgtgtgcaggtagagatgccgg -ggtctctgtgtgcag--------------------------------------------g -tagagatgccggggtctctgtgtgcaggtagagatgccggggtctctgtgtgcaggtaga -gatgccggggtctctgtgtgcaggtagagatgtagagatgctggggtctctgtgtgcagg -tagagatgctggggtctctgtgtgcaggcagagatgctgaagcccaggttagctcttatt -tatgtct ->p:HG002_2_chr20:37361752-37362058 -ctgagcaggggcagggcaggagtgctgctgagggc------------------------- ------------------------------------------------------------- ----------------ctctgtgtgcaggtagagatgccggggtctctgtgtgcaggtaga -gatgccggggtctctgtgtgcaggtagagatgtagagatgctggggtctctgtgtgcagg -tagagatgctggggtctctgtgtgcaggcagagatgctgaagcccaggttagctcttatt -tatgtct ->ref_chr20:37361752-37362058 -ctgagcaggggcagggcaggagtgctgctgagggcctctgtgtgcaggtagagatgccgg -ggtctctgtgtgcaggtagagatgtagagatgccggggtctctgtgtgcaggtagagatg -tagagatgccggggtctctgtgtgcaggtagagatgccggggtctctgtgtgcaggtaga -gatgccggggtctctgtgtgcaggtagagatgtagagatgctggggtctctgtgtgcagg -tagagatgctggggtctctgtgtgcaggcagagatgctgaagcccaggttagctcttatt -tatgtct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ae5709c59aa7d27ae6fea6fdb071269f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ae5709c59aa7d27ae6fea6fdb071269f.msa deleted file mode 100644 index 8003cae4..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ae5709c59aa7d27ae6fea6fdb071269f.msa +++ /dev/null @@ -1,640 +0,0 @@ ->syndip_1_chr20:63693325-63693884 -aaggcagtgtgggccagagtcctgggctgcttggggtgggcatcctcgggccctgcttgg -ccccgcctctctgttcccctatgggagtgatgggggcctccacctccaccaccagcacca -gcagcaccacctccaccttcaccaccaccacctccaccaccacctccaccacctccacct -ccaccacctccaccacctccaccaccaccacctccaccaccaccacctccaccaccacca -ccaccaccacctccaccaccaccaccaccaccaccacctccacctccaccacctccacca -ccacctccacctccaccaccacctccacctccacctccaccaccaccacctccaccacct -ccaccacctccacctccaccaccacctccacctccaccaccacctccacctccacctcca -cctccacctccaccaccaccacctccaccacctccaccacctccacctccaccaccacca -cctccacctccacctccaccacctccacctccaccacctccacctccaccacctccacca -ccaccaccaccaccaccaccacctccaccaccaccaccaccaccacctccaccacctcca -cctccaccacctccaccaccaccacctccaccaccacctccaccaccacctccacctcca -ccacctccacctccaccacctccacctccacctccaccaccacctccaccacctccacca -ccacctccaccacctccacctccaccaccaccacctccaccaccaccaccaccaccacct -ccaccacctccacctccaccacctccaccaccaccacctccaccaccacctccaccacca -cctccacctccaccacctccacctccaccacctccacctccacctccaccaccacctcca -ccacctccaccaccacctccaccacctccaccacctccaccaccacctccaccacctcca -cctccaccaccaccacctccacctccaccaccaccacctccaccaccacctccacctcca -ccaccaccacctccacctccaccaccaccacctccaccaccacctccaccaccaccacca -ccaccaccacctccacctccaccacctccaccaccaccaccaccacctccacctccacca -cctccaccacctccaccaccaccaccaccacctccaccacctccaccaccacctccacca -cctccacctccaccaccaccacctccaccaccaccacctccacctccacctccacctcca -cctccaccaccacctccacctccaccaccacctccaccaccacctccacctccaccacct -ccacctccacctccaccacctccaccaccaccaccaccaccaccaccaccaccaccacct -ccaccacctccacctccacctccaccaccaccaccaccacctccaccaccaccaccacca -cctccaccacctccaccaccacctccaccaccaccaccaccaccaccaccaccacctcca -ccacctccacctccacctccacctccaccacctccaccacctccaccaccacctccacca -ccaccaccaccacctccaccaccacctccacctccaccaccacctccaccaccacctcca -cctccaccacctccacctccaccacctccaccacctccacctccaccacctccacctcca -cctccaccacctccaccaccaccaccaccaccaccaccaccaccaccacctccaccacca -ccacctccaccaccacctccaccacctccaccaccacctccaccaccaccaccaccacca -ccaccaccaccaccacctccaccaccacctccacctccaccaccacctccaccaccacct -ccacctccaccacctccacctccaccacctccaccacctccaccaccaccaccaccacct -ccaccaccacctccacctccaccaccaccaccaccaccaccacctccaccaccaccacct -ccaccaccacctccaccacctccaccaccacctccacctccaccacctccaccaccacct -ccaccaccacctccaccaccaccacctccaccaccacctccaccacctccaccaccacct -ccacctccaccacctccaccaccacctccaccaccacctccaccaccaccacctccacca -ccacctccaccacctccaccaccacctccacctccaccacctccacctccacctccacca -cctccaccaccaccaccaccaccaccaccaccaccaccaccaccaccaccaccacctcca -cctccacctccaccacctccacctccaccacctccaccaccacctccacctccaccacct -ccacctccacctccaccacctccacctccaccacctccacctccacctccaccacctcca -ccaccaccacctccaccaccacctccaccacctccaccaccacctccacctccaccacct -ccaccaccacctccaccaccacctccaccaccaccacctccaccaccacctccaccacct -ccaccaccacctccacctccaccacctccacctccacctccaccacctccaccaccacca -ccaccaccaccaccaccaccaccacctccaccaccaccacctccaccaccacctccacca -ccaccaccaccacctccaccaccaccaccaccacctccaccaccacctccaccacctcca -ccaccaccaccaccaccaccaccacctccaccaccacctccaccaccaccaccaccacca -ccaccacctccaccacctccacctccaccaccaccaccacctccaccaccaccaccacca -ccacctccacctccaccaccaccacctccaccaccaccaccacctccaccaccacctcca -ccaccaccaccaccaccaccaccaccacctccaccacctccaccacctccaccaccacct -ccaccacctccaccaccaccaccaccacctccaccaccacctccaccaccaccaccacca -ccaccacctccacctccacctccaccacctccacctccaccacctccacctccaccacct -ccacctccacctccaccacctccaccaccacctccacctccaccaccacctcctccacca -ccaccacctccaccaccacctccaccaccaccacctccacctccaccacctccacctcca -ccaccaccacctccacctccaccaccaccacctccaccacctccaccaccacctccacca -cctccacctccaccaccaccacctccaccaccaccacctccacctccaccaccaccacca -ccaccacctccacctccaccaccacctccaccaccacctccacctccacctccaccacct -ccaccaccacctccaccacctccaccacctccacctccaccaccaccaccacctccacca -ccaccaccaccacctctaccacctctaccaccaccaccaccacctccaccaccaccacca -ccacctccaccaccaccaccaccaccacctccaccaccacctccaccacctccaccacca -ccaccaccacctctaccacctccacctccaccaccaccaccacctctaccaccaccacca -ccacctccaccaccaccaccacctccaccaccaccaccacctccaccaccacctccacca -ccacctccaccacctccaccaccaccaccacctccacctccaccacctccaccaccacct -ccaccaccaccaccaccaccacctccaccaccacctccaccacctccaccaccaccacca -ccacctctaccacctccacctccaccaccaccaccacctccacctccaccaccaccacca -ccaccaccaccaccaccacctccaccaccaccaccaccaccacctctaccaccaccacca -ccacctccaccaccaccaccacctccaccaccaccaccacctccaccaccacctccacca -ccaccaccaccaccaccaccacctctaccaccaccaccaccacctccaccaccaccacca -cctccaccaccaccaccacctccaccaccacctccaccaccaccaccacctccaccacca -cctccaccaccacctccaccacctccaccaccaccaccaccacctccaccaccacctcca -cctccaccaccaccaccaccacctccaccaccaccaccaccaccaccacctccaccacca 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-cctccacctccaccacctccacctccaccacctccaccaccacctccacctccaccacct -ccacctccacctccaccacctccacctccaccacctccacctccacctccaccacctcca -ccaccaccacctccaccaccacctccaccacctccaccaccacctccacctccaccacct -ccaccaccacctccaccaccacctccaccaccaccacctccaccaccacctccaccacct -ccaccaccacctccacctccaccacctccacctccacctccaccacctccaccaccacca -ccaccaccaccaccaccaccaccacctccaccaccaccacctccaccaccacctccacca -ccaccaccaccacctccaccaccaccaccaccacctccaccaccacctccaccacctcca -ccaccaccaccaccaccaccaccacctccaccaccacctccaccaccaccaccaccacca -ccaccacctccaccacctccacctccaccaccaccaccacctccaccaccaccaccacca -ccacctccacctccaccaccaccacctccaccaccaccaccacctccaccaccacctcca -ccaccaccaccaccaccaccaccaccacctccaccacctccaccacctccaccaccacct -ccaccacctccaccaccaccaccaccacctccaccaccacctccaccaccaccaccacca -ccaccacctccacctccacctccaccacctccacctccaccacctccacctccaccacct -ccacctccacctccaccacctccaccaccacctccacctccaccaccacctcctccacca -ccaccacctccaccaccacctccaccaccaccacctccacctccaccacctccacctcca -ccaccaccacctccacctccaccaccaccacctccaccacctccaccaccacctccacca -cctccacctccaccaccaccacctccaccaccaccacctccacctccaccaccaccacca -ccaccacctccacctccaccaccacctccaccaccacctccacctccacctccaccacct -ccaccaccacctccaccacctccaccacctccacctccaccaccaccaccacctccacca -ccaccaccaccacctctaccacctctaccaccaccaccaccacctccaccaccaccacca -ccacctccaccaccaccaccaccaccacctccaccaccacctccaccacctccaccacca -ccaccaccacctctaccacctccacctccaccaccaccaccacctctaccaccaccacca -ccacctccaccaccaccaccacctccaccaccaccaccacctccaccaccacctccacca -ccacctccaccacctccaccaccaccaccacctccacctccaccacctccaccaccacct -ccaccaccaccaccaccaccacctccaccaccacctccaccacctccaccaccaccacca -ccacctctaccacctccacctccaccaccaccaccacctccacctccaccaccaccacca -ccaccaccaccaccaccacctccaccaccaccaccaccaccacctctaccaccaccacca -ccacctccaccaccaccaccacctccaccaccaccaccacctccaccaccacctccacca -ccaccaccaccaccaccaccacctctaccaccaccaccaccacctccaccaccaccacca -cctccaccaccaccaccacctccaccaccacctccaccaccaccaccacctccaccacca -cctccaccaccacctccaccacctccaccaccaccaccaccacctccaccaccacctcca -cctccaccaccaccaccaccacctccaccaccaccaccaccaccaccacctccaccacca -cctccaccaccacctccaccacctccaccaccaccaccaccacctccaccaccacctcca -cctccaccaccaccaccaccacctccaccaccacctccaccaccaccaccaccaccacct -ccaccaccacctccaccacctccaccaccaccaccaccacctctaccacctctaccacca -ccaccaccacctccaccaccaccaccacctccaccaccaccaccacctccaccaccacca -cctccacctccaccaccaccacctccaccacctccaccaccacctccaccaccaccacct -ccacctccaccaccaccacctccaccacctccaccaccaccaccaccaccaccaccacct -ccaccaccaccaccaccaccacctccaccaccacctccaccacctccaccaccaccacca -ccacctctaccacctctaccaccaccaccaccacctccaccaccaccaccacctccacca -ccaccaccacctccaccaccacctccaccaccaccacctccacctccaccaccaccacct -ccaccaccaccacctccacctccaccaccaccacctccaccacctccaccaccacctcca -ccaccaccacctccacctccaccaccaccacctccaccacctccaccaccaccacctcca -ccaccaccacctccaccacctccaccaccaccaccaccacctccaccacctccaccacct -ccaccaccaccaccaccacctccacctccacctccaccacctccaccaccaccacctcca -ccaccaccaccaccaccaccaccacctccacctccacctccaccacctccacctccacca -ccaccaccaccaccaccaccaccaccaccacctccacctccacctccaccacctccacca -ccaccacctccaccaccaccacctccacctccaccacctccaccaccacctccaccacca -ccacctccacctccaccaccaccacctccaccaccaccacctccacctccaccaccacca -cctccaccacctccaccaccacctccaccaccaccacctccacctccaccaccaccacct -ccaccacctccaccaccaccacctccaccaccaccacctccaccacctccaccaccacca -ccaccacctccaccacctccaccacctccaccaccaccaccaccacctccacctccacct -ccaccacctccaccaccaccacctccaccaccaccaccaccaccacctccaccacctcca -ccaccaccaccaccacctccacctccacctccaccacctccaccaccaccacctccacca -ccaccaccaccaccaccaccaccacctccacctccacctccaccacctccacctccacca -ccaccaccaccaccaccacctccaccaccacctccacctccacctccaccacctccacct -ccaccaccaccaccaccaccaccaccaccaccaccacctccacctccacctccaccacca -ccacctctaccaccacctccaccaccaccaccaccaccaccaccaccacctccaccacct -ccaccaccaccacctccaccaccaccacctccacctccaccaccaccaccacctccacca -cctccaccaccacctccacctccacctccaccacctccaccaccaccacctccaccacca -ccaccaccaccaccacctccaccacctccaccaccaccacctccaccaccaccacctcca -cctccaccacctccaccacctccaccaccaccaccacctccaccaccaccaccaccacca -cctccacctccaccacctctaccaccacctccaccaccaccaccaccaccacctccacct -ccaccacctccacctccaccacctctaccaccacctccaccaccaccacctccacctcca -cctccaccaccaccacctccacctccacctccaccaccaccaccaccaccaccacctcca -ccaccaccaccaccaccaccaccaccacctccacctccaccaccaccacctccaccacca -ccacctccaccacctccaccaccacctccacctccaccaccaccacctccacctccacct -ccaccaccaccaccaccacctccaccaccaccacctccaccaccaacacctccacctcca -cctccaccaccaccaccaccacctccacctccaccaccacctccaccaccaccacctcca -cctccaccaccaccacctccaccaccacctccaccacctccaccaccaccacctccacca -ccacctccaccaccaccaccaccaccacctccacctccacctccaccaccaccacctcta -ccaccacctccaccaccaccaccaccaccaccaccaccacctccacctccacctccacca -cctccacctccaccaccaccaccaccaccaccacctccaccaccacctccacctccacct -ccaccacctccacctccaccaccaccaccaccaccaccaccaccaccaccacctccacct -ccacctccaccaccaccacctctaccaccacctccaccaccaccaccaccaccaccacca -ccacctccaccaccaccacctccacctccaccaccaccacctccacctccaccaccacca -cctccacctccaccaccaccaccaccaccaccacctccaccaccaccacctccaccacct -ccaccaccacctccaccaccaccacctccaccacctccaccaccacctccacctccacca -ccaccacctccaccaccaccacctccacctccaccaccaccacctccacctccacctcca -ccacctccacctccaccacctccaccaccaccacctccaccacctccaccaccacctcca -cctccaccaccaccacctccaccaccaccacctccaccacctccaccaccacctccacct -ccaccaccaccacctccacctccacctccaccaccaccaccaccacctccactaccacca -cctccacctccaccaccaccacctccaccaccaacacctccacctccacctccacctcca -ccaccaccacctccacctccaccaccaccacctccaccaccaccacctccaccacctcca -cctccaccaccaccacctccaccaccacctccaccaccaccaccacctccaccaccacca -cctccaccaccacctccaccaccaccacctccaccaccacctccaccaccacctccacct -ccaccaccaccacctgcaccaccacctccacctccaccaccaccaccacctccacctcca -ccagcagcagcatcacttgttggggagaccctgtgcaactccatgcacagccctgtccct -gccatagccccgacccctaagcacagccctgtccaactgccacacgtcccctgcctccc ->ref_chr20:63693325-63693884 -aaggcagtgtgggccagagtcctgggctgcttggggtgggcatcctcgggccctgcttgg -ccccgcctctctgttcccctatgggagtgatgggggcctccacctccaccaccagcacca -gcag-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------caccacctccacctccacctccacctcca -cctccaccaccacctccacctccaccaccacct--------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------------cct -ccaccaccaccacctccaccaccaccaccaccaccaccacctccacctccaccacct--- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------ccacctccaccaccaccacct -ccacctccacca------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------ccaccacctccacctccaccaccacctccaccaccaccacctcca -cctccacca--------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------ccacctccaccaccaccaccaccaccaccaccaccaccacca--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------ccacct -ccaccaccaccacctgcaccaccacctccacctccaccaccaccaccacctccacctcca -ccagcagcagcatcacttgttggggagaccctgtgcaactccatgcacagccctgtccct -gccatagccccgacccctaagcacagccctgtccaactgccacacgtcccctgcctccc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_af38c12092e6a7015d396ac4a67a84aa.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_af38c12092e6a7015d396ac4a67a84aa.msa deleted file mode 100644 index c2670ecf..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_af38c12092e6a7015d396ac4a67a84aa.msa +++ /dev/null @@ -1,150 +0,0 @@ ->syndip_1_chr20:61201612-61202452 -agctaaagcagtgctcagaggacaatctatactactagaggcttatattagaaaaaaaaa -tttaaatcaataacctaagctttcaccattagagaaggaatttcctcactcaggaccctc -tgcggatgtcgcctccatcctcatcaggaccctccatggtgtcacctccatcctcactca -ggacactccatggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatc -ctcactcaggaccctccatgagtgccacctccatcctcactcaggatcccctgtaagtgt -cacctccatcctcaccaggaccctccatg-gtgtcaccgccatcctcactcaggaccctc -catgagtgccacctccatcctcaccaggatcccctgtaagtgtcacctccatcctcac-c -aggaccctccatgagtgtcacctccatc----ctcaggaccctccatgagtgtcacctcc -atcctcactcaggaccctccat-ggtgtcaccgccatcctcactcaggaccctccatg-g -tgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggacc -ctccatggtgtcacctccatcctca----------------------------ccaggac -cctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctc -actcaggaccctccatgggtgtcacctccatcctcactcaggaccctccat-ggtgtcac -cgccatcctca-------------------------------ctcaggaccctccatgag -tgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggacc -ctccatggtgtcacctccatcctcaccaggatcccctgtaa-gtgtcacctccatcctca -ccagg-accctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacct -ccatcctcactcaggaccctccata-gtgccacctccatcctcaccaggatcccctgtaa -gtgtcacctccatcctcac-caggaccctccatgagtgtcacctccatcctcactcagga -ccctccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctc -actcaggaccctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacc -tccatcctcac-tcaggaccctccatggtgtcacctccatcctcac-caggaccctccat -gagtgtcacctccatc----ctcaggaccctccatg------------------------ --------------------------------------------agtgtcacctccatcct -cactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatg-gtgtcac -ctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctcca -tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg -accctccatggtgtcacctccatcctcactcaggaccctccgtgagtgccagctctgtct -accctcgggaccctccatgagtgtctcctctatctaccctcaggaccctctgtgaatg ->syndip_2_chr20:61201612-61202452 -agctaaagcagtgctcagaggacaatctatactactagaggcttatattagaaaaaaaaa -tttaaatcaataacctaagctttcaccattagagaaggaatttcctcactcaggaccctc -tgcggatgtcgcctccatcctcatcaggaccctccatggtgtcacctccatcctcactca -ggacactccatggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatc -ctcactcaggaccctccatgagtgccacctccatcctcac-caggatcccctgtaagtgt -cacctccatcctcaccaggaccctccatgagtgtcacctccatcctcactcaggaccctc -catg-gtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactc -aggaccctccatgggtgtcacctccatcctcactcaggaccctccatgagtgtcacctcc -atcctcactcaggaccctccat-ggtgtcaccgccatcctcactcaggaccctccatgag -tgccacctccatcctcaccaggatcccctgtaagtgtcacctccatcctcaccaggaccc -tccatgagtgtcacctccatcctcaggaccctccatgagtgtcacctccatcctcaggac -cctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctc -actcaggaccctccat-ggtgtcacctccatcctcactcaggaccctccatgggtgtcac -ctccatcctcactcaggaccctccatgagtgtcacctccatcctcaggaccctccatgag -tgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggacc -ctccatggtgtcacctccatcctcactcaggaccctccatg-gtgtcacctccatcctca -ctcag-gacactccatggtgtcacctccatccttactcaggaccctccatggtgtcaccg -ccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggatcccctgtaa -gtgtcacctccatcctcactcaggaccctccatgagtgtcacctccatcctca----gga -ccctccatggtgtcacctccatcctca---ggaccctccatgagtgtcacctccatcctc -actcaggaccctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacc -tccatcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccat -gagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg -accctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatcct -tactcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccac -ctccatcctcac-caggatcccctgtaagtgtcacctccatcctcactcaggaccctcca -tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg -accctccatggtgtcacctccatcctcactcaggaccctccgtgagtgccagctctgtct -accctcgggaccctccatgagtgtctcctctatctaccctcaggaccctctgtgaatg ->p:HG002_1_chr20:61201612-61202452 -agctaaagcagtgctcagaggacaatctatactactagaggcttatattagaaaaaaaaa -tttaaatcaataacctaagctttcaccattagagaaggaatttcctcactcaggaccctc -tgcggatgtcgcctccatcctcatcaggaccctccatggtgtcacctccatcctcactca -ggacactccatggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatc -ctcactcaggaccctccatgagtgccacctccatcctcac-caggatcccctgtaagtgt -cacctccatcctcaccaggaccctccatgagtgtcacctccatcctcactcaggaccctc -catg-gtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactc -aggaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtcacctcc -atcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatggg -tgccacctccatcctcaccaggatcccctgtaagtgtcacctccatcctcaccaggaccc -tccatgagtgtcacctccatcctcaggaccctccatgagtgtcacctccatcctcaggac -cctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctc -actcaggaccctccat-ggtgtcacctccatcctcactcaggaccctccatgggtgtcac -ctccatcctcactcaggaccctccatgagtgtcacctccatcctcaggaccctccatgag -tgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggacc -ctccatggtgtcacctccatcctcactcaggaccctccatg-gtgtcacctccatcctca -ctcgg-accctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcaccg -ccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggatcccctgtaa -gtgtcacctccatcctcac-caggaccctccatgagtgtcacctccatcctca----gga -ccctccatggtgtcacctccatcctca---ggaccctccatgagtgtcacctccatcctc -actcaggaccctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacc -tccatcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccat -gagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg -accctccatggtgtcacctccatcctcactcaggacactccatagtgtcacctccatcct -cactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatg-gtgtcac -ctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctcca -tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg -accctccatggtgtcacctccatcctcactcaggaccctccgtgagtgccagctctgtct -accctcgggaccctccatgagtgtctcctctatctaccctcaggaccctctgtgaatg ->p:HG002_2_chr20:61201612-61202452 -agctaaagcagtgctcagaggacaatctatactactagaggcttatattagaaaaaaaaa -tttaaatcaataacctaagctttcaccattagagaaggaatttcctcactcaggaccctc -tgcggatgtcgcctccatcctcatcaggaccctccatggtgtcacctccatcctcactca -ggacactccatggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatc -ctcactcaggaccctccatgagtgccacctccatcctcac-caggatcccctgtaagtgt -cacctccatcctcaccaggaccctccatgagtgtcacctccatcctcactcaggaccctc -catgagtgccacctccatcctcaccaggatcccctgtaagtgtcacctccatcctcac-c -aggaccctccatgagtgtcacctccatc----ctcaggaccctccatgagtgtcacctcc -atcctcactcaggaccctccat-ggtgtcacctccatcctcactcaggaccctccatg-g -tgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggacc -ctccatggtgtcacctccatcctca----------------------------ccaggac -cctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctc -actcaggaccctccatgggtgtcacctccatcctcactcaggaccctccat-ggtgtcac -cgccatcctca-------------------------------ctcaggaccctccatgag -tgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggacc -ctccatggtgtcacctccatcctcaccaggatcccctgtaa-gtgtcacctccatcctca -ccagg-accctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacct -ccatcctcactcaggaccctccatg-gtgtcacctccatcctcaccaggatcccctgtaa -gtgtcacctccatcctcac-caggaccctccatgagtgtcacctccatcctcactcagga -ccctccatggtgtcacctccatcctcactcggaccctccatgagtgtcacctccatcctc -actcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacc -tccatcctcac-caggatcccctgtaagtgtcacctccatcctcac-caggaccctccat -gagtgtcacctccatc----ctcaggaccctccatg------------------------ --------------------------------------------agtgtcacctccatcct -cactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatg-gtgtcac -ctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctcca -tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg -accctccatggtgtcacctccatcctcactcaggaccctccgtgagtgccagctctgtct -accctcgggaccctccatgagtgtctcctctatctaccctcaggaccctctgtgaatg ->ref_chr20:61201612-61202452 -agctaaagcagtgctcagaggacaatctatactactagaggcttatattagaaaaaaaaa -tttaaatcaataacctaagctttcaccattagagaaggaatttcctcactcaggaccctc -tgcggatgtcgcctccatcctcatcaggaccctccatggtgtcacctccatcctcactca -ggacactccatggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatc -ctcactcaggaccctccatgagtgccacctccatcctcac-caggatcccctgtaagtgt -cacctccatcctcaccaggaccctccatgagtgtcacctccatc----ctcaggaccctc -catgagtgtcacctccatcctcactcaggaccctccat---------------------- ------------------------------------------------------------- ------------------------ggtgtcaccgccatcctcactcaggaccctccatgag -tgccacctccatcctcaccaggatcccctgtaagtgtcacctccatcctcac-------- ------------------------caggaccctccatgagtgtcacctccatcctcaggac -cctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctc -actcaggaccctccat-ggtgtcacctccatcctcactcaggaccctccatgggtgtcac -ctccatcctcactcaggaccctccatg--------------------------------g -tgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggacc -ctccatggtgtcacctccatcctcactcaggaccctccgtgagtgccagctctgtctacc -ctcgggaccctccatgagtgtctcctctatctaccctcaggaccctctgtga-------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------atg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_afda56e0c84a9e3c780808affe542c4a.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_afda56e0c84a9e3c780808affe542c4a.msa deleted file mode 100644 index 926a7b0a..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_afda56e0c84a9e3c780808affe542c4a.msa +++ /dev/null @@ -1,80 +0,0 @@ ->syndip_1_chr20:61743988-61744854 -ccctgggcaggcacacaggccccacactcaggttcagacactatgccacggtcttgtcgc -tcttcatatgtttttgaacaaggggccccaaattttcatttcaaactgggcactgcaaat -tctggaatctctcctacctcccgaagtttgtagtccaccaggcccagggcgttctgaagc -ctggagggatgagaagcaagcggagactgtgtggttggaaaggagccaaccagagagtgg -ggaggcgatggagagaataacagagaggaaggcaggtgcagggagacagcaaaggagagg -gagaagagaatgagagagggatggggagaaagagagaagagaggtggagagagacaggaa -aggagagggagggagaggaagagagggagagagagaaggagggagagagatggaaagagg -tggagggagagagagaaggaaagggagggaga---------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------gagagagacagacagacagcttcacacagacataaaacatctgctgttcaggatc -ccagctgccctccgactctgcctccttctaacccggctgcctggctcacccgggtgacag -ggaggggcgccttcaccatgccctgtcctgaggctccctttcatcctggcatattccagc -aatccagcaccaggctcctgaacaacctgcgttcatccccagttctagctgttaggttcc -ccgtgcctgacggggaagtggccaggt ->syndip_2_chr20:61743988-61744854 -ccctgggcaggcacacaggccccacactcaggttcagacactatgccacggtcttgtcgc -tcttcatatgtttttgaacaaggggccccaaattttcatttcaaactgggcactgcaaat -tctggaatctctcctacctcccgaagtttgtagtccaccaggcccagggcgttctgaagc -ctggagggatgagaagcaagcggagactgtgtggttggaaaggagccaaccagagagtgg -ggaggcgatggagagaataagagagaggaaggcaggtgcagggagacagcaaaggagagg -gagaagagaatgagagagggatggggagaaagagagaagagaggtggagagagacaggaa -aggagagggagggagaggaagagagggagagagagaaggagggagagagatggaaagagg -tggagggagagagagaaggaaagggagggagaggaagagagggagagagagaaggaggga -gagagatggagagaggtggagggagagagagaaggaaagggagg---------------- ------------------------------------------------------------- ------gagagagagagacagacagcttcacacagacataaaacatctgctgttcaggatc -ccagctgccctccgactctgcctccttctaacccggctgcctggctcacccgggtgacag -ggaggggcgccttcaccatgccctgtcctgaggctccctttcatcctggcatattccagc -aatccagcaccaggctcctgaacaacctgcgttcatccccagttctagctgttaggttcc -ccgtgcctgacggggaagtggccaggt ->p:HG002_1_chr20:61743988-61744854 -ccctgggcaggcacacaggccccacactcaggttcagacactatgccacggtcttgtcgc -tcttcatatgtttttgaacaaggggccccaaattttcatttcaaactgggcactgcaaat -tctggaatctctcctacctcccgaagtttgtagtccaccaggcccagggcgttctgaagc -ctggagggatgagaagcaagcggagactgtgtggttggaaaggagccaaccagagagtgg -ggaggcgatggagagaataagagagaggaaggcaggtgcagggagacagcaaaggagagg -gagaagagaatgagagagggatggggagaaagagagaagagaggtggagagagacaggaa -aggagagggagggagaggaagagagggagagagagaaggagggagagagatggaaagagg -tggagggagagagagaaggaaagggagggagaggaagagagggagagagagaaggaggga -gagagatggagagaggtggagggagagagagaaggaaagggagg---------------- ------------------------------------------------------------- ------gagagagagagacagacagcttcacacagacataaaacatctgctgttcaggatc -ccagctgccctccgactctgcctccttctaacccggctgcctggctcacccgggtgacag -ggaggggcgccttcaccatgccctgtcctgaggctccctttcatcctggcatattccagc -aatccagcaccaggctcctgaacaacctgcgttcatccccagttctagctgttaggttcc -ccgtgcctgacggggaagtggccaggt ->p:HG002_2_chr20:61743988-61744854 -ccctgggcaggcacacaggccccacactcaggttcagacactatgccacggtcttgtcgc -tcttcatatgtttttgaacaaggggccccaaattttcatttcaaactgggcactgcaaat -tctggaatctctcctacctcccgaagtttgtagtccaccaggcccagggcgttctgaagc -ctggagggatgagaagcaagcggagactgtgtggttggaaaggagccaaccagagagtgg -ggaggcgatggagagaataacagagaggaaggcaggtgcagggagacagcaaaggagagg -gagaagagaatgagagagggatggggagaaagagagaagagaggtggagagagacaggaa -aggagagggagggagaggaagagagggagagagagaaggagggagagagatggaaagagg -tggagggagagagagaaggaaagggagggaga---------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------gagagagacagacagacagcttcacacagacataaaacatctgctgttcaggatc -ccagctgccctccgactctgcctccttctaacccggctgcctggctcacccgggtgacag -ggaggggcgccttcaccatgccctgtcctgaggctccctttcatcctggcatattccagc -aatccagcaccaggctcctgaacaacctgcgttcatccccagttctagctgttaggttcc -ccgtgcctgacggggaagtggccaggt ->ref_chr20:61743988-61744854 -ccctgggcaggcacacaggccccacactcaggttcagacactatgccacggtcttgtcgc -tcttcatatgtttttgaacaaggggccccaaattttcatttcaaactgggcactgcaaat -tctggaatctctcctacctcccgaagtttgtagtccaccaggcccagggcgttctgaagc -ctggagggatgagaagcaagcggagactgtgtggttggaaaggagccaaccagagagtgg -ggaggcgatggagagaataacagagaggaaggcaggtgcagggagacagcaaaggagagg -gagaagagaatgagagagggatggggagaaagagagaagagaggtggagagagacaggaa -aggagagggagggagaggaagagagggagagagagaaggagggagagagatggaaagagg -tggagggagagagagaaggaaagggagggagaggaagagagggagagagagaaggaggga -gagagatggagagaggtggagggagagagagaaggaaagggaggggagaggaagagaggg -agagagagaaggagggagagagatggagagaggtggagggagagagagaaggaaagggag -ggagagagagagacagacagacagcttcacacagacataaaacatctgctgttcaggatc -ccagctgccctccgactctgcctccttctaacccggctgcctggctcacccgggtgacag -ggaggggcgccttcaccatgccctgtcctgaggctccctttcatcctggcatattccagc -aatccagcaccaggctcctgaacaacctgcgttcatccccagttctagctgttaggttcc -ccgtgcctgacggggaagtggccaggt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b48c4b8600c916c02148abdc6273767c.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b48c4b8600c916c02148abdc6273767c.msa deleted file mode 100644 index 214317cf..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b48c4b8600c916c02148abdc6273767c.msa +++ /dev/null @@ -1,225 +0,0 @@ ->syndip_1_chr20:22081961-22084122 -acaaaaactatctttttcccgttcttttacttatatatgcttatttatatatattatata -tacacttttaatatatacttattaatatatattaatataatataataataatacaatata -atatatgtatatatgtaggtatataataatatacctacatatatacatatattatatata -ctatctgtatattatatgtataatatatgtatatataatatatgtatatactatacatgt -atatattatattatacatgtatatattataagtatatactatacatgcatgtattatatg -tatatac----------------------------tatacatgcatgtattatatgtata -tattatacatgcatgtattatatgtatatattatacatgcatgtattatatgtatatatt -atacatgtatgtattatatgtatagattatacatgtatatattatatatgtatatattac -acatgtacatatatgtatatattaaacacgtttatattatttattatacatgactatatt -atataggtatatatgatatatgcatatatgtcatataggtatatatgacatatatgcata -tatcatgtaggtatatatgacatatgcatatatcatataggtatatatgacatatgcata -tatcatataggtatatatgatatatgcgcatatatcatataggtatatatgatatatgcg -catatatcatataggtatatatgatatatgcgcatatatcatataggtatatatgatata -tgcgcatatatcatataggtatatatgatatatgcgcatatatcatataggtatatatga -tatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatacaggtatat -gtgcatatatcatataggtataggtataggtagatatatgatatatgcacacatatcata -taggtatatatgatatatgataggtatatatgatatatgataggtatatatgatatatat -catattggtatatatgatatatatcatatcggtatatatgatatatatcatatcggtata -tataggtatatatcataggtatatataggtatatatcacataggtatatataggtatata -tcatataggtatatataatatatgcatttatattatataggtatatatattacataggta -tatgtaatatgtgcatatatattatataggtatatatattatacaggcatatataatacg -tatatatattatatgggcatatatatgtatatatattatataggtatatataatatatgt -gtatatattatgtgggtatatataatatatgtgtacatattatgtgggtatatataatat -atgtgtacatattatgtgggtatatataatatatgtgtacatattatgtgggtatatata -atatatgtgtatatattatgtgggtatatataatatatgtgtatatattatgtgggtata -tataatatatgtgtatatattatgtgggtatatataatatatgtgtatatattatgtggg -tatatataatatatgtgtatatattatgtgggtatatataatatatgtgtatatattatg -tgggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatatat -tatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtat -atattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgt -gtatatattatatatgtaataggaagcaggaatgaatgcacagaagaccttagagtttaa -ggcattatttgtgtaatgagaaatattatatatacg------------------------ ----------tatattaatatagacgtatatataatatatacatatatacatatatagtat -atactatgtatacatatatactatacatacgtatattatatacatgtgtattatatacat -gtgtattatatatatgtgtatacatatatactatatatacatacattatatacatacatt -atatatgtgtattatatatgtatatattatgtatgtatatattatatatacgtatatatt -aatatgcatatatatgtgtctctttataccaataatgccttaaactctaaggtcttctgt -gcattcattcctgcttcctattacatatatattatatagatacatatataatatatacat -atatactacataatatatgcatatataatatatacatatgttgtatatgtatatataata -tatacatatgttgtatatgtatatataatatatacatatgttgtatatgtatatataata -tatacatatgttgtatatgtatatataatatatacatatgttgtatatgtatatataata -tatacatatgttgtatatgtatatataatatatacatatgttgtatatgtattatatgta -tatattacatattatatatacttatgtatgtataatatatatataatatatatatatctt -aggcaacttttcattgctcatttttat ->syndip_2_chr20:22081961-22084122 -acaaaaactatctttttcccgttcttttacttatatatgcttatttatatatattatata -tacacttttaatatatacttattactatatattaatataatataataataatacaatata -atatatgtatatatgtaggtatataataatatacctacatatatacatatattatatata -ctatctgtatattatatgtataatatatgtatatataatatatgtatatactatacatgt -atatattatattatacatgtatatattataagtatatactatacatgcatgtattatatg -tatatac----------------------------tatacatgcatgtattatatgtata -tattatacatgcatgtattatatgtatatattatacatgcatgtattatatgtatatatt -atacatgtatgtattatatgtatagattatacatgtatatattatatatgtatatattac -acatgtacatatatgtatatattaaacacgtttatattatttattata------------ ------------------------------------------------------------- ----catgtaggtatatatgacatatgcatatatcatataggtatatatgacatatgcata -tatcatataggtatatatgatatatgcgcatatatcatataggtatatatgatatatgcg -catatatcatacagg---------tatatgcgcatatatcatataggtataggt------ -------------ataggtagatatatgatatatgcacacatatcatataggtatatatga -tatatgcgcatatatcatataggtatatatgatatatg---------------------- ------------------------------------------------------------a -taggtatatatgatatatgata-------------------------------------- -------ggtatatatgatatatatcatatcggtatatatgatatatatcatatcggtata -tataggtatatatcataggtatatataggtatatatcacataggtatatataggtatata -tcatataggtatatataatatatgcatttatattatataggtatatatattacataggta -tatgtaatatgtgcatatatattatataggtatatatattatacaggcatatataatacg -tatatatattatatgggcatatatatgtgtatatattatata------------------ ------------------------------------------------------------- ---------------------------------------------------ggtatatata -atatatgtgtatatattatgtgggtatatataatatatgtgtatatattatgtgggtata -tataatatatgtgtacatattatgtgggtatatataatatatgtgtatatattatgtagg -tatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatatattatg -taggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatatat -tatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtat -atattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgt -gtatatattatatatgtaataggaagcaggaatgaatgcacagaagaccttagagtttaa -ggcattatttgtgtaatgagaaatattatatatacgtatattaatatagacgtatatata -atatatacatatattaatatagacgtatatataatatatacatatatacatatatagtat -atactatgtatacatatatactatacatacgtatattatatacatgtgtattatatacat -gtgtattatatatatgtgtatacatatatactatatatacatacattatatacatacatt -atatatgtgtattatatatgtatatattatgtatgtatatattatatatacgtatatatt -aatatacatatatatgtgtctcattataccaataatgccttaaactctaaggtcttctgt -gcattcattcctgcttcctattacatatatattatatagatacatatataatatatacat -atatactacataatatatgc---------------------------------------- ---------------------------------------------------atatataata -tatacatatgttgtatatgtatatataatatatacatatgttgtatatgtatatataata -tatacatatgttgtatatgtatatataatatatacatatgttgtatatgtattatatgta -tatattacatattatatatacttatgtatgtataatatatatataatatatatatatctt -aggcaacttttcattgctcatttttat ->p:HG002_1_chr20:22081961-22084122 -acaaaaactatctttttcccgttcttttacttatatatgcttatttatatatattatata -tacacttttaatatatacttattactatatattaatataatataataataatacaatata -atatatgtatatatgtaggtatataataatatacctacatatatacatatattatatata -ctatctgtatattatatgtataatatatgtatatataatatatgtatatactatacatgt -atatattatattatacatgtatatattataagtatatactatacatgcatgtattatatg -tatatac----------------------------tatacatgcatgtattatatgtata -tattatacatgcatgtattatatgtatatattatacatgcatgtattatatgtatatatt -atacatgtatgtattatatgtatagattatacatgtatatattatatatgtatatattac -acatgtacatatatgtatatattaaacacgtttatattatttattata------------ ------------------------------------------------------------- ----catgtaggtatatatgacatatgcatatatcatataggtatatatgacatatgcata -tatcatataggtatatatgatatatgcgcatatatcatataggtatatatgatatatgcg -catatatcatacagg---------tatatgcgcatatatcatataggtataggt------ -------------ataggtagatatatgatatatgcacacatatcatataggtatatatga -tatatgcgcatatatcatataggtatatatgatatatg---------------------- ------------------------------------------------------------a -taggtatatatgatatatgata-------------------------------------- -------ggtatatatgatatatatcatatcggtatatatgatatatatcatatcggtata -tataggtatatatcataggtatatataggtatatatcacataggtatatataggtatata -tcatataggtatatataatatatgcatttatattatataggtatatatattacataggta -tatgtaatatgtgcatatatattatataggtatatatattatacaggcatatataatacg -tatatatattatatgggcatatatatgtgtatatattatata------------------ ------------------------------------------------------------- ---------------------------------------------------ggtatatata -atatatgtgtatatattatgtgggtatatataatatatgtgtatatattatgtgggtata -tataatatatgtgtacatattatgtgggtatatataatatatgtgtatatattatgtagg -tatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatatattatg -taggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatatat -tatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtat -atattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgt -gtatatattatatatgtaataggaagcaggaatgaatgcacagaagaccttagagtttaa -ggcattatttgtgtaatgagaaatattatatatacgtatattaatatagacgtatatata -atatatacatatattaatatagacgtatatataatatatacatatatacatatatagtat -atactatgtatacatatatactatacatacgtatattatatacatgtgtattatatacat -gtgtattatatatatgtgtatacatatatactatatatacatacattatatacatacatt -atatatgtgtattatatatgtatatattatgtatgtatatattatatatacgtatatatt -aatatacatatatatgtgtctcattataccaataatgccttaaactctaaggtcttctgt -gcattcattcctgcttcctattacatatatattatatagatacatatataatatatacat -atatactacataatatatgc---------------------------------------- ---------------------------------------------------atatataata -tatacatatgttgtatatgtatatataatatatacatatgttgtatatgtatatataata -tatacatatgttgtatatgtatatataatatatacatatgttgtatatgtattatatgta -tatattacatattatatatacttatgtatgtataatatatatataatatatatatatctt -aggcaacttttcattgctcatttttat ->p:HG002_2_chr20:22081961-22084122 -acaaaaactatctttttcccgttcttttacttatatatgcttatttatatatattatata -tacacttttaatatatacttattaatatatattaatataatataataataatacaatata -atatatgtatatatgtaggtatataataatatacctacatatatacatatattatatata -ctatctgtatattatatgtataatatatgtatatataatatatgtatatactatacatgt -atatattatattatacatgtatatattataagtatatactatacatgcatgtattatatg -tatatac----------------------------tatacatgcatgtattatatgtata -tattatacatgcatgtattatatgtatatattatacatgcatgtattatatgtatatatt -atacatgtatgtattatatgtatagattatacatgtatatattatatatgtatatattac -acatgtacatatatgtatatattaaacacgtttatattatttattatacatgactatatt -atataggtatatatgatatatgcatatatgtcatataggtatatatgacatatatgcata -tatcatgtaggtatatatgacatatgcatatatcatataggtatatatgacatatgcata -tatcatataggtatatatgatatatgcgcatatatcatataggtatatatgatatatgcg -catatatcatataggtatatatgatatatgcgcatatatcatataggtatatatgatata -tgcgcatatatcatataggtatatatgatatatgcgcatatatcatataggtatatatga -tatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatacaggtatat -gtgcatatatcatataggtataggtataggtagatatatgatatatgcacacatatcata -taggtatatatgatatatgataggtatatatgatatatgataggtatatatgatatatat -catattggtatatatgatatatatcatatcggtatatatgatatatatcatatcggtata -tataggtatatatcataggtatatataggtatatatcacataggtatatataggtatata -tcatataggtatatataatatatgcatttatattatataggtatatatattacataggta -tatgtaatatgtgcatatatattatataggtatatatattatacaggcatatataatacg -tatatatattatatgggcatatatatgtatatatattatataggtatatataatatatgt -gtatatattatgtgggtatatataatatatgtgtacatattatgtgggtatatataatat -atgtgtacatattatgtgggtatatataatatatgtgtacatattatgtgggtatatata -atatatgtgtatatattatgtgggtatatataatatatgtgtatatattatgtgggtata -tataatatatgtgtatatattatgtgggtatatataatatatgtgtatatattatgtggg -tatatataatatatgtgtatatattatgtgggtatatataatatatgtgtatatattatg -tgggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatatat -tatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtat -atattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgt -gtatatattatatatgtaataggaagcaggaatgaatgcacagaagaccttagagtttaa -ggcattatttgtgtaatgagaaatattatatatacg------------------------ ----------tatattaatatagacgtatatataatatatacatatatacatatatagtat -atactatgtatacatatatactatacatacgtatattatatacatgtgtattatatacat -gtgtattatatatatgtgtatacatatatactatatatacatacattatatacatacatt -atatatgtgtattatatatgtatatattatgtatgtatatattatatatacgtatatatt -aatatgcatatatatgtgtctctttataccaataatgccttaaactctaaggtcttctgt -gcattcattcctgcttcctattacatatatattatatagatacatatataatatatacat -atatactacataatatatgcatatataatatatacatatgttgtatatgtatatataata -tatacatatgttgtatatgtatatataatatatacatatgttgtatatgtatatataata -tatacatatgttgtatatgtatatataatatatacatatgttgtatatgtatatataata -tatacatatgttgtatatgtatatataatatatacatatgttgtatatgtattatatgta -tatattacatattatatatacttatgtatgtataatatatatataatatatatatatctt -aggcaacttttcattgctcatttttat ->ref_chr20:22081961-22084122 -acaaaaactatctttttcccgttcttttacttatatatgcttatttatatatattatata -tacacttttaatatatacttattactatatattaatataatataataataatacaatata -atatatgtatatatgtaggtatataataatatacctacatatatacatatattatatata -ctatctgtatattatatgtataatatatgtatatataatatatgtatatactatacatgt -atatattatattatacatgtatatattataagtatatactatacatgcatgtattatatg -tatatactatacatgcatgtattatatgtatatattatacatgcatgtattatatgtata -tattatacatgcatgtattatatgtatatattatacatgcatgtattatatgtatatatt -atacatgtatgtattatatgtatagattatacatgtatatattatatatgtatatattac -acatgtacatatatgtatatattaaacacgtttatattatttattata------------ ------------------------------------------------------------- ----catgtaggtatatatgacatatgcatatatcatataggtatatatgacatatgcata -tatcatataggtatatatgatatatgcgcatatatcatataggtatatatgatatatgcg -catatatcatacagg---------tatatgcgcatatatcatataggtataggt------ -------------ataggtagatatatgatatatgcacacatatcatataggtatatatga -tatatgcgcatatatcatataggtatatatgatatatg---------------------- ------------------------------------------------------------a -taggtatatatgatatatgata-------------------------------------- -------ggtatatatgatatatatcatatcggtatatatgatatatatcatatcggtata -tataggtatatatcataggtatatataggtatatatcacataggtatatataggtatata -tcatataggtatatataatatatgcatttatattatataggtatatatattacataggta -tatgtaatatgtgcatatatattatataggtatatatattatacaggcatatataatacg -tatatatattatatgggcatatatatgtgtatatattatata------------------ ------------------------------------------------------------- ---------------------------------------------------ggtatatata -atatatgtgtatatattatgtgggtatatataatatatgtgtatatattatgtgggtata -tataatatatgtgtacatattatgtgggtatatataatatatgtgtatatattatgtagg -tatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatatattatg -taggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatatat -tatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtat -atattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgt -gtatatattatatatgtaataggaagcaggaatgaatgcacagaagaccttagagtttaa -ggcattatttgtgtaatgagaaatattatatatacgtatattaatatagacgtatatata -atatatacatatattaatatagacgtatatataatatatacatatatacatatatagtat -atactatgtatacatatatactatacatacgtatattatatacatgtgtattatatacat -gtgtattatatatatgtgtatacatatatactatatatacatacattatatacatacatt -atatatgtgtattatatatgtatatattatgtatgtatatattatatatacgtatatatt -aatatacatatatatgtgtctcattataccaataatgccttaaactctaaggtcttctgt -gcattcattcctgcttcctattacatatatattatatagatacatatataatatatacat -atatactacataatatatgc---------------------------------------- ---------------------------------------------------atatataata -tatacatatgttgtatatgtatatataatatatacatatgttgtatatgtatatataata -tatacatatgttgtatatgtatatataatatatacatatgttgtatatgtattatatgta -tatattacatattatatatacttatgtatgtataatatatatataatatatatatatctt -aggcaacttttcattgctcatttttat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b697d4213af9b212c21e41d1069cb6a4.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b697d4213af9b212c21e41d1069cb6a4.msa deleted file mode 100644 index a5091515..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b697d4213af9b212c21e41d1069cb6a4.msa +++ /dev/null @@ -1,125 +0,0 @@ ->syndip_1_chr20:53203987-53204473 -accgtagtgcacaatatctccttcatttttataatatgatactattatatcataatttta -taatatactattatatcatattatatgatactatttatatcatcatatgatgatatacta -t--tatatcatcatatgatgatata--ctattatatcatcatatgatgatatgatactat -atcatcatatgatgatatgatactatatcatcatatgatgat---atactatatcatcat -atgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgat -atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc -atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg -atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata -ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca -tcatatgatgatatgatactatatcatcacatgatgatatgatactatatcatcacatga -tgatatgatactatatcatcacatgatgatatgatactatatcatcacatgatgatatga -tactatatcatcacatgatgatatgatactatatcatcacatgatgatatgatactatat -catcacatgatgatatgatactatatcatcacatgatgatatgatactatatcatcatat -a---------------------acatgatgatatgatactatatcatcatata------- ---------------acatgatgatatgatactatatcatcat------------------ --------------------------------------------------------ataac -atgatgatatgatactatatcatcatataacatgatgatatgatactatatcatcatata -acatgatgatatgatactatatcatcatataacatgatgatatgatactattatatcata -atatgatataatattttggacatactaggttaaataaga--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------- ->syndip_2_chr20:53203987-53204473 -accgtagtgcacaatatctccttcatttttataatatgatactattatatcataatttta -taatatactattatatcatattatatgatactatttatatcatcatatgatgatatacta -t--tatatcatcatatgatgatatg--atactatatcatcatatgatgatatgatactat -atcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcat -atgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgat -atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc -atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg -atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata -ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca -tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga -tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatat -gatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatat -gatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactat -atcatcatatgatgatatgatactatatcataacatgatgatatgatactatatcataac -atgatgatatgatactatatcatcatataacatgatgatatgatactatatcatcatata -acatgatgatatgatactatatcatcatataacatgatgatatgatac---tatatcatc -atataacatgatgatatgatactatatcatcatataacatgatgatatgatactatatca -tcatataacatgatgatatgatactatatcatcatataacatgatgatatgatactatat -catcatataacatgatgatatgatactatatcatcatataacatgatgatatgatactat -atcatcatataacatgatgatatgatactattatatcataatatgatataatattttgga -catactaggttaaataaga ->p:HG002_1_chr20:53203987-53204473 -accgtagtgcacaatatctccttcatttttataatatgatactattatatcataatttta -taatatactattatatcatattatatgatactatttatatcatcatatgatgatatacta -t--tatatcatcatatgatgatatg--atactatatcatcatatgatgatatgatactat -atcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcat -atgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgat -atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc -atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg -atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata -ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca -tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga -tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatat -gatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatat -gatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactat -atcatcatatgatgatatgatactatatcataacatgatgatatgatactatatcataac -atgatgatatgatactatatcatcatataacatgatgatatgatactatatcatcatata -acatgatgatatgatactatatcatcatataacatgatgatatgatac---tatatcatc -atataacatgatgatatgatactatatcatcatataacatgatgatatgatactatatca -tcatataacatgatgatatgatactatatcatcatataacatgatgatatgatactatat -catcatataacatgatgatatgatactatatcatcatataacatgatgatatgatactat -atcatcatataacatgatgatatgatactattatatcataatatgatataatattttgga -catactaggttaaataaga ->p:HG002_2_chr20:53203987-53204473 -accgtagtgcacaatatctccttcatttttataatatgatactattatatcataatttta -taatatactattatatcatattatatgatactatttatatcatcatatgatgatatacta -t--tatatcatcatatgatgatata--ctattatatcatcatatgatgatatgatactat -atcatcatatgatgatatgatactatatcatcatatgatgat---atactatatcatcat -atgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgat -atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc -atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg -atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata -ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca -tcatatgatgatatgatactatatcatcacatgatgatatgatactatatcatcacatga -tgatatgatactatatcatcacatgatgatatgatactatatcatcacatgatgatatga -tactatatcatcacatgatgatatgatactatatcatcacatgatgatatgatactatat -catcacatgatgatatgatactatatcatcacatgatgatatgatactatatcatcatat -a---------------------acatgatgatatgatactatatcatcatata------- ---------------acatgatgatatgatactatatcatcat------------------ --------------------------------------------------------ataac -atgatgatatgatactatatcatcatataacatgatgatatgatactatatcatcatata -acatgatgatatgatactatatcatcatataacatgatgatatgatactattatatcata -atatgatataatattttggacatactaggttaaataaga--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------- ->ref_chr20:53203987-53204473 -accgtagtgcacaatatctccttcatttttataatatgatactattatatcataatttta -taatatactattatatcatattatatgatactatttatatcatcatatgatgatatgata -tactatatcatcatatgatgatatgatatactatatcatcatatgatgatatgatactat -atcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcat -atgatgatatgatactatatcatcatatgatgatatgatactatatcatcatata----- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------acatgatgatatgatactatatcatcat------------------ --------------------------------------------------------ataac -atgatgatatgatactatatcatcatataacatgatgatatgatactatatcatcatata -acatgatgatatgatactatatcatcatataacatgatgatatgatactattatatcata -atatgatataatattttggacatactaggttaaataaga--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b78e6b2bde8f809113bc2b6daa2b608a.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b78e6b2bde8f809113bc2b6daa2b608a.msa deleted file mode 100644 index 1a5e2924..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b78e6b2bde8f809113bc2b6daa2b608a.msa +++ /dev/null @@ -1,195 +0,0 @@ ->syndip_1_chr20:38123390-38124905 -caccctttcttggactgactcttcctccccaggctctcagcttccatagtagcttccaag -aaaggccttctctgacttccttgtctaggatattctccatttttaagtccacagcctgtg -accaatggcaacagagcagaaggttagagcaattactgtggatggagcttgcccagtagg -cctcctagctccattttctagctttgtgatctcaggcctgtcctgtaacctctctgggcc -tcagaaacctctctctctctc--tatatatatatatataataatatataataataatata -taatatgtataataataatatataatatttataataataatatatataatatgtatatat -aatatacatatacctattatatataatatacctattatatataatatacatatacctatt -atatataatatacctattatatataagatacctattatatataatatacatatacctatt -atatatataatatacctattatatatatataatatacctattatatataatatacctatt -atatatataatatacctattatatatataatatacctattatatatataatatacctatt -atatataatatacctattatatataaaatatacctattatatataatatacctattatat -acattatatataatatacctattatatgcattatatataatatacctattatatgcatta -tatataatatacctattatatgcattatatataatatacctattatatgcattatatata -atatacctattatatgcattatataatatattatatataatatgcatattatatgtatta -tatattatatattatatatataatatacatattatatgtattatatattatatattatat -atataatatacatattatatgtattatatattatatataatatacatattatatattata -tattatatacatattatatattatatattatatacatattatatattatatacatattat -atattatatattatatacatattatacattatatatatctaaaatatataatacacatta -tatattatataatacacattatatataatatataatacacattatatattatatataata -cacattatatattatatataatacacattatatat-----------------------ta -tataatacacattatatattatatataatacacattatatattatatataatacacatta -tatattatatataatacacattatatattatataatacacattatatattatatataata -cacattatatatataatacacattatatattatatataatacataatacacattatatat -tatatataatacacattatatataatatataacacacattatatataatatataacacac -attatatattatatataatacacattatatattatatataatacacatatattatatata -atacacattatatattatatataatacacatatattatatataatacacattatatatta -tatataatacacattatatataatatataatacacattatatataatacttattatatat -tatacataatatacatattatatataatacataatatacgtatattatataatatacata -ttatatataatacataatatacgtatattatataatatacatattatatatattatacta -tatataatactcatatatatacatattatatatacatattatatataatactcatattat -atgtacatattatacatacatattatatataatacacatatatacatattatatataata -cacacacacattatatatgtcttatatataatatacatattatatatgtattatattatt -atagatataatatacatattatatctatatataaaatatatatgtagagagagagagaca -gggtctcattttgtctcccaggctggagtgcagtggtgcaatcttggctcactacaacct -ccacctcccaggctcaagggatcctccagcttcagccccccgagtacctgggactacagg -aacgcgtcaccatgcctggctaatttttttttattttttgtagagatggggtttcgccat -gttgccgaggctggtgtcaaactcctggactcaagtgatcctcccacctcagcctcccaa -agtgctgagattacaggtgtgaaccactgcacctggacttacagtcttattttcacata ->syndip_2_chr20:38123390-38124905 -caccctttcttggactgactcttcctccccaggctctcagcttccatagtagcttccaag -aaaggccttctctgacttccttgtctaggatattctccatttttaagtccacagcctgtg -accaatggcaacagagcagaaggttagagcaattactgtggatggagcttgcccagtagg -cctcctagctccattttctagctttgtgatctcaggcctgtcctgtaacctctctgggcc -tcagaaacctctctctctctc--tatatatatatatataataatatataataataatata -taatatgtataataataatatataatatttataataataatatatataatatgtatatat -aatatacatatacctattatatataatatacctattatatataatatacatatacctatt -atatataatatacctattatatataagatacctattatatataatatacatatacctatt -atatatataatatacctattatatatatataatatacctattatatataatatacctatt -atatatataatatacctattatatatataatatacctattatatatataatatacctatt -atatataatatacctattatatataaaatatacctattatatataatatacctattatat -a---------------------------cattatatataatatacctattatatgcatta -tatataatatacctattatatgcattatatataatatacctattatatgcattatatata -atatacctattatatgcattatataatatattatatataatatgcatattatatgtatta -tatattatatattatatatataatatacatattatatgtattatatattatatattatat -atataatatacatattatatgtattatatattatatataatatacatattatatattata -tattatatacatattatatattatatattatatacatattatatattatatacatattat -atattatatattatatacatattatacattatatatatctaaaatatataatacacatta -tatattatataatacacattatatataatatataatacacattatatattatatataata -cacattatatattatatataatacacattatatattatataatacacattatatattata -tataatacacattatatattatatataatacacattatatattatatataatacacatta -tatattatatataatacacattatatattatataatacacattatatattatatataata -cacattatatatataatacacattatatattatatataatacataatacacattatatat -tatatataatacacattatatataatatataacacacattatatataatatataacacac -attatatattatatataatacacattatatattatatataatacacatatattatatata -atacacattatatattatatataatacacatatattatatataatacacattatatatta -tatataatacacattatatataatatataatacacattatatataatacttattatatat -tatacataatatacatattatatataatacataatatacgtatattatataatatacata -ttatatataatacataatatacgtatattatataatatacatattatatatattatacta -tatataatactcatatatatacatattatatatacatattatatataatactcatattat -atgtacatattatacatacatattatatataatacacatatatacatattatatataata -cacacacacattatatatgtcttatatataatatacatattatatatgtattatattatt -atagatataatatacatattatatctatatataaaatatatatgtagagagagagagaca -gggtctcattttgtctcccaggctggagtgcagtggtgcaatcttggctcactacaacct -ccacctcccaggctcaagggatcctccagcttcagccccccgagtacctgggactacagg -aacgcgtcaccatgcctggctaatttttttttattttttgtagagatggggtttcgccat -gttgccgaggctggtgtcaaactcctggactcaagtgatcctcccacctcagcctcccaa -agtgctgagattacaggtgtgaaccactgcacctggacttacagtcttattttcacata ->p:HG002_1_chr20:38123390-38124905 -caccctttcttggactgactcttcctccccaggctctcagcttccatagtagcttccaag -aaaggccttctctgacttccttgtctaggatattctccatttttaagtccacagcctgtg -accaatggcaacagagcagaaggttagagcaattactgtggatggagcttgcccagtagg -cctcctagctccattttctagctttgtgatctcaggcctgtcctgtaacctctctgggcc -tcagaaacctctctctctctc--tatatatatatatataataatatataataataatata -taatatgtataataataatatataatatttataataataatatatataatatgtatatat -aatatacatatacctattatatataatatacctattatatataatatacatatacctatt -atatataatatacctattatatataagatacctattatatataatatacatatacctatt -atatatataatatacctattatatatatataatatacctattatatataatatacctatt -atatatataatatacctattatatatataatatacctattatatatataatatacctatt -atatataatatacctattatatataaaatatacctattatatataatatacctattatat -a---------------------------cattatatataatatacctattatatgcatta -tatataatatacctattatatgcattatatataatatacctattatatgcattatatata -atatacctattatatgcattatataatatattatatataatatgcatattatatgtatta -tatattatatattatatatataatatacatattatatgtattatatattatatattatat -atataatatacatattatatgtattatatattatatataatatacatattatatattata -tattatatacatattatatattatatattatatacatattatatattatatacatattat -atattatatattatatacatattatacattatatatatctaaaatatataatacacatta -tatattatataatacacattatatataatatataatacacattatatattatatataata -cacattatatattatatataatacacattatatattatataatacacattatatattata -tataatacacattatatattatatataatacacattatatattatatataatacacatta -tatattatatataatacacattatatattatataatacacattatatattatatataata -cacattatatatataatacacattatatattatatataatacataatacacattatatat -tatatataatacacattatatataatatataacacacattatatataatatataacacac -attatatattatatataatacacattatatattatatataatacacatatattatatata -atacacattatatattatatataatacacatatattatatataatacacattatatatta -tatataatacacattatatataatatataatacacattatatataatacttattatatat -tatacataatatacatattatatataatacataatatacgtatattatataatatacata -ttatatataatacataatatacgtatattatataatatacatattatatatattatacta -tatataatactcatatatatacatattatatatacatattatatataatactcatattat -atgtacatattatacatacatattatatataatacacatatatacatattatatataata -cacacacacattatatatgtcttatatataatatacatattatatatgtattatattatt -atagatataatatacatattatatctatatataaaatatatatgtagagagagagagaca -gggtctcattttgtctcccaggctggagtgcagtggtgcaatcttggctcactacaacct -ccacctcccaggctcaagggatcctccagcttcagccccccgagtacctgggactacagg -aacgcgtcaccatgcctggctaatttttttttattttttgtagagatggggtttcgccat -gttgccgaggctggtgtcaaactcctggactcaagtgatcctcccacctcagcctcccaa -agtgctgagattacaggtgtgaaccactgcacctggacttacagtcttattttcacata ->p:HG002_2_chr20:38123390-38124905 -caccctttcttggactgactcttcctccccaggctctcagcttccatagtagcttccaag -aaaggccttctctgacttccttgtctaggatattctccatttttaagtccacagcctgtg -accaatggcaacagagcagaaggttagagcaattactgtggatggagcttgcccagtagg -cctcctagctccattttctagctttgtgatctcaggcctgtcctgtaacctctctgggcc -tcagaaacctctctctctctc--tatatatatatatataataatatataataataatata -taatatgtataataataatatataatatttataataataatatatataatatgtatatat -aatatacatatacctattatatataatatacctattatatataatatacatatacctatt -atatataatatacctattatatataagatacctattatatataatatacatatacctatt -atatatataatatacctattatatatatataatatacctattatatataatatacctatt -atatatataatatacctattatatatataatatacctattatatatataatatacctatt -atatataatatacctattatatataaaatatacctattatatataatatacctattatat -acattatatataatatacctattatatgcattatatataatatacctattatatgcatta -tatataatatacctattatatgcattatatataatatacctattatatgcattatatata -atatacctattatatgcattatataatatattatatataatatgcatattatatgtatta -tatattatatattatatatataatatacatattatatgtattatatattatatattatat -atataatatacatattatatgtattatatattatatataatatacatattatatattata -tattatatacatattatatattatatattatatacatattatatattatatacatattat -atattatatattatatacatattatacattatatatatctaaaatatataatacacatta -tatattatataatacacattatatataatatataatacacattatatattatatataata -cacattatatattatatataatacacattatatat-----------------------ta -tataatacacattatatattatatataatacacattatatattatatataatacacatta -tatattatatataatacacattatatattatataatacacattatatattatatataata -cacattatatatataatacacattatatattatatataatacataatacacattatatat -tatatataatacacattatatataatatataacacacattatatataatatataacacac -attatatattatatataatacacattatatattatatataatacacatatattatatata -atacacattatatattatatataatacacatatattatatataatacacattatatatta -tatataatacacattatatataatatataatacacattatatataatacttattatatat -tatacataatatacatattatatataatacataatatacgtatattatataatatacata -ttatatataatacataatatacgtatattatataatatacatattatatatattatacta -tatataatactcatatatatacatattatatatacatattatatataatactcatattat -atgtacatattatacatacatattatatataatacacatatatacatattatatataata -cacacacacattatatatgtcttatatataatatacatattatatatgtattatattatt -atagatataatatacatattatatctatatataaaatatatatgtagagagagagagaca -gggtctcattttgtctcccaggctggagtgcagtggtgcaatcttggctcactacaacct -ccacctcccaggctcaagggatcctccagcttcagccccccgagtacctgggactacagg -aacgcgtcaccatgcctggctaatttttttttattttttgtagagatggggtttcgccat -gttgccgaggctggtgtcaaactcctggactcaagtgatcctcccacctcagcctcccaa -agtgctgagattacaggtgtgaaccactgcacctggacttacagtcttattttcacata ->ref_chr20:38123390-38124905 -caccctttcttggactgactcttcctccccaggctctcagcttccatagtagcttccaag -aaaggccttctctgacttccttgtctaggatattctccatttttaagtccacagcctgtg -accaatggcaacagagcagaaggttagagcaattactgtggatggagcttgcccagtagg -cctcctagctccattttctagctttgtgatctcaggcctgtcctgtaacctctctgggcc -tcagaaacctctctctctctctatatatatatatatataataatatataataataatata -taatatgtataataataatatataatatttataataataatatatataatatgtatatat -aatatacatatacctattatatataatatacctattatatataatatacataaacctatt -atatataatatacctattatatataagatacctattatatataatatacctat------- ------------------------tatatataagatacctattatatataatatac----- ----------atatacctattatatatataatatacctattata----------------t -atatataatatacctattatatatataatatacctatta--------------------- --------------------------------tatatataatatacctattatatatataa -ta---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------tacctat -tatatataatacacattatatataatatataacacacattatatataatatataacacac -attatatattatatataatacacattatatattatatataatacacatatattatatata -atacacattatatattatatataatacacatatattatatataatacacattatatatta -tatataatacacattatatataatatataatacacattatatataatacttattatatat -tatacataatatacatattatatataatacataatatacgtatattatataatatacata -ttatatataatacataatatacgtatattatataatatacatattatatatattatacta -tatataatactcatatatatacatattatatatacatattatatataatactcatattat -atgtacatattatacatacatattatatataatacacatatatacatattatatataata -cacacacacattatatatgtcttatatataatatacatattatatatgtattatattatt -atagatataatatacatattatatctatatataaaatatatatgtagagagagagagaca -gggtctcattttgtctcccaggctggagtgcagtggtgcaatcttggctcactacaacct -ccacctcccaggctcaagggatcctccagcttcagccccccgagtacctgggactacagg -aacgcgtcaccatgcctggctaatttttttttattttttgtagagatggggtttcgccat -gttgccgaggctggtgtcaaactcctggactcaagtgatcctcccacctcagcctcccaa -agtgctgagattacaggtgtgaaccactgcacctggacttacagtcttattttcacata diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b9617e62946167b3934beacc3d1aca4f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b9617e62946167b3934beacc3d1aca4f.msa deleted file mode 100644 index 70d33b42..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b9617e62946167b3934beacc3d1aca4f.msa +++ /dev/null @@ -1,215 +0,0 @@ ->syndip_1_chr20:22082056-22084115 -tataatataataataatacaatataatatatgtatatatgtaggtatataataatatacc -tacatatatacatatattatatatactatctgtatattatatgtataatatatgtatata -taatatatgtatatactatacatgtatatattatattatacatgtatatattataagtat -atactatacatgcatgtattatatgtatatactatacatgcatgtattatatgtatatat -tatacatgcatgtattatatgtatatattatacatgcatgtattatatgtatatattata -catgtatgtattatatgtatagattatacatgtatatattatatatgtatatattacaca -tgtacatatatgtatatattaaacacgtttatattatttattatacatgactatattata -taggtatatatgatatatgcatatatgtcatataggtatatatgacatatatgcatatat -catgtaggtatatatgacatatgcatatatcatataggtatatatgacatatgcatatat -catataggtatatatgatatatgcgcatatatcatataggtatatatgatatatgcgcat -atatcatataggtatatatgatatatgcgcatat---------atcatataggtatatat -gatatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatataggtat -atatgatatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatacag -gtatatgcgcatatatcatataggtataggtataggtagatatatgatatatgcacacat -atcatataggtatatatgatatatg------------ataggtatatatgatatatgata -ggtatatatgatatatgataggtatatatgatatatatcatatcggtatatatgatatat -atcatatcggtatatataggtatatatcataggtatatataggtatatatcacataggta -tatataggtatatatcatataggtatatataatatatgcatttatattatataggtatat -atattacataggtatatgtaatatgtgcatatatattatataggtatatatattatacag -gcatatataatacgtatatatattatatgggcatatatatgtgtatatattatataggta -tatataatatatgtgtatatattatgtgggtatatataatatatgtgtacatattatgtg -ggtatatataatatatgtgtacatattatgtgggtatatataatatatgtgtacatatta -tgtgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtatat -attatgtgggtatatataatatatgtgtacatattatgtgggtatatataatatatgtgt -atatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatat -gtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataat -atatgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatata -taatatatgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggta -tatataatatatgtgtatatattatatatgtaataggaagcaggaatgaatgcacagaag -accttagagtttaaggcattatttgtgtaatgagaaatattatatatacg---------- ------------------------tatattaatatagacgtatatataatatatacatata -tacatatatagtatatactatgtatacatatatactatacatacgtatattatatacatg -tgtattatatacatgtgtattatatatatgtgtatacatatatactatatatacatacat -tatatacatacattatatatgtgtattatatatgtatatattatgtatgtatatattata -tatacgtatatattaatatacatatatatgtgtctcattataccaataatgccttaaact -ctaaggtcttctgtgcattcattcctgcttcctattacatatatattatatagatacata -tataatatatacatatatactacataatatatgcatatataatatatacatatgttgtat -atgtatatataatatatacatatgttgtatatgtatatataatatatacatatgttgtat -atgtatatataatatatacatatgttgtatatgtatatataatatatacatatgttgtat -atgtatatataatatatacatatgttgtatatgtatatataatatatacatatgttgtat -atgtattatatgtatatattacatattatatatacttatgtatgtataatatatatataa -tatatatatatcttaggcaacttttcattgctca ->syndip_2_chr20:22082056-22084115 -tataatataataataatacaatataatatatgtatatatgtaggtatataataatatacc -tacatatatacatatattatatatactatctgtatattatatgtataatatatgtatata -taatatatgtatatactatacatgtatatattatattatacatgtatatattataagtat -atactatacatgcatgtattatatgtatatac---------------------------- -tatacatgcatgtattatatgtatatattatacatgcatgtattatatgtatatattata -catgcatgtattatatgtatatattatacatgtatgtattatatgtatagat-------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------tatacatgtatatattatatatgtatatattacacatgtacat -atat-------gtatatattaaacacgtttatattatttattatacatgtaggtatatat -gacatat--gcatatatcatataggtatatatgacatat--gcatatatcatataggtat -atatgatatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatacag -gtatatgcgcatatatcatataggtataggtataggtagatatatgatatatgcacacat -atcatataggtatatatgatatatgcgcatatatcatataggtatatatgatatatgata -ggtatatatgatatatgataggtatatatgatatatatcatatcggtatatatgatatat -atcatatcggtatatataggtatatatcataggtatatataggtatatatcacataggta -tatataggtatatatcatataggtatatataatatatgcatttatattatataggtatat -atattacataggtatatgtaatatgtgcatatatattatataggtatatatattatacag -gcatatataatacgtatatatattatatgggcatatatatgtgtatatattatataggta -tatataatatatgtgtatatattatgtgggtatatataatatatgtgtatatattatgtg -ggtatatataatatatgtgtacatattatgtgggtatatataatatatgtgtatatatta -tgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatat -attatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgt -atatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatat -gtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataat -atatgtgtatatattatatatgta------------------------------------ ------------------------------------------------------------- ---------------------------------ataggaagcaggaatgaatgcacagaag -accttagagtttaaggcattatttgtgtaatgagaaatattatatatacgtatattaata -tagacgtatatataatatatacatatattaatatagacgtatatataatatatacatata -tacatatatagtatatactatgtatacatatatactatacatacgtatattatatacatg -tgtattatatacatgtgtattatatatatgtgtatacatatatactatatatacatacat -tatatacatacattatatatgtgtattatatatgtatatattatgtatgtatatattata -tatacgtatatattaatatacatatatatgtgtctcattataccaataatgccttaaact -ctaaggtcttctgtgcattcattcctgcttcctattacatatatattatatagatacata -tataatatatacatatatactacataatatatgc-------------------------- ------------------------------------------------------------- -----atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtat -atgtatatataatatatacatatgttgtatatgtatatataatatatacatatgttgtat -atgtattatatgtatatattacatattatatatacttatgtatgtataatatatatataa -tatatatatatcttaggcaacttttcattgctca ->p:HG002_1_chr20:22082056-22084115 -tataatataataataatacaatataatatatgtatatatgtaggtatataataatatacc -tacatatatacatatattatatatactatctgtatattatatgtataatatatgtatata -taatatatgtatatactatacatgtatatattatattatacatgtatatattataagtat -atactatacatgcatgtattatatgtatatac---------------------------- -tatacatgcatgtattatatgtatatattatacatgcatgtattatatgtatatattata -catgcatgtattatatgtatatattatacatgtatgtattatatgtatagat-------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------tatacatgtatatattatatatgtatatattacacatgtacat -atat-------gtatatattaaacacgtttatattatttattatacatgtaggtatatat -gacatat--gcatatatcatataggtatatatgacatat--gcatatatcatataggtat -atatgatatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatacag -gtatatgcgcatatatcatataggtataggtataggtagatatatgatatatgcacacat -atcatataggtatatatgatatatgcgcatatatcatataggtatatatgatatatgata -ggtatatatgatatatgataggtatatatgatatatatcatatcggtatatatgatatat -atcatatcggtatatataggtatatatcataggtatatataggtatatatcacataggta -tatataggtatatatcatataggtatatataatatatgcatttatattatataggtatat -atattacataggtatatgtaatatgtgcatatatattatataggtatatatattatacag -gcatatataatacgtatatatattatatgggcatatatatgtgtatatattatataggta -tatataatatatgtgtatatattatgtgggtatatataatatatgtgtatatattatgtg -ggtatatataatatatgtgtacatattatgtgggtatatataatatatgtgtatatatta -tgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatat -attatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgt -atatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatat -gtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataat -atatgtgtatatattatatatgta------------------------------------ ------------------------------------------------------------- ---------------------------------ataggaagcaggaatgaatgcacagaag -accttagagtttaaggcattatttgtgtaatgagaaatattatatatacgtatattaata -tagacgtatatataatatatacatatattaatatagacgtatatataatatatacatata -tacatatatagtatatactatgtatacatatatactatacatacgtatattatatacatg -tgtattatatacatgtgtattatatatatgtgtatacatatatactatatatacatacat -tatatacatacattatatatgtgtattatatatgtatatattatgtatgtatatattata -tatacgtatatattaatatacatatatatgtgtctcattataccaataatgccttaaact -ctaaggtcttctgtgcattcattcctgcttcctattacatatatattatatagatacata -tataatatatacatatatactacataatatatgc-------------------------- ------------------------------------------------------------- -----atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtat -atgtatatataatatatacatatgttgtatatgtatatataatatatacatatgttgtat -atgtattatatgtatatattacatattatatatacttatgtatgtataatatatatataa -tatatatatatcttaggcaacttttcattgctca ->p:HG002_2_chr20:22082056-22084115 -tataatataataataatacaatataatatatgtatatatgtaggtatataataatatacc -tacatatatacatatattatatatactatctgtatattatatgtataatatatgtatata -taatatatgtatatactatacatgtatatattatattatacatgtatatattataagtat -atactatacatgcatgtattatatgtatatactatacatgcatgtattatatgtatatat -tatacatgcatgtattatatgtatatattatacatgcatgtattatatgtatatattata -catgcatgtattatatgtatatattatacatgtatgtattatatgtatagatattacaca -tgtacatatatgtatatattaaacacgtttatattatttattatacatgactatattata -taggtatatatgatatatgcatatatgtcatataggtatatatgacatatatgcatatat -catgtaggtatatatgacatatgcatatatcatataggtatatatgacatatgcatatat -catataggtatatatgatatacatgtatatattatatatgtatatattacacatgtacat -atat-------gtatatattaaacacgtttatattatttattatacatgtaggtatatat -gacatat--gcatatatcatataggtatatatgacatat--gcatatatcatataggtat -atatgatatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatacag -gtatatgcgcatatatcatataggtataggtataggtagatatatgatatatgcacacat -atcatataggtatatatgatatatgcgcatatatcatataggtatatatgatatatgata -ggtatatatgat-----ataggtatatatgatatatatcatatcggtatatatgatatat -atcatatcggtatatataggtatatatcataggtatatataggtatatatcacataggta -tatataggtatatatcatataggtatatataatatatgcatttatattatataggtatat -atattacataggtatatgtaatatgtgcatatatattatataggtatatatattatacag -gcatatataatacgtatatatattatatgggcatatatatgtgtatatattatataggta -tatataatatatgtgtatatattatgtgggtatatataatatatgtgtatatattatgtg -ggtatatataatatatgtgtacatattatgtgggtatatataatatatgtgtatatatta -tgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatat -attatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgt -atatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatat -gtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataat -atatgtgtatatattatatatgtatatataatatatgtgtatatattatgtaggtatata -taatatatgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggt- ---------------------------------ataggaagcaggaatgaatgcacagaag -accttagagtttaaggcattatttgtgtaatgagaaatattatatatacgtatattaata -tagacgtatatataatatatacatatattaatatagacgtatatataatatatacatata -tacatatatagtatatactatgtatacatatatactatacatacgtatattatatacatg -tgtattatatacatgtgtattatatatatgtgtatacatatatactatatatacatacat -tatatacatacattatatatgtgtattatatatgtatatattatgtatgtatatattata -tatacgtatatattaatatacatatatatgtgtctcattataccaataatgccttaaact -ctaaggtcttctgtgcattcattcctgcttcctattacatatatattatatagatacata -tataatatatacatatatactacataatatatgcatatataatatatacatatgttgtat -atgtatatataatatatacatatgttgtatatgtatatataatatatacatatgttgtat -atgtatatataatatatacatatgttgtatatgtatatataatatatacatatgttgtat -atgtatatataatatatacatatgttgtatatgtatatataatatatacatatgttgtat -atgtattatatgtatatattacatattatatatacttatgtatgtataatatatatataa -tatatatatatcttaggcaacttttcattgctca ->ref_chr20:22082056-22084115 -tataatataataataatacaatataatatatgtatatatgtaggtatataataatatacc -tacatatatacatatattatatatactatctgtatattatatgtataatatatgtatata -taatatatgtatatactatacatgtatatattatattatacatgtatatattataagtat -atactatacatgcatgtattatatgtatatactatacatgcatgtattatatgtatatat -tatacatgcatgtattatatgtatatattatacatgcatgtattatatgtatatattata -catgcatgtattatatgtatatattatacatgtatgtattatatgtatagat-------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------tatacatgtatatattatatatgtatatattacacatgtacat -atat-------gtatatattaaacacgtttatattatttattatacatgtaggtatatat -gacatat--gcatatatcatataggtatatatgacatat--gcatatatcatataggtat -atatgatatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatacag -gtatatgcgcatatatcatataggtataggtataggtagatatatgatatatgcacacat -atcatataggtatatatgatatatgcgcatatatcatataggtatatatgatatatgata -ggtatatatgatatatgataggtatatatgatatatatcatatcggtatatatgatatat -atcatatcggtatatataggtatatatcataggtatatataggtatatatcacataggta -tatataggtatatatcatataggtatatataatatatgcatttatattatataggtatat -atattacataggtatatgtaatatgtgcatatatattatataggtatatatattatacag -gcatatataatacgtatatatattatatgggcatatatatgtgtatatattatataggta -tatataatatatgtgtatatattatgtgggtatatataatatatgtgtatatattatgtg -ggtatatataatatatgtgtacatattatgtgggtatatataatatatgtgtatatatta -tgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatat -attatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgt -atatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatat -gtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataat -atatgtgtatatattatatatgta------------------------------------ ------------------------------------------------------------- ---------------------------------ataggaagcaggaatgaatgcacagaag -accttagagtttaaggcattatttgtgtaatgagaaatattatatatacgtatattaata -tagacgtatatataatatatacatatattaatatagacgtatatataatatatacatata -tacatatatagtatatactatgtatacatatatactatacatacgtatattatatacatg -tgtattatatacatgtgtattatatatatgtgtatacatatatactatatatacatacat -tatatacatacattatatatgtgtattatatatgtatatattatgtatgtatatattata -tatacgtatatattaatatacatatatatgtgtctcattataccaataatgccttaaact -ctaaggtcttctgtgcattcattcctgcttcctattacatatatattatatagatacata -tataatatatacatatatactacataatatatgc-------------------------- ------------------------------------------------------------- -----atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtat -atgtatatataatatatacatatgttgtatatgtatatataatatatacatatgttgtat -atgtattatatgtatatattacatattatatatacttatgtatgtataatatatatataa -tatatatatatcttaggcaacttttcattgctca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b9f51cff314a22617a81ae12c84eb296.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b9f51cff314a22617a81ae12c84eb296.msa deleted file mode 100644 index 9c8bd308..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b9f51cff314a22617a81ae12c84eb296.msa +++ /dev/null @@ -1,65 +0,0 @@ ->syndip_1_chr20:50775436-50776042 -gccttgcttgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtca -cataccaaaggcttgtgtctttaaatctatctctagacttggtattctgctttctcattc -tgtctctccaaagatttccatatatatatatatatatatatatatatatatatatatata -taaatataaatatattctatatattcatatatatatattctatatattcatatatataaa -tatattctatatattcatatataaatatattccatatatataaatatattccatatatt- ---tatatataaatatatatcatatatttatatataaatatatatcatatatttatatata -aatatatatcatatatttatatat-aatatatatcatatatttatatataaatatatatc -atatatttatatataaatatatatcatatatttatatataatatatatcatata-ttata -tataaatatatatcatatatttatatataaatatatatcatatattaatatatatcatat -atttatatattaatatatatcatatatttatatattaatatatatcatatatttatatat -aaatatatatcatatatttatatataaatatatatctacattttttgagacagagtctgg -ctctgtcaccccagctggagtgcag ->syndip_2_chr20:50775436-50776042 -gccttgcttgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtca -cataccaaaggcttgtgtctttaaatctatctctagacttggtattctgctttctcattc -tgtctctccaaagatttccatatatatatatatatatatatatatatatatatatatata -taaatataaatatattctatatattcatatatatatattctatatattcatatatataaa -tatattctatatattcatatatataaatatattctatatattcatata-taaatatattc -catatatataaatatattccatatatttatatataaatatatatcatatatttatatata -aatatatatcatatatttatatataaatatatatcatatatttatatat-aatatatatc -atatatttatatataaatatatatcatatatttatatataatatatatcatata-ttata -tataaatatatatcatatatttatatataaatatatatcatatattaatatatatcatat -atttatatattaatatatatcatatatttatatattaatatatatcatatatttatatat -aaatatatatcatatatttatatataaatatatatctacattttttgagacagagtctgg -ctctgtcaccccagctggagtgcag ->p:HG002_1_chr20:50775436-50776042 -gccttgcttgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtca -cataccaaaggcttgtgtctttaaatctatctctagacttggtattctgctttctcattc -tgtctctccaaagatttccatatatatatatatatatatatatatatatatatatatata -taaatataaatatattctatatattcatatatatatattctatatattcatatatataaa -tatattctatatattcatatataaatatatattctatatattcatata-taaatatattc -catatatataaatatattccatatatttatatataaatatatatcatatccatatatata -aatatattccatatatttatatataaatatatatcatatatttatatataaatatatatc -atatatttatatataaatatatatcatatatttatatataatatatatcatatatttata -tataaatatatatcatatatttatatataaatatatatcatatattaatatatatcatat -atttatatattaatatatatcatatatttatatattaatatatatcatatatttatatat -aaatatatatcatatatttatatataaatatatatctacattttttgagacagagtctgg -ctctgtcaccccagctggagtgcag ->p:HG002_2_chr20:50775436-50776042 -gccttgcttgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtca -cataccaaaggcttgtgtctttaaatctatctctagacttggtattctgctttctcattc -tgtctctccaaagatttccatatatatatatatatatatatatatatatatatatatata -taaatataaatatattctatatattcatatatatatattctatatattcatatatataaa -tatattctatatattcatatataaatatattccatatatataaatatattccatatatt- ---tatatataaatatatatcatatatttatatataaatatatatcatatatttatatata -aatatatatcatatatttatatat-aatatatatcatatatttatatataaatatatatc -atatatttatatataaatatatatcatatatttatatataatatatatcatata-ttata -tataaatatatatcatatatttatatataaatatatatcatatattaatatatatcatat -atttatatattaatatatatcatatatttatatattaatatatatcatatatttatatat -aaatatatatcatatatttatatataaatatatatctacattttttgagacagagtctgg -ctctgtcaccccagctggagtgcag ->ref_chr20:50775436-50776042 -gccttgcttgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtca -cataccaaaggcttgtgtctttaaatctatctctagacttggtattctgctttctcattc -tgtctctccaaagatttccatatatatatatatatatatatatatatatatatatatata -taaatataaatatattctatatattcatatatatatattctatatattcatatatataaa -tatattctatatattcatatataaatatattccatatatataaatatattccatatatt- ---tatatataaatatatatcatatatttatatataaatatatatcatatatttatatata -aatatatatcatatatttatatat-aatatatatcatatat------------------- --------------------------------------------------------ttata -tataaatatatatcatatatttatatataaatatatatcatatattaatatatatcatat -atttatatattaatatatatcatatatttatatattaatatatatcatatatttatatat -aaatatatatcatatatttatatataaatatatatctacattttttgagacagagtctgg -ctctgtcaccccagctggagtgcag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ba516a449ff76749d3e01d677727df4e.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ba516a449ff76749d3e01d677727df4e.msa deleted file mode 100644 index 9cb3d144..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ba516a449ff76749d3e01d677727df4e.msa +++ /dev/null @@ -1,80 +0,0 @@ ->syndip_1_chr20:62270203-62271037 -ggagcctgagaggcttagcagctcatgtgtgtgtcagctgggaacccacagcaagtggat -tccaaagcctgccatgtccctgttgccactagcacctcctcctccactccctcctggcct -ctctgggtcctctccttgtccctcctggcctctctgggtcctctccttgtccctccctga -cctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctct -ctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctc-ctggc -ctctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctc -tgggtcctctctgacctctctgagtcctctccttgtccctctctgggtcctctccttgtc -cctctctgg--------------------------------------------------- --gtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcc -tctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcc -ttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcct -ctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctcct -tgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtcc -ctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctttcctt -gtccctttctggtctc ->syndip_2_chr20:62270203-62271037 -ggagcctgagaggcttagcagctcatgtgtgtgtcagctgggaacccacagcaagtggat -tccaaagcctgccatgtccctgttgccactagcacctcctcctccactccctcctggcct -ctctgggtcctctccttgtccctcctggcctctctgggtcctctccttgtccctccctga -cctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctct -ctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggc -ctctctgggtcctctccttgtccctctctgggtcctctccttgtccctc----------- -----------ctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtc -cctctctga--------------------------------------------------- ----------------cctctctgggtcctctccttgtc---------cctctctgggtcc -tctccttgtc---------cctctctgggtcctctccttgtccctctctgggtcctctcc -ttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcct -ctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctcct -tgtccctctctggcctctctgggtcctttccttgtccctttctggtctc----------- ------------------------------------------------------------- ----------------- ->p:HG002_1_chr20:62270203-62271037 -ggagcctgagaggcttagcagctcatgtgtgtgtcagctgggaacccacagcaagtggat -tccaaagcctgccatgtccctgttgccactagcacctcctcctccactccctcctggcct -ctctgggtcctctccttgtccctcctggcctctctgggtcctctccttgtccctccctga -cctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctct -ctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggc -ctctctgggtcctctccttgtccctctctgggtcctctccttgtccctc----------- -----------ctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtc -cctctctgg--------------------------------------------------- ----------------cctctctgggtcctctc------------------ctctgggtcc -tctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcc -ttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcct -ctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctcct -tgtccctctctggcctctctgggtcctttccttgtccctttctggtctc----------- ------------------------------------------------------------- ----------------- ->p:HG002_2_chr20:62270203-62271037 -ggagcctgagaggcttagcagctcatgtgtgtgtcagctgggaacccacagcaagtggat -tccaaagcctgccatgtccctgttgccactagcacctcctcctccactccctcctggcct -ctctgggtcctctccttgtccctcctggcctctctgggtcctctccttgtccctccctga -cctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctct -ctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggc -ctctctgggtcctctccttgtccctctctgggtcctctccttgtccctc----------- -----------ctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtc -cctctctgg-----------------------------gtcctctccttgtccctctctg -ggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcc -tctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcc -ttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcct -ctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctcct -tgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtcc -ctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctttcctt -gtccctttctggtctc ->ref_chr20:62270203-62271037 -ggagcctgagaggcttagcagctcatgtgtgtgtcagctgggaacccacagcaagtggat -tccaaagcctgccatgtccctgttgccactagcacctcctcctccactccctcctggcct -ctctgggtcctctccttgtccctcctggcctctctgggtcctctccttgtccctccctga -cctctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctct -ctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggc -ctctctgggtcctctccttgtccctctctgggtcctctccttgtccctc----------- -----------ctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtc -cctctctggcctctctgggtcctctctgacctctctgggtcctctccttgtccctctctg -ggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcc -tctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcc -ttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcct -ctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctcct -tgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtcc -ctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctttcctt -gtccctttctggtctc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_bb7fd33627eeebb611fd58a76e4c129f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_bb7fd33627eeebb611fd58a76e4c129f.msa deleted file mode 100644 index 92f76260..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_bb7fd33627eeebb611fd58a76e4c129f.msa +++ /dev/null @@ -1,50 +0,0 @@ ->syndip_1_chr20:61562009-61562352 -ctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctcccggagaga -gagaggggcctccgtgtggagaggtggaccccagggctcccggagagagggacttccgtg -tggagaggtggaccccagggctcccggagagagagagggacctccctgagagagagaggg -acctccgtgtggagaggtggaccccagggctcccggagagagagagggacctccctgtgg -agaggtggaccccagggctcccagagagagagagggaccttcgtgtggagaggtggaccc -cagggctcccggagagagagagggacctccgtgtggagaggtggaccccagggctcccgg -agagagagagggacctccgtgtggagaggtggaccccagggctcccg--gagagagggac -ctccgtgtggagaggtggaccccagggctcccggagagagagagggacctctgtgtggag -aggtggaccccagggctcccggagagaga ->syndip_2_chr20:61562009-61562352 -ctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctcccggagaga -gagaggggcctccgtgtggagaggtggaccccagggctcccggagagagggacctccgtg -tggagaggtggaccccagggctcccggagagagagagggacctccc-------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------tgtggagaggtggaccccagggctcccag -agagagagagggaccttcgtgtggagaggtggaccccagggctcccggagagagagggac -ctccgtgtggagaggtggaccccagggctcccggagagagagagggacctctgtgtggag -aggtggaccccagggctcccggagagaga ->p:HG002_1_chr20:61562009-61562352 -ctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctcccggagaga -gagaggggcctccgtgtggagaggtggaccccagggctcccggagagagggacctccgtg -tggagaggtggaccccagggctcccggagagagagagggacctccc-------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------tgtggagaggtggaccccagggctcccag -agagagagagggaccttcgtgtggagaggtggaccccagggctcccggagagagagggac -ctccgtgtggagaggtggaccccagggctcccggagagagagagggacctctgtgtggag -aggtggaccccagggctcccggagagaga ->p:HG002_2_chr20:61562009-61562352 -ctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctcccggagaga -gagaggggcctccgtgtggagaggtggaccccagggctcccggagagagggacctccgtg -tggagaggtggaccccagggctcccggagagagagagggacctccctgagagagagaggg -acctccctgtggagaggtggaccccagggctcccggagagagagagggacctccctgtgg -agaggtggaccccagggctcccagagagagagagggaccttcgtgtggagaggtggaccc -cagggctcccggagagagagagggacctccgtgtggagaggtggaccccagggctcccag -agagagagagggaccttcgtgtggagaggtggaccccagggctcccggagagagagggac -ctccgtgtggagaggtggaccccagggctcccggagagagagagggacctctgtgtggag -aggtggaccccagggctcccggagagaga ->ref_chr20:61562009-61562352 -ctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctcccggagaga -gagaggggcctccgtgtggagaggtggaccccagggctcccggagagagggacctccgtg -tggagaggtggaccccagggctcccggagagagagagggacctccc-------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------tgtggagaggtggaccccagggctcccag -agagagagagggaccttcgtgtggagaggtggaccccagggctcccggagagagagggac -ctccgtgtggagaggtggaccccagggctcccggagagagagagggacctctgtgtggag -aggtggaccccagggctcccggagagaga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_bcb71c9e5547e2d793157a11880bdab7.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_bcb71c9e5547e2d793157a11880bdab7.msa deleted file mode 100644 index b2fa67f8..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_bcb71c9e5547e2d793157a11880bdab7.msa +++ /dev/null @@ -1,210 +0,0 @@ ->syndip_1_chr20:63948384-63948863 -ccacagatgccagttacgcccgaaaacgacacagaacacaggtgcggacagggaacggca -tcctcagagcatggtcaggggagaaaagcaagctggaaggagagatgattccatctgtat -aaaatccaggaaacgaaggacgctcaccgccatgcgcctcggtgtgaggagggaggcgtg -tgtgagagggaggggatgtgtgtgagaggga-ggggcgtgtgtgagagggaggggcgtgt -gtgaggg---aggggtgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtg -tgagaggcagggg-gcgtgtgtgtga-ggggcgtgtgtgagagggaggggcgtgtgtgag -agggagggg-gcgtgtgtgagggggggcgtgtgtgagaggtaggggcgtgtgtgagaggg -aggggcgtgtgtgagggagggggcgtgtgtgagaggg-----------------aggggc -gtgtgtgtgagggaggggcgtgtgagag-ggagggggcgtgtgtgagaggcaggggcgtg -tgtgtgagggaggggcgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgag -ggggggcgtgtgtgagaggtaggggcgtgtgt----gggagggggcgtgtgtgagaggga -gggggcgtgtgtgagagggaggggcgtgtgtgagacggaggggcgtgtgtgagagggagg -gggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggagggg-- --gcgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagaggcg -tgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagagggaggggcgtgtg -agaggg-aggggcgtgtgtgagagg----------gagggggcgtgtgtgagagggaggg -ggcgtgtgtgagagggaggggcgtgtgtgaagggaggggcgtgtgtgagagggagggggc -gtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgt -gagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgag -aggcaggggcgtgtgtgagggaggggcgtgtgtgagag--------ggagggggcgtgtg -agagggagggggcgtgtgtgagagggagaggcgtgtgtgagaggga-ggggcgtgtgtga -gaggcaggggcgtgtgtgagggaggggcgtgtgtgagagggagggggcgtgtgtgagagg -gagggggcgtgt-------------gtgagagggagaggcgtgtgtgagagggaggggcg -tgtgtgagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggagggggcgtgt -gtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtga -gagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgaga -gggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggg -ag--------------ggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcg -tgtgtgagagggagggggcgtgtgtgagaggga-ggggcgtgtgtgagagggaggggcgt -gtgtgaagggaggggcgtgtgtgagagtgggggcgtgtgtgagttaggggcgtgagaggt -aggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtg-----agaggga -ggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaagg -ggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggc -gtgtgtgagggaggggcgtgtgtgagagggagggg-gcgtgtgagagggaggggcgtgtg -tgagagggaggggc--gtgtgagagggaggggcgtgtgtgagaggga-ggggcgtgtgtg -agagggaggggcgtgtgtgagagggaggggcgtgagagggagggggcgtgtgtgagggag -gggcgtgtgtgagagggaggggggcgtgtgtgagagggagggggcgtgtgtgagagggag -ggggtgtgtgtgagaccgagggggcgtgtaagggagggggtgtgtgtgagagggaagcgt -gtgcacacaccagccctaaccatgatcactctctggccaccaagatttggaacagcaact -tctgtcacatttgaatgtttttaaagcaggtgccactttgttgccataaaccaaaccgta -gtctgtcttt ->syndip_2_chr20:63948384-63948863 -ccacagatgccagttacgcccgaaaacgacacagaacacaggtgcggacagggaacggca -tcctcagagcatggtcaggggagaaaagcaagctggaaggagagatgattccatctgtat -aaaatccaggaaacgaaggacgctcaccgccatgcgcctcggtgtgaggagggaggcgtg -tgtgagagggaggggatgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgt -gtgagag---aggggtgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtg -tgaaagggaggggcgtgtgtgaggga-ggggcgtgtgtgagagggaggggcgtgtgtgag -aggcaggggcgtgtgtgagggagggggcgtgtgtgagagggaggggcgtgtgtgagaggc -aggggcgtgtgtgagagtgggggcgtgtgtgagggggggcgtgtgtgagagggagggggc -gtgtgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtg -tgtgagaggcaggggcgtgtgtggggggggcgtgtgtgag-gggggggcgtgtgtgagag -ggagggggcgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgtgaggga --ggggcgtgtgtgagagggaggggcgtgtgtga---agggaggggtgtgtgtgagagtgg -gggcgtgtgtgagaggg--------gcgtgagaggtaggggcgtgtgtgagagggagggg -tgtgtgtgagagggaggggcgtgtgtgagaggga-ggggcgtgtgtgag-ggagggggcg -tgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagagggaggggcgtgtg -tgagagtgggggcgtgtgtgggggggcgtgtgtgagggggggcgtgtgtgagaggta-gg -ggcgtgtgtgagagggaggggcgtgtgtg-agggaggggcgtgtgtgagaggcaggggcg -tgtgtgggggggggcgtgtgt--gaggggggggcgtgtgtgagagggagggggcgtgtgt -gagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgag -aggcaggggcgtgtgtggggggggcgtgtgtgaggggggcgtgtgagagggaggggcgtg -tgtggggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtga -gagggaggggcgtgtgtgagagggaggggcgtgtgtgaagggaggggtgtgtgtgagagt -gggggcgtgtgtgagagttaggggcgtgagaggtaggggcgtgtgtgagagggaggggcg -tgtgtgaggga-ggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgt -gtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgcga -gagggaggggcgtgtgtgagagggagggggcgtgtgtgag-ggagggggcgtgtgtgaga -gggaggggcgtgtgagag-ggagggggcgtgtgtgagaggcaggggcgtgtgtgtgaggg -aggggcgtgagagggaggggcgtgtgtga---gggggggcgtgtgtgagaggtaggggcg -tgtgtgagagggagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgt -gtgtgagggagggggcgtgt-------------------------------gtgagaggg -aggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggag -ggggcgtgtgtgagagggaggggcgtgtgtga-agggaggggcgtgtgtgagagtg--gg -ggcgtgtgtgagaggg--------gcgtgagaggtaggggcgtgtgtgagagggagggg- -gcgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtg -tgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagagggagggggcgtgtgtg -agagggaggggcgtgt---------------gtgagagggaaggggcgtgtgagagggag -gggcgtgtgtgagaggaaggggcgtgtgtgaga---gggaggggcgtgtgtgagagggag -ggggtgtgtgtgagaccgagggggcgtgtaagggagggggtgtgtgtgagagggaagcgt -gtgcacacaccagccctaaccatgatcactctctggccaccaagatttggaacagcaact -tctgtcacatttgaatgtttttaaagcaggtgccactttgttgccataaaccaaaccgta -gtctgtcttt ->p:HG002_1_chr20:63948384-63948863 -ccacagatgccagttacgcccgaaaacgacacagaacacaggtgcggacagggaacggca -tcctcagagcatggtcaggggagaaaagcaagctggaaggagagatgattccatctgtat -aaaatccaggaaacgaaggacgctcaccgccatgcgcctcggtgtgaggagggaggcgtg -tgtgagagggaggggatgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgt -gtgagag---aggggtgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtg -tgaaagggaggggcgtgtgtgaggga-ggggcgtgtgtgagagggaggggcgtgtgtgag -aggcaggggcgtgtgtgagggagggggcgtgtgtgagagggaggggcgtgtgtgagaggc -aggggcgtgtgtgagagtgggggcgtgtgtgagggggggcgtgtgtgagagggagggggc -gtgtgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtg -tgtgagaggcaggggcgtgtgtggggggggcgtgtgtgag-gggggggcgtgtgtgagag -ggagggggcgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgtgaggga --ggggcgtgtgtgagagggaggggcgtgtgtga---agggaggggtgtgtgtgagagtgg -gggcgtgtgtgagaggg--------gcgtgagaggtaggggcgtgtgtgagagggagggg -tgtgtgtgagagggaggggcgtgtgtgagaggga-ggggcgtgtgtgag-ggagggggcg -tgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagagggaggggcgtgtg -tgagagtgggggcgtgtgtgggggggcgtgtgtgagggggggcgtgtgtgagaggta-gg -ggcgtgtgtgagagggaggggcgtgtgtg-agggaggggcgtgtgtgagaggcaggggcg -tgtgtgggggggggcgtgtgt--gaggggggggcgtgtgtgagagggagggggcgtgtgt -gagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgag -aggcaggggcgtgtgtggggggggcgtgtgtgaggggggcgtgtgagagggaggggcgtg -tgtggggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtga -gagggaggggcgtgtgtgagagggaggggcgtgtgtgaagggaggggtgtgtgtgagagt -gggggcgtgtgtgagagttaggggcgtgagaggtaggggcgtgtgtgagagggaggggcg -tgtgtgaggga-ggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgt -gtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgcga -gagggaggggcgtgtgtgagagggagggggcgtgtgtgag-ggagggggcgtgtgtgaga -gggaggggcgtgtgagag-ggagggggcgtgtgtgagaggcaggggcgtgtgtgtgaggg -aggggcgtgagagggaggggcgtgtgtga---gggggggcgtgtgtgagaggtaggggcg -tgtgtgagagggagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgt -gtgtgagggagggggcgtgt-------------------------------gtgagaggg -aggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggag -ggggcgtgtgtgagagggaggggcgtgtgtga-agggaggggcgtgtgtgagagtg--gg -ggcgtgtgtgagaggg--------gcgtgagaggtaggggcgtgtgtgagagggagggg- -gcgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtg -tgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagagggagggggcgtgtgtg -agagggaggggcgtgt---------------gtgagagggaaggggcgtgtgagagggag -gggcgtgtgtgagaggaaggggcgtgtgtgaga---gggaggggcgtgtgtgagagggag -ggggtgtgtgtgagaccgagggggcgtgtaagggagggggtgtgtgtgagagggaagcgt -gtgcacacaccagccctaaccatgatcactctctggccaccaagatttggaacagcaact -tctgtcacatttgaatgtttttaaagcaggtgccactttgttgccataaaccaaaccgta -gtctgtcttt ->p:HG002_2_chr20:63948384-63948863 -ccacagatgccagttacgcccgaaaacgacacagaacacaggtgcggacagggaacggca -tcctcagagcatggtcaggggagaaaagcaagctggaaggagagatgattccatctgtat -aaaatccaggaaacgaaggacgctcaccgccatgcgcctcggtgtgaggagggaggcgtg -tgtgagagggaggggatgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgt -gtgag-----aggggtgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtg -tgagaggcagggg-gcgtgtgtgtga-ggggcgtgtgtgagagggaggggcgtgtgtgag -agggagggg-gcgtgtgtgagggggggcgtgtgtgagaggtaggggcgtgtgtgagaggg -aggggcgtgtgtgagggagggggcgtgtgtgagaggg-----------------aggggc -gtgtgtgtgagggaggggcgtgtgagag-ggagggggcgtgtgtgagaggcaggggcgtg -tgtgtgagggaggggcgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgag -ggggggcgtgtgtgagaggtaggggcgtgtgt----gggagggggcgtgtgtgagaggga -gggggcgtgtgtgagagggaggggcgtgtgtgagacggaggggcgtgtgtgagagggagg -gggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggagggg-- --gcgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagaggcg -tgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagagggaggggcgtgtg -agaggg-aggggcgtgtgtgagagg----------gagggggcgtgtgtgagagggaggg -ggcgtgtgtgagagggaggggcgtgtgtgaagggaggggcgtgtgtgagagggagggggc -gtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgt -gagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgag -aggcaggggcgtgtgtgagggaggggcgtgtgtgagag--------ggagggggcgtgtg -agagggagggggcgtgtgtgagagggagaggcgtgtgtgagaggga-ggggcgtgtgtga -gaggcaggggcgtgtgtgagggaggggcgtgtgtgagagggagggggcgtgtgtgagagg -gagggggcgtgt-------------gtgagagggagaggcgtgtgtgagagggaggggcg -tgtgtgagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggagggggcgtgt -gtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtga -gagggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgaga -gggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggg -ag--------------ggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcg -tgtgtgagagggagggggcgtgtgtgagaggga-ggggcgtgtgtgagagggaggggcgt -gtgtgaagggaggggcgtgtgtgagagtgggggcgtgtgtgagttaggggcgtgagaggt -aggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtg-----agaggga -ggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggaggg -ggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggc -gtgtgtgagggaggggcgtgtgtgagagggagggg-gcgtgtgagagggaggggcgtgtg -tgagagggaggggc--gtgtgagagggaggggcgtgtgtgagaggga-ggggcgtgtgtg -agagggaggggcgtgtgtgagagggaggggcgtgagagggagggggcgtgtgtgaggaag -gggcgtgtgtgagagggaggggggcgtgtgtgagagggagggggcgtgtgtgagagggag -ggggtgtgtgtgagaccgagggggcgtgtaagggagggggtgtgtgtgagagggaagcgt -gtgcacacaccagccctaaccatgatcactctctggccaccaagatttggaacagcaact -tctgtcacatttgaatgtttttaaagcaggtgccactttgttgccataaaccaaaccgta -gtctgtcttt ->ref_chr20:63948384-63948863 -ccacagatgccagttacgcccgaaaacgacacagaacacaggtgcggacagggaacggca -tcctcagagcatggtcaggggagaaaagcaagctggaaggagagatgattccatctgtat -aaaatccaggaaacgaaggacgctcaccgccatgcgcctcggtgtgaggagggaggcgtg -tgtgagagggaggggatgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgt -gtgagagggaaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggtgtgtg -tgagaccgagggg-gcgtgtaagggagggggtgtgtgtgagagggaagcgtgtgcaca-- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- 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------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------caccagccctaaccatgatcactctctggccaccaagatttggaacagcaact -tctgtcacatttgaatgtttttaaagcaggtgccactttgttgccataaaccaaaccgta -gtctgtcttt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_bddf55a76d381806ed830ff9366b3db1.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_bddf55a76d381806ed830ff9366b3db1.msa deleted file mode 100644 index b85ffcbc..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_bddf55a76d381806ed830ff9366b3db1.msa +++ /dev/null @@ -1,150 +0,0 @@ ->syndip_1_chr20:62349431-62350036 -ggactctcccaagcacctggagaggtgaagagacagtcaaatcatttctccaaagtgctg -agagatgcagctatcaaccacgaatcctacagtcagctcaactatcattcaagagggagg -acaaaacagccgttttcagacaattccggatagactgtcatggaatagaaaaactacagg -gtgcatttcaggaaggaggaagcagcaacccaggggatggggatggggatggggatgggg -atggtgggggtgatgggggtgatgatggtgatggtgatggtgatggtgatggtgatggtg -atggtggg---------ggtggtgatggtgggggtgggggtggtgatggtgggggtgggg -gtgatgatggtgatggtgggggtgatgacggtggggctgggggtgatgatggtgggggtg -atgacggtgatgatgggggtggaggggtgatgacggtgatgatgggggtgggggggtgat -gacggtgatgtgggggtgatgacggtgggggtgg--gggtgatgacggtgat-------- --------------ggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgg -gggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgatggtgatgg -tgggggtgatgatggtgggggtgggggtgatgatggtgagggtgatgatggtgggggtaa -tgacggtggggtgggggtgatgacggtgggagtgggggtgatgacggtgatggtgggggt -gatgacggtgatggtgggggtgatgacggtgatggcggtgggggtgatgacggtgggggt -gggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtggg -ggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggt -gggggtgggggtgatgacggtgatggtagaggtgatgatggtgggggtgatggtgggggt -gggggtggg---------ggtgggggtgatgatggtgatggtgggggtgatgatggtgag -ggtgatgatggtgggggtgatggtgggggtgggggtgggg-------------------- ------------------------------------------------------------- -------------------gtgggggtgatgac---------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------ggtgatggtgggg -gtgatgatggtgggagtgggctggtagtgggggtgatggtttgggtgggagtaaggtgat -ggtggaggtaaagaggcagaaaattgctggctgatgacatggagcccccttccctggagg -agaggtggggtggcgggtaaagggtgcagggagaacatgggcaggctaatgttttgggac -actggtgggtgaccaggtcctgg ->syndip_2_chr20:62349431-62350036 -ggactctcccaagcacctggagaggtgaagagacagtcaaatcatttctccaaagtgctg -agagatgcagctatcaaccacgaatcctacagtcagctcaactatcattcaagagggagg -acaaaacagccgttttcagacaattccggatagactgtcatggaatagaaaaactacagg -gtgcatttcaggaaggaggaagcagcaaccca------ggggatggggatggggatgggg -atggggatggtgggggtgatgggggtgatgatggtgatggtgggggtgatgatggtgatg -gtgatggt---------gatggtgat------ggtgggggtggtgatggtgggggtgggg -gtgatgatggtgatggtgggggtgatgacggtggggctgggggtgatgatggtgggggtg -atgacggtgatgatgggggtggaggggtgatgacggtgatgatgggggtgggggggtgat -gacggtgatgtgggggtgatgacggtgggggtgg--gggtgatgacggtgatggtggggg -tgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgg -gggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgatggtgatgg -tgggggtgatgatggtgggggtgggggtgatgatggtgagggtgatgatggtgggggtaa -tgacggtggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtgggggt -gatgacgatgatggtgggggtgatgacggtgatggcggtgggggtgatgacggtgggggt -gggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtggg -ggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggt -gggggtgggggtgatgacggtgatggtagaggtgatgatggtgggggtgggggtgggggt -gggggtgagggtgatgatggtgggggtgatgatggtgatggtgggggtgatgatggtgag -ggtgatgatggtgggggtgatggtgggggtgggggtgggggtaatgacggtggggtgggg -gtaatgacggtgggggtgggggtgatgacggtgggagtgggggtgatgacggtgatggtg -ggggtgatgacggtgatggtgggggtgatgacggtgatggcggtgggggtgatgacggtg -ggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacg -gtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtagaggtgatg -atggtgggggtgatggtgggggtgggggtgggggtgggggtgatgatggtgatggtgggg -gtgatgatggtgagggtgatgatggtgggggtgatggtgggggtgggggtgggggtgggg -gtgatgatggtgggagtgggctggtagtgggggtgatggtttgggtgggagtaaggtgat -ggtggaggtaaagaggcagaaaattgctggctgatgacatggagcccccttccctggagg -agaggtggggtggcgggtaaagggtgcagggagaacatgggcaggctaatgttttgggac -actggtgggtgaccaggtcctgg ->p:HG002_1_chr20:62349431-62350036 -ggactctcccaagcacctggagaggtgaagagacagtcaaatcatttctccaaagtgctg -agagatgcagctatcaaccacgaatcctacagtcagctcaactatcattcaagagggagg -acaaaacagccgttttcagacaattccggatagactgtcatggaatagaaaaactacagg -gtgcatttcaggaaggaggaagcagcaaccca------ggggatggggatggggatgggg -atggtgggggtgatgggggtgatgatggtgatggtgatggtgatggtgatggtgatggtg -atggtggg---------ggtggtgat-----gggtgggggtgatgacggtgggagtgggg -gtgatgacggtgatggtgggggtgatgacggtgatggtgggggtgatgatggtgggggtg -atgacggtgatgatgggggtggaggggtgatgacggtgatgatgggggtgggggggtgat -gacggtgatgtgggggtgatgacggtgggggtgg--gggtgatgacggtgatggtggggg -tgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgg -gggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgatggtgatgg -tgggggtgatgatggtgggggtgggggtgatgatggtgagggtgatgatggtgggggtaa -tgacggtggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtgggggt -gatgacgatgatggtgggggtgatgacggtgatggcggtgggggtgatgacggtgggggt -gggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtggg -ggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggt -gggggtgggggtgatgacggtgatggtagaggtgatgatggtgggggtgggggtgggggt -gggggtgagggtgatgatggtgggggtgatgatggtgatggtgggggtgatgatggtgag -ggtgatgatggtgggggtgatggtgggggtgggggtgggggtaatgacggtggggtgggg -gtaatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtg -ggggtgatgacgatgatggtgggggtgatgacggtgatggcggtgggggtgatgacggtg -ggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacg -gtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtagaggtgatg -atggtgggggtgatggtgggggtgggggtgggggtgggggtgatgatggtgatggtgggg -gtgatgatggtgagggtgatgatggtgggggtgatggtgggggtggcggtgatggtgggg -gtgatgatggtgggagtgggctggtagtgggggtgatggtttgggtgggagtaaggtgat -ggtggaggtaaagaggcagaaaattgctggctgatgacatggagcccccttccctggagg -agaggtggggtggcgggtaaagggtgcagggagaacatgggcaggctaatgttttgggac -actggtgggtgaccaggtcctgg ->p:HG002_2_chr20:62349431-62350036 -ggactctcccaagcacctggagaggtgaagagacagtcaaatcatttctccaaagtgctg -agagatgcagctatcaaccacgaatcctacagtcagctcaactatcattcaagagggagg -acaaaacagccgttttcagacaattccggatagactgtcatggaatagaaaaactacagg -gtgcatttcaggaaggaggaagcagcaaccca------ggggatggggatggggatgggg -atggtgggggtgatgggggtgatgatggtgatggtgatggtgatggtgatggtgatggtg -atggtgggggtggtgatggtggtgatggtgggggtgggggtggtgatggtgggggtgggg -gtgatgatggtgatggtgggggtgatgacggtggggctgggggtgatgatggtgggggtg -atgacggtgatgatgggggtggaggggtgatgacggtgatgatgggggtgggggggtgat -gacggtgatgtgggggtgatgacggtgggggtgg--gggtgatgacggtgat-------- --------------ggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgg -gggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgatggtgatgg -tgggggtgatgatggtgggggtgggggtgatgatggtgagggtgatgatggtgggggtaa -tgacggtggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtgggggt -gatgacgatgatggtgggggtgatgacggtgatggcggtgggggtgatgacggtgggggt -gggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtggg -ggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggt -gggggtgggggtgatgacggtgatggtagaggtgatgatggtgggggtgatggtgggggt -gggggtggg---------ggtgggggtgatgatggtggtgggggtgatgacggtgggagt -gggggtgatgacggtgatggtgggggtgatgacggtgatg-------------------- ------------------------------------------------------------- -------------------gtgggggtgatgac---------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------ggtgatggtgggg -gtgatgatggtgggagtgggctggtagtgggggtgatggtttgggtgggagtaaggtgat -ggtggaggtaaagaggcagaaaattgctggctgatgacatggagcccccttccctggagg -agaggtggggtggcgggtaaagggtgcagggagaacatgggcaggctaatgttttgggac -actggtgggtgaccaggtcctgg ->ref_chr20:62349431-62350036 -ggactctcccaagcacctggagaggtgaagagacagtcaaatcatttctccaaagtgctg -agagatgcagctatcaaccacgaatcctacagtcagctcaactatcattcaagagggagg -acaaaacagccgttttcagacaattccggatagactgtcatggaatagaaaaactacagg -gtgcatttcaggaaggaggaagcagcaaccca------ggggatggggatggggatgggg -atggtgggggtgatgggggtgatgatggtgatggtgatggtgatggtgatggtgatggtg -atggtggg---------ggtggtgat-----gggtgggggtgatgacggtgggagtgggg -gtgatgacggtgatggtgggggtgatgacggtgatggtgggggtgatgacggtgatggtg -ggggtgatgatggtgggagtgggctggtagtgggggtgatggtttgggtgggagtaaggt -gatg-----gtggaggtaaagaggcagaaaattgctggctgatgacatggag-------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------cccccttccctggagg -agaggtggggtggcgggtaaagggtgcagggagaacatgggcaggctaatgttttgggac -actggtgggtgaccaggtcctgg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_be67c95cf42d6e9d273a3da441adf015.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_be67c95cf42d6e9d273a3da441adf015.msa deleted file mode 100644 index a82480ef..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_be67c95cf42d6e9d273a3da441adf015.msa +++ /dev/null @@ -1,140 +0,0 @@ ->syndip_1_chr20:641636-642665 -caaaataataacaataacagcgacgacaacagcaacaacacctccgagcagtaacagcat -tttccactgcagacggcggcgctgagggtacagggataagatcatccggtgacagggatc -atcatccctgcctggcatagaaacccggacatcggaccctgccctcccgctgcttccgca -gggacagggggcagccagcagagcctccctctgggggtgccccccaatctggttgcctgg -gaggggggcccagcgggggtggagttgcctgggggggggggcccagcgggggtggagttg -cctgggggggg-ggcccagcgggggtggagttgcctgggggggggaggcccagcgggggt -ggagttgcctgggggggg--gcccagcgggggtggagttgcctggg-------------- ----------------ggggggaggcccagcgggggtggagttgcctgggggggggcccag -cgggggtggagttgcctgggggggg-ggcccagcgggggtggagttgcctggggggggga -ggcccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagttgcctggg -g---------------------------gggggaggcccagcgggggtggagttgcctgg -gggggg-------------------------------ggcccagcgggggtggagttgcc -tggggggg---ggcccagcgggggtggagttgcctggggggg---gcccagcgggggtgg -agttgcctggggggggcccagcgggggtggagttgcctggggggggccccagcgggggtg -gagttgcctggggggg--ggcccagcgggggtggagttgcctgggggggg--gcccagcg -ggggtggagttgcctggggggggcccagcgggggtggagttgcctggggggggccccagc -gggggtggagttgcctgggggggggcccagcgggggtggagttgcctggggggggggccc -agcgggggtggagttgcctggggggggggcccagcgggggtggagttgcctggggggggg -ggcccagcgggggtggagttgcctgggggggggcccagcgggggtggagttgcctg-ggg -ggggggcccagcgggggtggagttgcct-ggggggggcccagcgggggtggagttgcct- -gggggggggcccagcgggggtggagttgcctg-gggggggggcccagcgggggtggagtt -gcctg-gggggggcccagcgggggtggagttgcctgtgggggggggcccagcgggggtgg -agttgcctggggggggcccagcgggggtggagttgcctgggggggggcccagcgggggtg -gagcaccctggacggccccgcggagccccctgcgggaggcgagggcggccctcgggctct -ggaaggggccgcgcggcctggaagacattacacggctgtcgggcggggggcggcgctcgc -agttccggaggggggtcccggcggcggacgcgcggggtgaggggaccgcccggccacaga -gcgcgctttgttctgcgccgcccccgggagctggaaccaatggattggcggca ->syndip_2_chr20:641636-642665 -caaaataataacaataacagcgacgacaacagcaacaacacctccgagcagtaacagcat -tttccactgcagacggcggcgctgagggtacagggataagatcatccggtgacagggatc -atcatccctgcctggcatagaaacccggacatcggaccctgccctcccgctgcttccgca -gggacagggggcagccagcagagcctccctctgggggtgccccccaatctggttgcctgg -gacgggggcccagcgggggtggagttgcct-ggggggggggcccagcgggggtggagttg -cctggggggggaggcccagcgggggtggagttgcctgggggggggaggcccagcgggggt -ggagttgcctgggggggggtgcccagcgggggtggagttgcctggggggggcccagcggg -ggtggagttgcctgtggggggaggcccagcgggggtggagttgcct-ggggggggcccag -cgggggtggggttgcctggggggggaggcccagcgggggtggagttgcctggggggggga -ggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtggagttgcctggg -ggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggggttgcctgg -ggggggcccagcgggggtggggttgcctggggggggaggcccagcgggggtggagttgcc -tgggggggggaggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtgg -agttgcctggggggggcccagcgggggtggggttgcctgggggggg-cccagcgggggtg -gggttgcctggggggggaggcccagcaggggtggagttgcctgggggggggtgcccagcg -ggggtggagttgcctggggggggcccagcgggggtggagttgcctgggggggg-cccagc -gggggtggagttgcctgggggggggcccagcggggatggggttgcct-gggggggggccc -agcgggggtggggttgcct-gggggggggcccagcgggggtggagttgcct--ggggggg -ggcccagcgggggtggagttgcct-ggggggggcccagcgggggtggagttgcctgtggg -ggggggcccagcgggggtggagttgcctgggggggggcccagcgggggtggagttgcctg -gggggggggcccagcgggggtggagttgcctgtggtggggggcccagcgggggtggagtt -gcctgtgggggggcccagcgggggtggagttgcctgtgggggggggcccagcgggggtgg -agttgcctggggggggcccagcgggggtggagttgcct-ggggggggcccagcgggggtg -gagcaccctggacggccccgcggagccccctgcgggaggcgagggcggccctcgggctct -ggaaggggccgcgcggcctggaagacattacacggctgtcgggcggggggcggcgctcgc -agttccggaggggggtcccggcggcggacgcgcggggtgaggggaccgcccggccacaga -gcgcgctttgttctgcgccgcccccgggagctggaaccaatggattggcggca ->p:HG002_1_chr20:641636-642665 -caaaataataacaataacagcgacgacaacagcaacaacacctccgagcagtaacagcat -tttccactgcagacggcggcgctgagggtacagggataagatcatccggtgacagggatc -atcatccctgcctggcatagaaacccggacatcggaccctgccctcccgctgcttccgca -gggacagggggcagccagcagagcctccctctgggggtgccccccaatctggttgcctgg -gacgggggcccagcgggggtggagttgcct-ggggggggggcccagcgggggtggagttg -cctggggggggaggcccagcgggggtggagttgcctgggggggggaggcccagcgggggt -ggagttgcctgggggggggtgcccagcgggggtggagttgcctggggggggcccagcggg -ggtggagttgcctgtggggggaggcccagcgggggtggagttgcct-ggggggggcccag -cgggggtggggttgcctggggggggaggcccagcgggggtggagttgcctggggggggga -ggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtggagttgcctggg -ggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggggttgcctgg -ggggggcccagcgggggtggggttgcctggggggggaggcccagcgggggtggagttgcc -tgggggggggaggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtgg -agttgcctggggggggcccagcgggggtggggttgcctgggggggg-cccagcgggggtg -gggttgcctggggggggaggcccagcaggggtggagttgcctgggggggggtgcccagcg -ggggtggagttgcctggggggggcccagcgggggtggagttgcctgggggggg-cccagc -gggggtggagttgcctgggggggggcccagcggggatggggttgcct-gggggggggccc -agcgggggtggggttgcct-gggggggggcccagcgggggtggagttgcct--ggggggg -ggcccagcgggggtggagttgcct-ggggggggcccagcgggggtggagttgcctgtggg -ggggggcccagcgggggtggagttgcctgggggggggcccagcgggggtggagttgcctg -gggggggggcccagcgggggtggagttgcctgtggtggggggcccagcgggggtggagtt -gcctgtgggggggcccagcgggggtggagttgcctgtgggggggggcccagcgggggtgg -agttgcctggggggggcccagcgggggtggagttgcct-ggggggggcccagcgggggtg -gagcaccctggacggccccgcggagccccctgcgggaggcgagggcggccctcgggctct -ggaaggggccgcgcggcctggaagacattacacggctgtcgggcggggggcggcgctcgc -agttccggaggggggtcccggcggcggacgcgcggggtgaggggaccgcccggccacaga -gcgcgctttgttctgcgccgcccccgggagctggaaccaatggattggcggca ->p:HG002_2_chr20:641636-642665 -caaaataataacaataacagcgacgacaacagcaacaacacctccgagcagtaacagcat -tttccactgcagacggcggcgctgagggtacagggataagatcatccggtgacagggatc -atcatccctgcctggcatagaaacccggacatcggaccctgccctcccgctgcttccgca -gggacagggggcagccagcagagcctccctctgggggtgccccccaatctggttgcctgg -gaggggggcccagcgggggtggagttgcctgggggggggggcccagcgggggtggagttg -cctgggggggg-ggcccagcgggggtggagttgcctgggggggggaggcccagcgggggt -ggagttgcctgggggggg--gcccagcgggggtggagttgcctggg-------------- ----------------ggggggaggcccagcgggggtggagttgcctgggggggggcccag -cgggggtggagttgcctgggggggg-ggcccagcgggggtggagttgcctggggggggga -ggcccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagttgcctggg -g---------------------------gggggaggcccagcgggggtggagttgcctgg -gggggg-------------------------------ggcccagcgggggtggagttgcc -tggggggg---ggcccagcgggggtggagttgcctggggggg---gcccagcgggggtgg -agttgcctggggggggcccagcgggggtggagttgcctggggggggccccagcgggggtg -gagttgcctggggggg--ggcccagcgggggtggagttgcctgggggggg--gcccagcg -ggggtggagttgcctggggggggcccagcgggggtggagttgcctggggggggccccagc -gggggtggagttgcctgggggggggcccagcgggggtggagttgcctggggggggggccc -agcgggggtggagttgcctggggggggggcccagcgggggtggagttgcctggggggggg -ggcccagcgggggtggagttgcctgggggggggcccagcgggggtggagttgcctg-ggg -ggggggcccagcgggggtggagttgcct-ggggggggcccagcgggggtggagttgcct- -gggggggggcccagcgggggtggagttgcctg-gggggggggcccagcgggggtggagtt -gcctg-gggggggcccagcgggggtggagttgcctgtgggggggggcccagcgggggtgg -agttgcctggggggggcccagcgggggtggagttgcctgggggggggcccagcgggggtg -gagcaccctggacggccccgcggagccccctgcgggaggcgagggcggccctcgggctct -ggaaggggccgcgcggcctggaagacattacacggctgtcgggcggggggcggcgctcgc -agttccggaggggggtcccggcggcggacgcgcggggtgaggggaccgcccggccacaga -gcgcgctttgttctgcgccgcccccgggagctggaaccaatggattggcggca ->ref_chr20:641636-642665 -caaaataataacaataacagcgacgacaacagcaacaacacctccgagcagtaacagcat -tttccactgcagacggcggcgctgagggtacagggataagatcatccggtgacagggatc -atcatccctgcctggcatagaaacccggacatcggaccctgccctcccgctgcttccgca -gggacagggggcagccagcagagcctccctctgggggtgccccccaatctggttgcctgg -gacgggggcccagcgggggtggagttgcct-ggggggggggcccagcgggggtggagttg -cctggggggggaggcccagcgggggtggagttgcctgggggggggaggcccagcgggggt -ggagttgcctgggggggggtgcccagcgggggtggagttgcctggggggggcccagcggg -ggtggagttgcctgtggggggaggcccagcgggggtggagttgcct-ggggggggcccag -cgggggtggggttgcctggggggggaggcccagcgggggtggagttgcctggggggggga -ggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtggagttgcct--- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------ggggggggcccagcgggggtggagttgcctg-tgg -tggggggccagcgggggtgaagttgcct-gggggggg----------------------- --------------------------------------------ccagcgggggtggagtt -gcctg-ggggggggccagcgggggtggagttgcctgtggggggggg-ccagcgggggtgg -agttgcctgggggggg-ccagcgggggtggagttgcctgggggggg--ccagcgggggtg -gagcaccctggacggccccgcggagccccctgcgggaggcgagggcggccctcgggctct -ggaaggggccgcgcggcctggaagacattacacggctgtcgggcggggggcggcgctcgc -agttccggaggggggtcccggcggcggacgcgcggggtgaggggaccgcccggccacaga -gcgcgctttgttctgcgccgcccccgggagctggaaccaatggattggcggca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_c1beed4ff87d6482a746ae3c7f9ba90b.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_c1beed4ff87d6482a746ae3c7f9ba90b.msa deleted file mode 100644 index ccf7cd65..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_c1beed4ff87d6482a746ae3c7f9ba90b.msa +++ /dev/null @@ -1,250 +0,0 @@ ->syndip_1_chr20:20356320-20358020 -aagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcacactgagggga -ggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggag -gtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgagggga -gatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggag -gtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacactgtgaggggagg -tggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtgg -tcaca--ctgaggggaggtggtcatagtgtgaggggaggtggtcacactgtgaggggagg -tggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtgg -tcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtca -cactgtgaggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtc -acactgaggggaagtggtcacactgagaggaggtggtcacactg---------------- ------------------------------------------------------------- ------------------------------------------------------------- --aggggaggtggtcatactg---------------------------------------- --------------------tgaggggaggtggtcatactgtgagtgaggaggtagtcaca -ctgaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcac -actgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatact -gtgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacac -tgaggggaggtggtcacagtgtgaggggaggtggtcacact----gaggggaggtggtca -cactgaggggaggtggtcacagtgtgagaggaggtggtcacactgaggggaggtggtcac -agtgtga--ggggagatggtcacactgaggggaggtggtcacagtgtgaggggaggtggt -cacactgaggggaggtggtcac-------------------agtgtgaggggaggtggtc -acactgaggggaggtggtcacactgaggggaggtggtcaca------------------- ---gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggagatggtc -acactgaggggaggtggtcacagtgtga--ggggaggtggtcacactgagg--------- -------------ggaggtggtcacagtgtgcggggaggtggtcatactgaggggaggtgg -tcacactgaggggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggta -gtcacactgaggggaagtggtcacact-----------------------gaggggaggt -ggtcacactgaggggagggggtcatactgcgagtggaggtagtcacact--gtgaagggt -ggtagtcacactgagaggaggtggtcacac--tgaggggaagtggtcacactgaggggag -gtggtcatactgtga--ggggaagtggtcacactgaggggaggtggtcatagtgtgaggg -gaggtggtcacac--tgaggggaggtggtcacactgaggggaggtggtcacagtgtgagg -ggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtcatactgaggg -gaggtggtcacagtgtgaggggaggtggtcaca---------------------ctgagg -ggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggg -gaggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgagg -ggaggtggtcacactgaggggaggtggtcaca--ctgaggagaggtggtcatagtgtgag -gggaggtggtcacac--tgaggggaggtggtcacactgaggggaggtggtcatagtgtga -ggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcacactgag -gggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacagtg--- ------------------------------------tgaggggaggtggtcacactgaggg -gaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactgagggg -aggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtcacattgagga -gaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactgagggg -aggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgcggg -gaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtgtgagggg -aggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggg -gaggtggtcacactgaggggaggtggtcacactgagggaaggtggtcacactgaggggag -gtggtcatagtgtgaggggaggtggtcatagtgtgaggggaggtggtcacagtgtgaggg ->syndip_2_chr20:20356320-20358020 -aagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcacactgagggga -ggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggag -gtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgagggga -gatggtcacactgaggggaggtggtcacagtg-------------------tgaggggag -gtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacactgtgaggggagg -tggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtgg -tcatagtgtgaggggaggtggtcacact----ggggaggtggtcacactgtgaggggagg -tggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtgg -tcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtca -cactgtgaggggaggtggtcacac--tgagaggaggtggtcacactgaggggaagtggtc -acactgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtca -cactggggaggtggtcacactgtgaggggaggtggtcacactgtgaggggaggtggtcac -actgagaggaggtggtcacactgaggggaagtggtcacactgagaggaggtggtcacact -gaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggaagtggtcacac -tgaggggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcaca -ctgaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcac -actgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatact -gtgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacac -tgaggggaggtggtcacagtgtgaggggaggtggtcacact----gaggggaggtggtca -cactgaggggaggtggtcacagtgtgcggggaggtggtcatactgaggggaggtggtcac -agtgtga--ggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggt -cacactgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtc -acactgaggggaggtggtcacactgagaggaggtggtcacactgaggggaggtggtcata -ctgtgagtgaggaagtagtcacactgaggggaagtggtcaca--ctgaggggaggtggtc -acactgaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggagggggt -catactgcgagtggaggtagtcacactgtgaagggtggtagtcacactgagaggaggtgg -tcacactgaggggaagtggtcacactgaggggaggtggtcatactgtga--ggggaagtg -gtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggt -ggtcacactgagaggaggtggtcacac--tgaggggaggtggtcatactgtgagtgagga -ggtagtcacactgaggggaagtggtcacac--tgaggggaggtggtcacactgaggggag -gtggtcatactgtgagtgaggaggtagtcacactgaggggagggggtcatactgcgagtg -gaggtagtcacactgtgaagggtggtagtcacactgagaggaggtggtcaca--ctgagg -ggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcacactgaggg -gaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgagg -ggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtcatactgaggg -gaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcgg -ggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcata--ctgag -gggaggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcacactgtga -ggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcacactgag -gggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactgagg -agaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggg -gaggtggtcatagtgtgaggggaggtggtgacactgaggggaggtggtcacactgagggg -aggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtcacattgagga -gaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactgagggg -aggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggg -gaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtgtgagggg -aggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggg -gaggtggtcacactgaggggaggtggtcacactgagggaaggtggtcacactgaggggag -gtggtcatagtgtgaggggaggtggtcatagtgtgaggggaggtggtcacagtgtgaggg ->p:HG002_1_chr20:20356320-20358020 -aagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcacactgagggga -ggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggag -gtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgagggga -gatggtcacactgaggggaggtggtcacagtg-------------------tgaggggag -gtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacactgtgaggggagg -tggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtgg -tcatagtgtgaggggaggtggtcacact----ggggaggtggtcacactgtgaggggagg -tggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtgg -tcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtca -cactgtgaggggaggtggtcacac--tgagaggaggtggtcacactgaggggaagtggtc -acactgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtca -cactggggaggtggtcacactgtgaggggaggtggtcacactgtgaggggaggtggtcac -actgagaggaggtggtcacactgaggggaagtggtcacactgagaggaggtggtcacact -gaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggaagtggtcacac -tgaggggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcaca -ctgaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcac -actgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatact -gtgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacac -tgaggggaggtggtcacagtgtgaggggaggtggtcacact----gaggggaggtggtca -cactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcac -agtgtga--ggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggt -cacactgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtc -acactgaggggaggtggtcacactgagaggaggtggtcacactgaggggaggtggtcata -ctgtgagtgaggaagtagtcacactgaggggaagtggtcaca--ctgaggggaggtggtc -acactgaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggagggggt -catactgcgagtggaggtagtcacactgtgaagggtggtagtcacactgagaggaggtgg -tcacactgaggggaagtggtcacactgaggggaggtggtcatactgtga--ggggaagtg -gtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggt -ggtcacactgagaggaggtggtcacac--tgaggggaggtggtcatactgtgtgcgggga -ggtggtcatactgaggggaggtggtcacac--tgaggggaggtggtcacactgaggggag -gtggtcatactgtgagtgaggaggtagtcacactgaggggagggggtcatactgcgagtg -gaggtagtcacactgtgaagggtggtagtcacactgagaggaggtggtcaca--ctgagg -ggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcacactgaggg -gaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgagg -ggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtcatactgaggg -gaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcgg -ggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcata--ctgag -gggaggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcacactgtga -ggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcacactgag -gggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactgagg -agaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggg -gaggtggtcatagtgtgaggggaggtggtgacactgaggggaggtggtcacactgagggg -aggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtcacattgagga -gaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactgagggg -aggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggg -gaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtgtgagggg -aggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggg -gaggtggtcacactgaggggaggtggtcacactgagggaaggtggtcacactgaggggag -gtggtcatagtgtgaggggaggtggtcatagtgtgaggggaggtggtcacagtgtgaggg ->p:HG002_2_chr20:20356320-20358020 -aagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcacactgagggga -ggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggag -gtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgagggga -gatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggag -gtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacactgtgaggggagg -tggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtgg -tcatagtgtgaggggaggtggtcacact----ggggaggtggtcacactgtgaggggagg -tggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtgg -tcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtca -cactgtgaggggaggtggtcacac--tgagaggaggtggtcacactgaggggaagtggtc -acactgaggggaggtggtcacactgaggggaggtggtcatagtg---------------- ------------------------------------------------------------- ------------------------------------------------------------- --aggggaggtggtcacagtg---------------------------------------- --------------------tgaggggaggtggtcatactgtgagtgaggaggtagtcaca -ctgaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcac -actgaggggaggtggtcacactggggaggtggtcacactgtgaggggaggtggtcacact -gtgaggggaggtggtcacactgagaggaggtggtcaca--ctgaggggaagtggtcacac -tgagaggaggtggtcaca--ctgaggggaggtggtcatactgtgagtgaggaggtagtca -cactgaggggaagtggtcaca--ctgaggggaggtggtcacactgaggggaggtggtcat -actgtgagtgaggaggtagtcacactgaggggagggggtcatactgcgagtggaggtagt -cacactgtgaagggtggtagtc-------------------acactgagaggaggtggtc -acactgaggggaagtggtcacactgaggggaggtggtcata------------------- ---ctgtgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtc -acactgaggggaggtggtcacagtgtga--ggggaggtggtcacactgagg--------- -------------ggaggtggtcacagtgtgcggggaggtggtcatactgaggggaggtgg -tcacactgaggggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggta -gtcacactgaggggagggggtcatactg---------------------cgagtggaggt -agtcacactgtgaagggtggtagtcacactgagaggaggtggtcacac----tgagggga -agtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggag -gtggtcatagtgtga--ggggaggtggtcacactgaggggaggtggtcacagtgtgaggg -gaggtggtcacac--tgaggggaggtggtcacagtgaggggaggtggtcacagtgtgagg -ggaggtggtcacactgaggggaggtggtcacagtgtacggggaggtggtcatactgaggg -gaggtggtcacagtgtgaggggaggtggtcaca---------------------ctgagg -ggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggg -gaggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgagg -ggaggtggtcacactgaggggaggtggtcaca--ctgaggagaggtggtcatagtgtgag -gggaggtggtcacac--tgaggggaggtggtcacactgaggggaggtggtcatagtgtga -ggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcacactgag -gggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacagtg--- ------------------------------------tgaggggaggtggtcacactgaggg -gaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactgagggg -aggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtcacattgagga -gaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactgagggg -aggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgcggg -gaggtggtcacactgcggggaggtggtcatactgaggggaggtggtcacagtgtgagggg -aggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggg -gaggtggtcacactgaggggaggtggtcacactgagggaaggtggtcacactgaggggag -gtggtcatagtgtgaggggaggtggtcatagtgtgaggggaggtggtcacagtgtgaggg ->ref_chr20:20356320-20358020 -aagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcacactgagggga -ggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggag -gtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgagggga -gatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggag -gtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacactgtgaggggagg -tggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtgg -tcatagtgtgaggggaggtggtcacact----ggggaggtggtcacactgtgaggggagg -tggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtgg -tcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtca -cactgtgaggggaggtggtcacac--tgagaggaggtggtcacactgaggggaagtggtc -acactgaggggaggtggtcacactgaggggaggtggtcatagtg---------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---tgaggggaggtggtcacactggggaggtggtcacactgtgaggggaggtggtcacact -gtgaggggaggtggtcacactgagaggaggtggtcaca--ctgaggggaagtggtcacac -tgagaggaggtggtcaca--ctgaggggaggtggtcatactgtgagtgaggaggtagtca -cactgaggggaagtggtcaca--ctgaggggaggtggtcacactgaggggaggtggtcat -actgtgagtgaggaggtagtcacactgaggggagggggtcatactgcgagtggaggtagt -cacactgtgaagggtggtagtc-------------------acactgagaggaggtggtc -acactgaggggaagtggtcacactgaggggaggtggtcata------------------- ---ctgtgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtc -acactgaggggaggtggtcacagtgtga--ggggaggtggtcacactgagg--------- -------------ggaggtggtcacagtgtgcggggaggtggtcatactgaggggaggtgg -tcacactgaggggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggta -gtcacactgaggggagggggtcatactg---------------------cgagtggaggt -agtcacactgtgaagggtggtagtcacactgagaggaggtggtcacac----tgagggga -agtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggag -gtggtcatagtgtga--ggggaggtggtcacac--------------------------- -----------------------------------tgaggggaggtggtcacagtgtgagg -ggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtcatactgaggg -gaggtggtcacagtgtgaggggaggtggtcaca-------------------gtgtgagg -ggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggg -gaggtggtcacac--tgagggaaggtggtcacactgaggggaggtggtcatagtgtgagg -ggaggtggtcatagtg-------------------tgaggggaggtggtcacagtgtgag -gg---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_c3c96241ade48ae0003101107ab5e74b.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_c3c96241ade48ae0003101107ab5e74b.msa deleted file mode 100644 index a0e11621..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_c3c96241ade48ae0003101107ab5e74b.msa +++ /dev/null @@ -1,165 +0,0 @@ ->syndip_1_chr20:59383804-59385235 -ccatcctcaaatgtgagagctgatgattggggtggaggaggaggtgagtggggagggggt -gggggagaaggaggtgatggggaagagatgagtgggcaggaggtgagcagggaggaggtg -agcagggatgagtggaggaaggaggtgatagggaggaggtgagtgggcaggaggtgagca -gggagaagatgagcaggggggtggtgagcggggaggaggtggaggggaaggaagtgatgg -gggaggaggtggggggaaggaggtgatggggaggaggtgaatgggcaggaggtgactggg -gaggaggtgagcagggaggaggtgagcagggaggaggtgagtggagtggggatgggagtg -gagtggggggaaggaagtgatagggaggagatgagtgggcaggaggtgagcagagaggag -atgagtagagcagggatgagtaggggaaggaggtgataggaggtgagtgggcaggaggtg -agcagggaggaggcgagcagggaggaggtagaggggaaggaagtgatggggaggaggtga -ggggggaaagaggtggcgggggaaggaggtgatggggaggaggtgagtggggaggaaggt -gggaggaaggaggtgatggggaggatgtgggggaggtggggagcaaggaggtgatgggga -ggaggtgagtggggaggtggtgagca---------------------------------- ----------------------------gggaggaggtgagggggcaagggaggtgatggg -gaggaaggaggttatggggaggtggtgagtggggagggaggtaaggggtaaggtggtgat -gtggaggtggtgagtggggaggtggtgagaggggaggagatgagggggcaagggaggtga -tggggaggaggtgagtggggaggaaggtggggggaaggaggtgatggggaggatgtgggg -gaggtgggggggaaggaggtgaggcagaggaggggagtggggagggagatgagtaaggaa -gtgatggggagagggtgagtggggaagtggtgagaggggaggaggtgagggggcaaggga -ggtgatgcggaggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggag -gaagtggggaggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggagg -aagtgggggggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggagga -agtgggggggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaa -gtgggggggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaag -tggggaggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagt -gggggggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtg -ggggggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgg -gggggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggg -ggggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggg -gggaaggaggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaagtggggg -ggaaggaggtgatggggaggaggtgagaggggaggagctgaggggggaaggaggtaatga -ggacaaggtgaggggaaaggaggtaagggaggggaaggggagggaaggagctgagcgggg -cagagcatgtctcctctc ->syndip_2_chr20:59383804-59385235 -ccatcctcaaatgtgagagctgatgattggggtggaggaggaggtgagtggggagggggt -gggggagaaggaggtgatggggaagagatgagtgggcaggaggtgagcagggaggaggtg -agcagggatgagtggaggaaggaggtgatagggaggaggtgagtgggcaggaggtgagca -gggagaagatgagcaggggggtggtgagcggggaggaggtggaggggaaggaagtgatgg -gggaggaggtggggggaaggaggtgatggggaggaggtgaatgggcaggaggtgactggg -gaggaggtgagcagggaggaggtgagcagggaggaggtgagtggagtggggatgggagtg -gagtggggggaaggaagtgatagggaggagatgagtgggcaggaggtgagcagagaggag -atgagtagagcagggatgagtaggggaaggaggtgataggaggtgagtgggcaggaggtg -agcagggaggaggcgagcagggaggaggtagaggggaaggaagtgatggggaggaggtga -ggggggaaagaggtggcgggggaaggaggtgatggggaggaggtgagtggggaggaaggt -gggaggaaggaggtgatggggaggatgtgggggaggtggggagcaaggaggtgatgggga -ggaggtgagtggggaggtggtgagcagggaggaggtgagggggcaagggaggtgatgggg -aggaggtgagtggggaggtggtgagcggggaggaggtgagggggcaagggaggtgatggg -gaggaaggaggttatggggaggtggtgagtggggagggaggtaaggggtaaggtggtgat -gtggaggtggtgagtggggaggtggtgagaggggaggagatgagggggcaagggaggtga -tggggaggaggtgagtggggaggaaggtggggggaaggaggtgatggggaggatgtgggg -gaggtgggggggaaggaggtgaggcagaggaggggagtggggagggagatgagtaaggaa -gtgatggggagagggtgagtggggaagtggtgagaggggaggaggtgagggggcaaggga -ggcgatgcggaggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggag -gaagtggggaggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggagg -aagtgggggggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggagga -agtgggggggaaggaggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaa -gtggggaggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaag -tgggggggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagt -gggggggaaggaggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaagtg -ggggggaaggaggtgatggggaggaggtgag----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------aggggaggagctgaggggggaaggaggtaatga -ggacaaggtgaggggaaaggaggtaagggaggggaaggggagggaaggagctgagcgggg -cagagcatgtctcctctc ->p:HG002_1_chr20:59383804-59385235 -ccatcctcaaatgtgagagctgatgattggggtggaggaggaggtgagtggggagggggt -gggggagaaggaggtgatggggaagagatgagtgggcaggaggtgagcagggaggaggtg -agcagggatgagtggaggaaggaggtgatagggaggaggtgagtgggcaggaggtgagca -gggagaagatgagcaggggggtggtgagcggggaggaggtggaggggaaggaagtgatgg -gggaggaggtggggggaaggaggtgatggggaggaggtgaatgggcaggaggtgactggg -gaggaggtgagcagggaggaggtgagcagggaggaggtgagtggagtggggatgggagtg -gagtggggggaaggaagtgatagggaggagatgagtgggcaggaggtgagcagagaggag -atgagtagagcagggatgagtaggggaaggaggtgataggaggtgagtgggcaggaggtg -agcagggaggaggcgagcagggaggaggtagaggggaaggaagtgatggggaggaggtga -ggggggaaagaggtggcgggggaaggaggtgatggggaggaggtgagtggggaggaaggt -gggaggaaggaggtgatggggaggatgtgggggaggtggggagcaaggaggtgatgggga -ggaggtgagtggggaggtggtgagcagggaggaggtgagggggcaagggaggtgatgggg -aggaggtgagtggggaggtggtgagcggggaggaggtgagggggcaagggaggtgatggg -gaggaaggaggttatggggaggtggtgagtggggagggaggtaaggggtaaggtggtgat -gtggaggtggtgagtggggaggtggtgagaggggaggagatgagggggcaagggaggtga -tggggaggaggtgagtggggaggaaggtggggggaaggaggtgatggggaggatgtgggg -gaggtgggggggaaggaggtgaggcagaggaggggagtggggagggagatgagtaaggaa -gtgatggggagagggtgagtggggaagtggtgagaggggaggaggtgagggggcaaggga -ggcgatgcggaggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggag -gaagtggggaggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggagg -aagtgggggggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggagga -agtgggggggaaggaggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaa -gtggggaggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaag -tgggggggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagt -gggggggaaggaggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaagtg -ggggggaaggaggtgatggggaggaggtgag----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------aggggaggagctgaggggggaaggaggtaatga -ggacaaggtgaggggaaaggaggtaagggaggggaaggggagggaaggagctgagcgggg -cagagcatgtctcctctc ->p:HG002_2_chr20:59383804-59385235 -ccatcctcaaatgtgagagctgatgattggggtggaggaggaggtgagtggggagggggt -gggggagaaggaggtgatggggaagagatgagtgggcaggaggtgagcagggaggaggtg -agcagggatgagtggaggaaggaggtgatagggaggaggtgagtgggcaggaggtgagca -gggagaagatgagcaggggggtggtgagcggggaggaggtggaggggaaggaagtgatgg -gggaggaggtggggggaaggaggtgatggggaggaggtgaatgggcaggaggtgactggg -gaggaggtgagcagggaggaggtgagcagggaggaggtgagtggagtggggatgggagtg -gagtggggggaaggaagtgatagggaggagatgagtgggcaggaggtgagcagagaggag -atgagtagagcagggatgagtaggggaaggaggtgataggaggtgagtgggcaggaggtg -agcagggaggaggcgagcagggaggaggtagaggggaaggaagtgatggggaggaggtga -ggggggaaagaggtggcgggggaaggaggtgatggggaggaggtgagtggggaggaaggt -gggaggaaggaggtgatggggaggatgtgggggaggtggggagcaaggaggtgatgggga -ggaggtgagtggggaggtggtgagca---------------------------------- ----------------------------gggaggaggtgagggggcaagggaggtgatggg -gaggaaggaggttatggggaggtggtgagtggggagggaggtaaggggtaaggtggtgat -gtggaggtggtgagtggggaggtggtgagaggggaggagatgagggggcaagggaggtga -tggggaggaggtgagtggggaggaaggtggggggaaggaggtgatggggaggatgtgggg -gaggtgggggggaaggaggtgaggcagaggaggggagtggggagggagatgagtaaggaa -gtgatggggagagggtgagtggggaagtggtgagaggggaggaggtgagggggcaaggga -ggtgatgcggaggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggag -gaagtggggaggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggagg -aagtgggggggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggagga -agtgggggggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaa -gtgggggggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaag -tggggaggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagt -gggggggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtg -ggggggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgg -gggggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggg -ggggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggg -gggaaggaggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaagtggggg -ggaaggaggtgatggggaggaggtgagaggggaggagctgaggggggaaggaggtaatga -ggacaaggtgaggggaaaggaggtaagggaggggaaggggagggaaggagctgagcgggg -cagagcatgtctcctctc ->ref_chr20:59383804-59385235 -ccatcctcaaatgtgagagctgatgattggggtggaggaggaggtgagtggggagggggt -gggggagaaggaggtgatggggaagagatgagtgggcaggaggtgagcagggaggaggtg -agcagggatgagtggaggaaggaggtgatagggaggaggtgagtgggcaggaggtgagca -gggagaagatgagcaggggggtggtgagcggggaggaggtggaggggaaggaagtgatgg -gggaggaggtggggggaaggaggtgatggggaggaggtgaatgggcaggaggtgactggg -gaggaggtgagcagggaggaggtgagcagggaggaggtgagtggagtggggatgggagtg -gagtggcgggaaggaagtgatagggaggagatgagtgggcaggaggtgagcagagaggag -atgagtagagcagggatgagtaggggaaggaggtgataggaggtgagtgggcaggaggtg -agcagggaggaggcgagcagggaggaggtagaggggaaggaagtgatggggaggaggtga -ggggggaaagaggtggcgggggaaggaggtgatggggaggaggtgagtggggaggaaggt -ggggggaaggaggtgatagggaggatgtgggggaggtgggggggaaggaggtgaggcaga -ggaggggagtggggagg-------------------gagatgagtaaggaagtgatgggg -agagggtgagtggggaagtggtgagaggggaggaggtgagggggcaagggaggcgatgcg -gaggaaggaggtgatgggaaggaggtgag------------------------------- ------------------------------------------------------------- -tgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagga------- ------------------------------------------------------------- --------------ggtgagtgtgtaggaggtaagcagggaggaagtggggg--------- ------------ggaaggaggtgatggggaggaggtgagtgtgtaggaggtaagcagggag -gaagtgggggggaaggaggtgatggggaggaggtgagtgtgtaggaggtaagcagggagg -aagtgggggggaaggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggagga -agtgggggggaaggaggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaa -gtgggggggaaggaggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaag -tgggggggaaggaggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaagt -gggggggaaggaggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaagtg -ggggggaaggaggtgatggggaggaggtgag----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------aggggaggagctgagtggggaaggaggtaatga -ggacaaggtgaggggaaaggaggtaagggaggggaaggggagggaaggagctgagcgggg -cagagcatgtctcctctc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_c3ca784845992e7f185ad2e6a992de0e.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_c3ca784845992e7f185ad2e6a992de0e.msa deleted file mode 100644 index 24a437db..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_c3ca784845992e7f185ad2e6a992de0e.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:57948901-57949446 -gatggatggatggatagtggatagatggatgaatagtggatggataaatggattaatgga -tggatgaatggatgatggatggatgaatgagatggatggatt----------------ga -tggatggatggatggatggatggatggaagaatggatgatggatggatga---------- -----------gatggatggatggatggatggaagaatggatgatggatggatga------ ---gatggatggatggatggggggttggatggatggatggatggatggatggatagtggat -agatggatgaatagtggatggataaatggattaatggatggatgaatggatgatggatgg -atgaatgagatggatggattgatggatggatggatggatggaagaatggatgatggatgg -atgaatgagatgggtggattgatggatggatggatggatggatggatggatggatggatg ------------------------------------------------------------- ------------- ->syndip_2_chr20:57948901-57949446 -gatggatggatggatagtggatagatggatgaatagtggatggataaatggattaatgga -tggatgaatggatgatggatggatgaatgagatggatggattgatggatggatggatgga -tggatggatggatggatggatggatggaagaatggatgatggatggatgagatggatgga -tggatggatggatggatggatggatggatggaagaatggatgatggatggatgagatgga -tggatggatggatggatggggggttggatggatggatggatggatggatggatagtggat -agatggatgaatagtgaatggataaatggattaatggatggatggatagtggatagatgg -atgaat------agtggatggataaatggattaatggatggatgaatggatgatggatgg -atgaatgagatggatggattgatggatggatggatggatggatggatggatggaagaatg -gatgatggatggatgaatgagatgggtggattgatggatggatggatggatggatggatg -gatggatggatg ->p:HG002_1_chr20:57948901-57949446 -gatggatggatggatagtggatagatggatgaatagtggatggataaatggattaatgga -tggatgaatggatgatggatggatgaatgagatggatggattgatggatggatggatgga -tggatggatggatggatggatggatggaagaatggatgatggatggatgagatggatgga -tggatggatggatggatggatggatggatggaagaatggatgatggatggatgagatgga -tggatggatggatggatggggggttggatggatggatggatggatggatggatagtggat -agatggatgaatagtgaatggataaatggattaatggatggatggatagtggatagatgg -atgaat------agtggatggataaatggattaatggatggatgaatggatgatggatgg -atgaatgagatggatggattgatggatggatggatggatggatggatggatggaagaatg -gatgatggatggatgaatgagatgggtggattgatggatggatggatggatggatggatg -gatggatggatg ->p:HG002_2_chr20:57948901-57949446 -gatggatggatggatagtggatagatggatgaatagtggatggataaatggattaatgga -tggatgaatggatgatggatggatgaatgagatggatggattgatggatggatggatgga -tggatggatggatggatggatggatggaaga----------------------------- --------atggatggatggatggatggatggaagaatggatgatggatggatgagatgga -tggatggatggatggatggggggttggatggatggatggatggatggatggatagtggat -agatggatgaatagtgaatggataaatggattaatggatggatggatagtggatagatg- --tgatg------gatggatggatggatggatggatggatggaagaatggatgatggatgg -atgaatgagatgggtggattgatggatggatggatggatggatggatggatggatggatg ------------------------------------------------------------- ------------- ->ref_chr20:57948901-57949446 -gatggatggatggatagtggatagatggatgaatagtggatggataaatggattaatgga -tggatgaatggatgatggatggatgaatgagatggatggattgatggatggatggatgga -tggatggatggatggatggatggatggaagaatggatgatggatggatgagatggatgga -tggatggatggatggatggatggatggatggaagaatggatgatggatggatgagatgga -tggatggatggatggatggggggttggatggatggatggatggatggatggatagtggat -agatggatgaatagtgaatggataaatggattaatggatggatggatagtggatagatgg -atgaat------agtggatggataaatggattaatggatggatgaatggatgatggatgg -atgaatgagatggatggattgatggatggatggatggatggatggatggatggaagaatg -gatgatggatggatgaatgagatgggtggattgatggatggatggatggatggatggatg -gatggatggatg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_c42bbcec24917db34a0c5391f80eabbb.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_c42bbcec24917db34a0c5391f80eabbb.msa deleted file mode 100644 index ff4ea8dc..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_c42bbcec24917db34a0c5391f80eabbb.msa +++ /dev/null @@ -1,150 +0,0 @@ ->syndip_1_chr20:4032147-4033438 -cagtgctcagtggtgtccaggctggagtgcagcggcgtgatctcggctcgctacaaccac -ctcccagccgcctgccttggcctcccaaagagccgagattgcagcctctgcccggccgcc -accccgtctgggaagtgaggagcgtctctgcttggccacccatcgtctgggatatgagga -gcccctctgcctggctgcccagtctggaaagt---------------------------- -------------gaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcg -cctcttcccggctgccatcccatctaggaactgaggagcgtctctgcccggccgcccatc -gtctgagatgtggggagcacctctgccccaccgccctgtctgggatgtgaggagcgcctc -tgctgggccgcaaccctgtctgggaggtgaggagcgtctctgccccgccgctccgtctga -gaagtgaggaaaccctctgcctggcaaccgccccgtctgagaagtgaggagcccctccgt -ccggcaaccaccccgt-------------------------------------------- --------------------------------------------ctgggaagtgaggagcg -tctccgcccggcagccaccccgtccgggagggaggtggggggggtcagccccccgcccgg -ccagccgccccgtccgggaggtgaggggctcctctgcccggccgcccctactgggaagtg -aggagcccctctgcccggccagccgccccgtccgggagggaggcgggggggggggtcggc -cagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccgccccg -tccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggacccctctg -cccggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggct -gccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggagc -ccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagccccccgcctg -gccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagccgccc -cgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccgggagg -gaggtggggggggg--tcagccccccgcccggccagccgccccgtccgggagggaggtgg -ggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggcgcctctgccc -ggccacccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggagg -gaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagccc -cctttccggcc--gccgcctgtccgggaggtgaggggcgcctctgcctggccgcccctac -tgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtggggggga -cagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccggccgc -ccctactgggaagtgaggagcccctctgcctggccagccgccccgtc ->syndip_2_chr20:4032147-4033438 -cagtgctcagtggtgtccaggctggagtgcagcggcgtgatctcggctcgctacaaccac -ctcccagccgcctgccttggcctcccaaagagccgagattgcagcctctgcccggccgcc -accccgtctgggaagtgaggagcgtctctgcttggccacccatcgtctgggatatgagga -gcccctctgcctggctgcccagtctggaaagtgaggagcgtctctgcccggccgccatcc -catctaggaagcgaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcg -cctcttcccggctgccatcccatctaggaactgaggagcgtctctgcccggccgcccatc -gtctgagatgtggggagcacctctgccccaccgccctgtctgggatgtgaggagcgcctc -tgctgggccgcaaccctgtctgggaggtgaggagcgtctctgccccgccgctccgtctga -gaagtgaggaaaccctctgcctggcaaccgccccgtctgagaagtgaggagcccctccgt -ccggcaaccaccccgt-------------------------------------------- --------------------------------------------ctgggaagtgaggagcg -tctccgcccggcagccaccccgtccgggagggaggt------------------------ ------------------------------------------------------------- ---------------------------------------------gggggggggggtcggc -cagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccgccccg -tccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggacccctctg -cccggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggct -gccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggagc -ccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagccccccgcctg -gccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagccgccc -cgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccgggagg -gaggtgggggggggggtcagccccccgcccggccagccgccccgtccgggagggaggtgg -ggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggcgcctctgccc -ggccacccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggagg -gaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagccc -cctttccggcc--gccgcctgtccgggaggtgaggggcgcctctgcctggccgcccctac -tgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtggggggga -cagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccggccgc -ccctactgggaagtgaggagcccctctgcctggccagccgccccgtc ->p:HG002_1_chr20:4032147-4033438 -cagtgctcagtggtgtccaggctggagtgcagcggcgtgatctcggctcgctacaaccac -ctcccagccgcctgccttggcctcccaaagagccgagattgcagcctctgcccggccgcc -accccgtctgggaagtgaggagcgtctctgcttggccacccatcgtctgggatatgagga -gcccctctgcctggctgcccagtctggaaagtgaggagcgtctctgcccggccgccatcc -catctaggaagcgaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcg -cctcttcccggctgccatcccatctaggaactgaggagcgtctctgcccggccgcccatc -gtctgagatgtggggagcacctctgccccaccgccctgtctgggatgtgaggagcgcctc -tgctgggccgcaaccctgtctgggaggtgaggagcgtctctgccccgccgctccgtctga -gaagtgaggaaaccctctgcctggcaaccgccccgtctgagaagtgaggagcccctccgt -ccggcaaccaccccgt-------------------------------------------- --------------------------------------------ctgggaagtgaggagcg -tctccgcccggcagccaccccgtccgggagggaggt------------------------ ------------------------------------------------------------- ---------------------------------------------gggggggggggtcggc -cagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccgccccg -tccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggacccctctg -cccggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggct -gccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggagc -ccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagccccccgcctg -gccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagccgccc -cgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccgggagg -gaggtggggggggggtcagccccctttccggcccagccgccccgtccgggagggaggtgg -ggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggcgcctctgccc -ggccacccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggagg -gaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagccc -cccttccggccgggccgcctgtccgggaggtgaggggcgcctctgcctggccgcccctac -tgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtggggggga -cagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccggccgc -ccctactgggaagtgaggagcccctctgcctggccagccgccccgtc ->p:HG002_2_chr20:4032147-4033438 -cagtgctcagtggtgtccaggctggagtgcagcggcgtgatctcggctcgctacaaccac -ctcccagccgcctgccttggcctcccaaagagccgagattgcagcctctgcccggccgcc -accccgtctgggaagtgaggagcgtctctgcttggccacccatcgtctgggatatgagga -gcccctctgcctggctgcccagtctggaaagtgaggagcgtctctgcccggccgccatcc -catctaggaagcgaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcg -cctcttcccggctgccatcccatctaggaactgaggagcgtctctgcccggccgcccatc -gtctgagatgtggggagcacctctgccccaccgccctgtctgggatgtgaggagcgcctc -tgctgggccgcaaccctgtctgggaggtgaggagcgtctctgccccgccgctccgtctga -gaagtgaggaaaccctctgcctggcaaccgccccgtctgagaagtgaggagcccctccgt -ccggcaaccaccccgtccgggagggaggtggggggggtcagccccccgcccggccagccg -ccccgtccgggaggtgaggggctcctctgcccggccgcccctactgggaagtgaggagcg -tctccgcccggcagccaccccgtccgggagggaggt------------------------ ------------------------------------------------------------- ---------------------------------------------gggggggggggtcggc -cagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccgccccg -tccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggacccctctg -cccggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggct -gccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggagc -ccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagccccccgcctg -gccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagccgccc -cgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccgggagg -gaggtggggggggggtcagccccctttccggcc--gccgccccgtccgggagggaggtgg -ggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggcgcctctgccc -ggccacccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggagg -gaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagccc -cccttccggccggccgccctgtccgggaggtgaggggcgcctctgcctggccgcccctac -tgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtggggggga -cagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccggccgc -ccctactgggaagtgaggagcccctctgcctggccagccgccccgtc ->ref_chr20:4032147-4033438 -cagtgctcagtggtgtccaggctggagtgcagcggcgtgatctcggctcgctacaaccac -ctcccagccgcctgccttggcctcccaaagagccgagattgcagcctctgcccggccgcc -accccgtctgggaagtgaggagcgtctctgcttggccacccatcgtctgggatatgagga -gcccctctgcctggctgcccagtctggaaagtgaggagcgtctctgcccggccgccatcc -catctaggaagcgaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcg -cctcttcccggctgccatcccatctaggaactgaggagcgtctctgcccggccgcccatc -gtctgagatgtggggagcacctctgccccaccgccctgtctgggatgtgaggagcgcctc -tgctgggccgcaaccctgtctgggaggtgaggagcgtctctgccccgccgctccgtctga -gaagtgaggaaaccctctgcctggcaaccgccccgtctgagaagtgaggagcccctccgt -ccggcaaccaccccgt-------------------------------------------- --------------------------------------------ctgggaagtgaggagcg -tctccgcccggcagccaccccgtccgggagggaggt------------------------ ------------------------------------------------------------- ---------------------------------------------gggggggggggtcggc -cagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccgccccg -tccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggacccctctg -cccggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggct -gccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggagc -ccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagccccccgcctg -gccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagccgccc -cgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccgggagg -gaggtggggggggg---------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------gtcagccc -cctttccggcc--gccgcctgtccgggaggtgaggggcgcctctgcctggccgcccctac -tgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtggggggga -cagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccggccgc -ccctactgggaagtgaggagcccctctgcctggccagccgccccgtc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_c5069c0545b22809b43e824442304f5d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_c5069c0545b22809b43e824442304f5d.msa deleted file mode 100644 index 98792768..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_c5069c0545b22809b43e824442304f5d.msa +++ /dev/null @@ -1,65 +0,0 @@ ->syndip_1_chr20:63641779-63642135 -cccaccccagctcagcgcctcggagtccccggccccgctctgcgcccctccgagctccgc -cctagccccgcccccgcccagtgccccgccccctgcctgctgctagccctgcccccgccc -cggcccctgcccgctccgagctccgccctggccccgccccggcccctgcccgctccgagc -tccgccctggccccgccccccgcccagtgccccgccccctgcctgctgctagccctgccc -ccgccccggcccctgcccgctccgagctccgccccggccccg------------------ ------------------------------------------------------------- --------------------------------------------------------ccccg -gcccctgcccgctccgagctccgccctggccccgcccccgcccagtgccccgccccctga -ctgctgctagccctgcccccgccccggcccctgcccgctccgagctccgccccggccccg -ccccggcccctgcccgctccgagctccgccccggccccgccccggcccctgcccgctccg -agcttcgccccggccccgccccggcccctgcccgctccgagctccgccccggccccgccc -ccgcaccttctcgcgcagccgctcgcgcagtgcg ->syndip_2_chr20:63641779-63642135 -cccaccccagctcagcgcctcggagtccccggccccgctctgcgcccctccgagctccgc -cctagccccgcccccgcccagtgccccgccccctgcctgctgctagccctgcccccgccc -cggcccctgcccgctccgagctccgccctggccccgccccggcccctgcccgctccgagc -tccgccctggccccg-cccccgcccagtgccccgccccctgcctgctgctagccctgccc -ccgccccggcccctgcccgctccgagctccaccctggccccgcccccgcccagtgccccg -ccccctgcctgctgcttgccctgccccctccccggcccctgcccgctccgagctccgccc -cggccccgccccggcccagtgccccgccccctgcctgctgctagccctgcccccgccccg -gcccctgcccgctccgagctccgccctggccccgcccccgcccagtgccccgccccctgc -ctgctgcttgccctgccccctccccggcccctgcccgctccgagctccgccccggcctcg -ccccggcccctgcccgctccgagcttcgccccggccccgccccggcccctgcccgctccg -agcttcgccccggccccgccccggcccctgcccgctccgaactccgccccggccccgccc -ccgcaccttctcgcgcagccgctcgcgcagtgcg ->p:HG002_1_chr20:63641779-63642135 -cccaccccagctcagcgcctcggagtccccggccccgctctgcgcccctccgagctccgc -cctagccccgcccccgcccagtgccccgccccctgcctgctgctagccctgcccccgccc -cggcccctgcccgctccgagctccgccctggccccgccccggcccctgcccgctccgagc -tccgccctggccccg-cccccgcccagtgccccgccccctgcctgctgctagccctgccc -ccgccccggcccctgcccgctccgagctccaccctggccccgcccccgcccagtgccccg -ccccctgcctgctgcttgccctgccccctccccggcccctgcccgctccgagctccgccc -cggccccgccccggcccagtgccccgccccctgcctgctgctagccctgcccccgccccg -gcccctgcccgctccgagctccgccctggccccgcccccgcccagtgccccgccccctgc -ctgctgcttgccctgccccctccccggcccctgcccgctccgagctccgccccggcctcg -ccccggcccctgcccgctccgagcttcgccccggccccgccccggcccctgcccgctccg -agcttcgccccggccccgccccggcccctgcccgctccgaactccgccccggccccgccc -ccgcaccttctcgcgcagccgctcgcgcagtgcg ->p:HG002_2_chr20:63641779-63642135 -cccaccccagctcagcgcctcggagtccccggccccgctctgcgcccctccgagctccgc -cctagccccgcccccgcccagtgccccgccccctgcctgctgctagccctgcccccgccc -cggcccctgcccgctccgagctccgccctggccccgccccggcccctgcccgctccgagc -tccgccctggccccgccccccgcccagtgccccgccccctgcctgctgctagccctgccc -ccgccccggcccctgcccgctccgagctccgccccggccccg------------------ ------------------------------------------------------------- --------------------------------------------------------ccccg -gcccctgcccgctccgagctccgccctggccccgcccccgcccagtgccccgccccctga -ctgctgctagccctgcccccgccccggcccctgcccgctccgagctccgccccggccccg -ccccggcccctgcccgctccgagctccgccccggccccgccccggcccctgcccgctccg -agcttcgccccggccccgccccggcccctgcccgctccgagctccgccccggccccgccc -ccgcaccttctcgcgcagccgctcgcgcagtgcg ->ref_chr20:63641779-63642135 -cccaccccagctcagcgcctcggagtccccggccccgctctgcgcccctccgagctccgc -cctagccccgcccccgcccagtgccccgccccctgcctgctgctagccctgcccccgccc -cggcccctgcccgctccgagctccgccccggccccgccccggcccctgcccgctccgagc -tccgccctggccccg-cccccgcccagtgccccgccccctgactgctgctagccctgccc -ccgccccggcccctgcccgctccgagcttcgccccggccccg------------------ ------------------------------------------------------------- --------------------------------------------------------ccccg -gcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagcc--- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------gctcgcgcagtgcg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_c50e1186af8d764e9f4a7ebc3e6ca294.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_c50e1186af8d764e9f4a7ebc3e6ca294.msa deleted file mode 100644 index 2b643f53..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_c50e1186af8d764e9f4a7ebc3e6ca294.msa +++ /dev/null @@ -1,145 +0,0 @@ ->syndip_1_chr20:20320239-20320619 -ggaaatttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcag -taaagatggtatttcagatatatagatatatatatattatatatatgtaatatatataat -atatgtaatatatattatatatatgtaatatatataatatatgtaatatattatatatat -gtaatatatataatatatgtaatatatattatatatgtaatatatataatatatgtaata -tatattatatatgtaatata----atatatgtaatatatattatatatgtaatatataat -atatgtaatatatattatatatgtaatataatatatgtaatatatattatatatgtaata -tatattacatatattatatatgcaatatatattatatatattatatatgcaatatatatt -atatatattatatatgcaatatatattatatatgcaatatatattatatatattatatat -gcaatatatattatatatattacatatgtaatatatattacatatgtaatatataatata -ttatatattacatatgtaatatataatatattatatattacatatgtaatatataatata -tattacatatgtaatatataatatatattacatatgtaatatattatatattacatatgt -aatatattatatattacatatgtaatatattatatattacatatgtaatatattatatat -tacatatgtaatatattatatattacatatgtaatatatataatatattacatatgtaat -atataatatattatatatgtaatatatattacatatataatatatataatatatatgtaa -tatattatatatattatatatgtaatatatattacatatataatatatattatatatatt -acatatattatatatgtaatatatattacatatgtaatatatgtaatatatattacatat -gtaatatatattatatatgtaatatatattacatatattatatatgtaatatatattata -tatattatatatgtaatgtataatatatatattatatatgtaatatatattatatataat -atatgtaatatatattatatatgtaatgtatattatatatattatatatgtaatgtatat -tatatataatatatgtaatgtatattatatatgtaatatatattatgtatattatatatg -taatatatattatatatattatatatgtaatatatattatatatattatatatgtaatat -atattatatatattatatatgtaatatatattatatatattatatatgtaatatatatta -tatatattatatatgtaatatatattatatatattatatatgtaatatatattatatata -ttatatatgtaatatatattatatatattatatatgtaatatatattatatatattatat -atgtaatatatattatatatattatatatgtaatatatattatatatattatatatgtaa -tatatattatatatattatatatgtaatatatattatatatattatatatgtaatatata -ttatatatattatatatgtaatatatatatatttaaaaacagaaccattatcttttagag -atacatactgaagtgtctggagacatgcttcaagataaccca ->syndip_2_chr20:20320239-20320619 -ggaaatttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcag -taaagatggtatttcagatatatagatatatatatattatatatatgtaatatatataat -atatgtaatatata---------------------------ttatatatatgtaatatat -ataatatatgtaatatatgtaatatatattatatatgta----atataatatatgtaata -tatattatatatgtaatatata--------------------atatatgtaatatataat -atatgtaatatatattatatatgtaatata-------taatatatattatatatgtaata -tatatatatttaaaaacagaaccattatcttttagagatac------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----atactgaagtgtctggagacatgcttcaagataaccca ->p:HG002_1_chr20:20320239-20320619 -ggaaatttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcag -taaagatggtatttcagatatatagatatatatatattatatatatgtaatatatataat -atatgtaatatata---------------------------ttatatatatgtaatatat -ataatatatgtaatatatgtaatatatattatatatgta----atataatatatgtaata -tatattatatatgtaatatata--------------------atatatgtaatatataat -atatgtaatatatattatatatgtaatata-------taatatatattatatatgtaata -tatatatatttaaaaacagaaccattatcttttagagatac------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----atactgaagtgtctggagacatgcttcaagataaccca ->p:HG002_2_chr20:20320239-20320619 -ggaaatttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcag -taaagatggtatttcagatatatagatatatatatat--tatatatgtaatatatataat -atatgtaatatgta--atatatataatatatgtaatatatattatatatatgtaatatat -ataatatatgtaatatatgtaatatatattatatatgta----atataatatatgtaata -tatattatatatgtaatatataatatatgtaatatatatattatatatgtaatatataat -atatgtaatatatattatatatgtaatataatatatgtaatatatattatatatgtaata -tatattacatatattatatatgcaatatatattatatatattatatatgcaatatatatt -atatatattatatatgcaatatatattatatatgcaatatatattatatatattatatat -gcaatatatattatatatattacatatgtaatatatattacatatgtaatatataatata -ttatatattacatatgtaatatataatatattatatattacatatgtaatatataatata -tattacatatgtaatatataatatatattacatatgtaatatattatatattacatatgt -aatatattatatattacatatgtaatatattatatattacatatgtaatatattatatat -tacatatgtaatatattatatattacatatgtaatatatataatatattacatatgtaat -atataatatattatatatgtaatatatattacatatataatatatataatatatatgtaa -tatattatatatattatatatgtaatatatattacatatataatatatattatatatatt -acatatattatatatgtaatatatattacatatgtaatatatgtaatatatattacatat -gtaatatatattatatatgtaatatatattacatatattatatatgtaatatatattata -tatattatatatgtaatgtataatatatatattatatatgtaatatatattatatataat -atatgtaatatatattatatatgtaatgtatattatatatattatatatgtaatgtatat -tatatataatatatgtaatgtatattatatatgtaatatatattatgtatattatatatg -taatatatattatatatattatatatgtaatatatattatatatattatatatgtaatat -atattatatatattatatatgtaatatatattatatatattatatatgtaatatatatta -tatatattatatatgtaatatatattatatatattatatatgtaatatatattatatata -ttatatatgtaatatatattatatatattatatatgtaatatatattatatatattatat -atgtaatatatattatatatattatatatgtaatatatattatatatattatatatgtaa -tatatattatatatattatatatgtaatatatatgtaatatatattatatatgtaatata -taatatatattatatatgtaatatatatatatttaaaaacagaaccattatcttttagag -atacatactgaagtgtctggagacatgcttcaagataaccca ->ref_chr20:20320239-20320619 -ggaaatttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcag -taaagatggtatttcagatatatagatatatatatattatatatatgtaatatatataat -atatgtaatatata---------------------------ttatatatatgtaatatat -ataatatatgtaatatatgtaatatatattatatatgta----atataatatatgtaata -tatattatatatgtaatatata--------------------atatatgtaatatataat -atatgtaatatatattatatatgtaatata-------taatatatattatatatgtaata -tatatatatttaaaaacagaaccattatcttttagagatac------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----atactgaagtgtctggagacatgcttcaagataaccca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_c84764c85e3bc2208c93471f25974884.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_c84764c85e3bc2208c93471f25974884.msa deleted file mode 100644 index 9df36af2..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_c84764c85e3bc2208c93471f25974884.msa +++ /dev/null @@ -1,640 +0,0 @@ ->syndip_1_chr20:63693349-63693832 -ggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccctatgg -gagtgatgggggcctccacctccaccaccagcaccagcagcaccacctccaccttcacca -ccaccacctccaccaccacctccaccacctccacctccaccacctccaccacctccacca -ccaccacctccaccaccaccacctccaccaccaccaccaccaccacctccaccaccacca -ccaccaccaccacctccacctccaccacctccaccaccacctccacctccaccaccacct -ccacctccacctccaccaccaccacctccaccacctccaccacctccacctccaccacca 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-ccaccaccacctccaccaccaccacctccaccacctccaccaccacctccacctccacca -ccaccacctccacctccacctccaccaccaccaccaccacctccactaccaccacctcca -cctccaccaccaccacctccaccaccaacacctccacctccacctccacctccaccacca -ccacctccacctccaccaccaccacctccaccaccaccacctccaccacctccacctcca -ccaccaccacctccaccaccacctccaccaccaccaccacctccaccaccaccacctcca -ccaccacctccaccaccaccacctccaccaccacctccaccaccacctccacctccacca -ccaccacctgcaccaccacctccacctccaccaccaccaccacctccacctccaccagca -gcagcatcacttgttggggagaccctgtgcaactccatgcacagccctgtccctgccata -g ->syndip_2_chr20:63693349-63693832 -ggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccctatgg -gagtgatgggggcctccacctccaccaccagcaccagcagcaccacctccac---cacct -ccacctcca---ccacctccacctccacctccaccaccacctccacctccacctccacct -ccacctccaccaccaccaccaccacctccaccacctc----------------------- --------------------------------------cacctccacctccacctccacct -ccacctccacctccacctccaccacgtccaccacctccacca---ccacctccaccacca -cctccacctccacct------------ccacctccaccaccacctccaccaccac---ct 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------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------ccaccacctccaccacctccaccaccacca -ccaccaccacctccacctccaccacctccacctccacctccaccacct------------ ------------------------------------------------------------- ------------------------------------------------------------- -ccacctccacctccaccaccacctccaccacctccaccacctccaccacctccacctcca -ccacctccaccacctccaccacca------------------------------------ ----------------------ccaccaccaccacctccaccaccacct------------ -------------------------ccaccaccacctccaccaccacctccaccaccacct -ccaccacctccacctccacctccaccacctccacctccacctccaccaccaccacctcca -cctccaccaccacctccaccaccaccacct------ccacctccaccacctccaccacca -gcaccacctccaccaccaccacctccacctccacc------------------------- ---------------------tccacctccacctccacctccacctcca------------ ------------------------------------------------------------- ----ccaccacctccacctccaccaccacctcctccaccaccaccacctccaccaccacca -ccaccacctccacctccaccaccacctccaccacctccaccacctccaccaccaccacct -cca--------------------------------------------------------- ------------------------------------------------------------- -------------------ccacctccacctccaccacctccaccaccacctccaccacca -ccacctccacctccaccaccacctccaccacctccaccacctccaccaccaccaccacca -cctcca------------------------------------------------------ -------------ccacctccaccaccacc------------------------------- ------------------------------------acctccacctccacctccaccacca -ccaccaccacctccaccacctccaccaccaccacctccacctccaccaccacctccacca -cctccaccaccaccaccaccacctccacca------------------------------ ------------------------------------------------------------- ----------------------------------------------cctccaccaccacca -cctccaccaccacctccaccaccaccacctccacct------------------------ ----------------ccaccaccacctccaccacct---ccaccacctccaccacctcca -cct--------------------------------------------------------- ----------------------------------------ccacctccaccacctccacca -ccacctccaccacct--------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------ccacca -ccacctccaccacctccacctccacctccacctccacctccaccaccacctccaccacct -ccaccaccacctccacctcca--------------------------------------- ----------------ccacctccacctccacctccaccacctccaccaccacct------ -ccaccacctccaccacctccaccaccaccaccaccacctccaccacctccaccaccacct -ccaccacctccacctccacctccacctccacctcca------------------------ ------------------------------------------------------------- -------------------------------------------------ccaccacctcca -ccacctccaccaccacctccaccaccacctccaccacctccacctccacctccacctcca -cctccaccaccacct---ccaccacctccaccaccacctccacct---ccaccacctcca -cctccacctccaccacctccaccaccacctccaccacctccaccaccacctccacctcca -ccacctcca--------------------------------------------------- ------------------------------------------------------------- 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------------------------------------------------------------- ------------------------------------------------------------- -------------------------------ccaccacctccaccacctccaccaccacca -ccaccaccacctccacctccaccacctccacctccacctccaccacct------------ ------------------------------------------------------------- ------------------------------------------------------------- -ccacctccacctccaccaccacctccaccacctccaccacctccaccacctccacctcca -ccacctccaccacctccaccacca------------------------------------ ----------------------ccaccaccaccacctccaccaccacct------------ -------------------------ccaccaccacctccaccaccacctccaccaccacct -ccaccacctccacctccacctccaccacctccacctccacctccaccaccaccacctcca -cctccaccaccacctccaccaccaccacct------ccacctccaccacctccaccacca -gcaccacctccaccaccaccacctccacctccacc------------------------- ---------------------tccacctccacctccacctccacctcca------------ ------------------------------------------------------------- ----ccaccacctccacctccaccacctccacctccaccaccaccaccaccaccaccacca 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-ccacctccaccacct--------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------ccacca -ccacctccaccacctccacctccacctccacctccacctccaccaccacctccaccacct -ccaccaccacctccacctcca--------------------------------------- ----------------ccacctccacctccacctccaccacctccaccaccacct------ -ccaccacctccaccacctccaccaccaccaccaccacctccaccacctccaccaccacct -ccaccacctccacctccacctccacctccacctcca------------------------ ------------------------------------------------------------- -------------------------------------------------ccaccacctcca -ccacctccaccaccacctccaccaccacctccaccacctccacctccacctccacctcca -cctccaccaccacct---ccaccacctccaccaccacctccacct---ccaccacctcca -cctccacctccaccacctccaccaccacctccaccacctccaccaccacctccacctcca -ccacctcca--------------------------------------------------- ------------------------------------------------------------- -------------------ccaccacctccaccacctccaccacctccaccaccaccacca 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-------------ccacctccaccaccaccacctccacctccaccaccaccaccaccacca -cctccaccaccacctccacctccacca---------------ccacctccacctccacca -cctccaccaccagcaccaccaccacctccaccaccaccacctccacctccaccaccacca -ccaccaccacctccaccaccacct------------------------------------ -------------------------------------ccacctccacctccacctccacca -ccacctccaccaccacctccaccacctccaccaccacctccacctccaccacctccacct -ccac------------------ctccaccacctccacctccacctccaccacctccacct -ccacctccacctccaccaccacca------------------------------------ ----------cctccacctccacctccacctccaccacgtccaccacctccaccacctcca -cctccacctccacctccacctccaccacctccacc------------------------- ------------------------------------tccacctccaccacctccacct--- ----------------------------------------------------ccacctcca -cctccaccacgtccaccaccaccacctccaccaccaccaccaccacctccaccaccacct -ccacctccaccaccacctccaccaccacctccaccaccaccacctccacctccaccacca -------ccacctccacct------------------------------ccaccaccacca -ccaccaccacctccaccaccacctccacctccaccaccacctccacctccaccacctcca -ccaccaccaccacctccacctccaccaccaccacctccacctccacctccacctccacca -ccacctccaccaccacctccaccaccaccacctccacct--------------------- -ccaccaccaccaccaccaccacctccaccaccacctcca------------------cct -ccaccaccacctccaccaccacctccaccacctccaccaccacca--------------- -------------------------ccacctccacctccaccaccaccacctccacctcca -ccaccaccaccaccaccacctccaccacca------------------------------ -cctccacctccaccaccacctccaccacctccacctccacctccacctccacctccacca -cctccacct------ccacctccaccaccaccaccacctccaccacctccaccaccacct -ccaccacctccacctccacctccacctccaccaccacctccaccacctccaccaccacct -ccaccacctccaccacctccacctccaccaccacctccacctccacctccaccacctcca -ccaccacca------------------------ccaccaccacctccaccaccacctcca ----------------------ccaccacctccacctccacctccaccacctccaccacca -cctccaccaccacca---------------------------------------ccacct -ccacctccaccacctccacctccacctcc------------------accaccacctcca -ccacctccaccaccaccaccaccacctccaccacctccacctccacctccacctccacct -ccaccacctccacctccacctccaccaccacca------------------------cca -cctccaccacctccaccaccacctccaccacctccacctccacctccacctccaccacca -cctccaccacctccaccaccacctccaccacctccaccaccacctccacctccaccacca -ccacctccacctccaccaccacctcca---------------ccaccaccacctccacct -ccaccaccacctccaccaccaccaccaccaccaccaccaccaccaccaccacctccacca -ccaccacctgcaccaccacctccacctccaccaccaccaccacctccacctccaccagca -gcagcatcacttgttggggagaccctgtgcaactccatgcacagccctgtccctgccata -g ->p:HG002_2_chr20:63693349-63693832 -ggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccctatgg -gagtgatgggggcctccacctccaccaccagcaccagcagcaccacctccacctccacct -ccacctccacctccaccaccacctccacctccaccaccacctcctccaccaccaccacct -ccaccaccaccaccaccaccaccacctccacctccaccacctccacctccaccaccacca -cctccacctccaccaccaccacctccacctccaccaccacctccacctccaccaccacct -ccacctccacctccaccaccaccacctccaccacctccaccacctccacctccaccacca -cctccacctccaccaccacctccacctccacctccacctccacctccaccaccaccacct -ccaccacctccaccacctccacctccaccaccaccacctccacctccacctccaccacct -ccacctccaccacctccacctccaccacctccaccaccaccaccaccaccaccaccacct -ccaccaccaccaccaccaccacctccaccacctccacctccaccacctccaccaccacca -cctccaccaccacctccaccaccacctccacctccaccacctccacctccaccacctcca -cctccacctccaccaccacctccaccacctccaccaccacctccaccacctccacctcca -ccaccaccacctccaccaccaccaccaccaccacctccaccacctccacctccaccacct -ccaccaccaccacctccaccaccacctccaccaccacctccacctccaccacctccacct -ccaccacctccacctccacctccaccaccacctccaccacctccaccaccacctccacca -cctccaccacctccaccaccacctccaccacctccacctccaccaccaccacctccacct -ccaccaccaccacctccaccaccacctccacctccaccaccaccacctccacctccacca -ccaccacctccaccaccacctccaccaccaccaccaccaccaccacctccacctccacca -cctccaccaccaccaccaccacctccacctccaccacctccaccacctccaccaccacca -ccaccacctccaccacctccaccaccacctccaccacctccacctccaccaccaccacct -ccaccaccaccacctccacctccacctccacctccacctccaccaccacctccacctcca -ccaccacctccaccaccacctccacctccaccacctccacctccacctccaccacctcca -ccaccaccaccaccaccaccaccaccaccaccacctccaccacctccacctccacctcca -ccaccaccaccaccacctccaccaccaccaccaccacctccaccacctccaccaccacct -ccaccaccaccaccaccaccaccaccaccacctccaccacctccacctccacctccacct -ccaccacctccaccacctccaccaccacctccaccaccaccaccaccacctccaccacca -cctccacctccaccaccacctccaccaccacctccacctccaccacctccacctccacca -cctccaccacctccacctccaccacctccacctccacctccaccacctccaccaccacca -ccaccaccaccaccaccaccaccacctccaccaccaccacctccaccaccacctccacca -cctccaccaccacctccaccaccaccaccaccaccaccaccaccaccaccacctccacca -ccacctccacctccaccaccacctccaccaccacctccacctccaccacctccacctcca -ccacctccaccacctccaccaccaccaccaccacctccaccaccacctccacctccacca -ccaccaccaccaccaccacctccaccaccaccacctccaccaccacctccaccacctcca -ccaccacctccacctccaccacctccaccaccacctccaccaccacctccaccaccacca -cctccaccaccacctccaccacctccaccaccacctccacctccaccacctccaccacca -cctccaccaccacctccaccaccaccacctccaccaccacctccaccacctccaccacca -cctccacctccaccacctccacctccacctccaccacctccaccaccaccaccaccacca -ccaccaccaccaccaccaccaccaccaccacctccacctccacctccaccacctccacct -ccaccacctccaccaccacctccacctccaccacctccacctccacctccaccacctcca -cctccaccacctccacctccacctccaccacctccaccaccaccacctccaccaccacct -ccaccacctccaccaccacctccacctccaccacctccaccaccacctccaccaccacct -ccaccaccaccacctccaccaccacctccaccacctccaccaccacctccacctccacca -cctccacctccacctccaccacctccaccaccaccaccaccaccaccaccaccaccacca -cctccaccaccaccacctccaccaccacctccaccaccaccaccaccacctccaccacca -ccaccaccacctccaccaccacctccaccacctccaccaccaccaccaccaccaccacca -cctccaccaccacctccaccaccaccaccaccaccaccaccacctccaccacct------ -------------ccacctccaccaccaccaccacctccaccaccaccaccaccaccacct -ccacctccaccaccaccacctccaccaccaccaccacctccaccaccacctccaccacca -ccaccaccaccaccaccaccacctccaccacctccaccacctccaccaccacctccacca -cctccaccaccaccaccaccacctccaccaccacctccaccaccaccaccaccaccacca -cctccacctccacctccaccacctccacctccaccacctccacctccaccacctccacct -ccacctccaccacctccaccaccacctccacctccaccaccacctcctccaccaccacca -cctccaccaccacctccaccaccaccacctccacctccaccacctccacctccaccacca -ccacctccacctccaccaccaccacctccaccacctccaccaccacctccaccacctcca -cctccaccaccaccacctccaccaccaccacctccacctccaccaccaccaccaccacca -cctccacctccaccaccacctccaccaccacctccacctccacctccaccacctccacca -ccacctccaccacctccaccacctccacctccaccaccaccaccacctccaccaccacca -ccaccacctctaccacctctaccaccaccaccaccacctccaccaccaccaccaccacct -ccaccaccaccaccaccaccacctccaccaccacctccaccacctccaccaccaccacca -ccacctctaccacctccacctccaccaccaccaccacctctaccaccaccaccaccacct -ccaccaccaccaccacctccaccaccaccaccacctccaccaccacctccaccaccacct -ccaccacctccaccaccaccaccacctccacctccaccacctccaccaccacctccacca -ccaccaccaccaccacctccaccaccacctccaccacctccaccaccaccaccaccacct -ctaccacctccacctccaccaccaccaccacctccacctccaccaccaccaccaccacca -ccaccaccaccacctccaccaccaccaccaccaccacctctaccaccaccaccaccacct -ccaccaccaccaccacctccaccaccaccaccacctccaccaccacctccaccaccacca -ccaccaccaccaccacctctaccaccaccaccaccacctccaccaccaccaccacctcca -ccaccaccaccacctccaccaccacctccaccaccaccaccacctccaccaccacctcca -ccaccacctccaccacctccaccaccaccaccaccacctccaccaccacctccacctcca -ccaccaccaccaccacctccaccaccaccaccaccaccaccacctccaccaccacctcca -ccaccacctccaccacctccaccaccaccaccaccacctccaccaccacctccacctcca -ccaccaccaccaccacctccaccaccacctccaccaccaccaccaccaccacctccacca -ccacctccaccacctccaccaccaccaccaccacctctaccacctctaccaccaccacca -ccacctccaccaccaccaccacctccaccaccaccaccacctccaccaccaccacctcca -cctccaccaccaccacctccaccacctccaccaccacctccaccaccaccacctccacct -ccaccaccaccacctccaccacctccaccaccaccaccaccaccaccaccacctccacca -ccaccaccaccaccacctccaccaccacctccaccacctccaccaccaccaccaccacct -ctaccacctctaccaccaccaccaccacctccaccaccaccaccacctccaccaccacca -ccacctccaccaccacctccaccaccaccacctccacctccaccaccaccacctccacca -ccaccacctccacctccaccaccaccacctccaccacctccaccaccacctccaccacca -ccacctccacctccaccaccaccacctccaccacctccaccaccaccacctccaccacca -ccacctccaccacctccaccaccaccaccaccacctccaccacctccaccacctccacca -ccaccaccaccacctccacctccacctccaccacctccaccaccaccacctccaccacca -ccaccaccaccaccaccacctccacctccacctccaccacctccacctccaccaccacca -ccaccaccaccaccaccaccaccacctccacctccacctccaccacctccaccaccacca -cctccaccaccaccacctccacctccaccacctccaccaccacctccaccaccaccacct -ccacctccaccaccaccacctccaccaccaccacctccacctccaccaccaccacctcca -ccacctccaccaccacctccaccaccaccacctccacctccaccaccaccacctccacca -cctccaccaccaccacctccaccaccaccacctccaccacctccaccaccaccaccacca -cctccaccacctccaccacctccaccaccaccaccaccacctccacctccacctccacca -cctccaccaccaccacctccaccaccaccaccaccaccacctccaccacctccaccacca -ccaccaccacctccacctccacctccaccacctccaccaccaccacctccaccaccacca -ccaccaccaccaccaccacctccacctccacctccaccacctccacctccaccaccacca -ccaccaccaccacctccaccaccacctccacctccacctccaccacctccacctccacca -ccaccaccaccaccaccaccaccaccaccacctccacctccacctccaccaccaccacct -ctaccaccacctccaccaccaccaccaccaccaccaccaccacctccaccacctccacca -ccaccacctccaccaccaccacctccacctccaccaccaccaccacctccaccacctcca -ccaccacctccacctccacctccaccacctccaccaccaccacctccaccaccaccacca -ccaccaccacctccaccacctccaccaccaccacctccaccaccaccacctccacctcca -ccacctccaccacctccaccaccaccaccacctccaccaccaccaccaccaccacctcca -cctccaccacctctaccaccacctccaccaccaccaccaccaccacctccacctccacca -cctccacctccaccacctctaccaccacctccaccaccaccacctccacctccacctcca -ccaccaccacctccacctccacctccaccaccaccaccaccaccaccacctccaccacca -ccaccaccaccaccaccaccacctccacctccaccaccaccacctccaccaccaccacct -ccaccacctccaccaccacctccacctccaccaccaccacctccacctccacctccacca -ccaccaccaccacctccaccaccaccacctccaccaccaacacctccacctccacctcca -ccaccaccaccaccacctccacctccaccaccacctccaccaccaccacctccacctcca -ccaccaccacctccaccaccacctccaccacctccaccaccaccacctccaccaccacct -ccaccaccaccaccaccaccacctccacctccacctccaccaccaccacctctaccacca -cctccaccaccaccaccaccaccaccaccaccacctccacctccacctccaccacctcca -cctccaccaccaccaccaccaccaccacctccaccaccacctccacctccacctccacca -cctccacctccaccaccaccaccaccaccaccaccaccaccaccacctccacctccacct -ccaccaccaccacctctaccaccacctccaccaccaccaccaccaccaccaccaccacct -ccaccaccaccacctccacctccaccaccaccacctccacctccaccaccaccacctcca -cctccaccaccaccaccaccaccaccacctccaccaccaccacctccaccacctccacca -ccacctccaccaccaccacctccaccacctccaccaccacctccacctccaccaccacca -cctccaccaccaccacctccacctccaccaccaccacctccacctccacctccaccacct -ccacctccaccacctccaccaccaccacctccaccacctccaccaccacctccacctcca -ccaccaccacctccaccaccaccacctccaccacctccaccaccacctccacctccacca -ccaccacctccacctccacctccaccaccaccaccaccacctccactaccaccacctcca -cctccaccaccaccacctccaccaccaacacctccacctccacctccacctccaccacca -ccacctccacctccaccaccaccacctccaccaccaccacctccaccacctccacctcca -ccaccaccacctccaccaccacctccaccaccaccaccacctccaccaccacctccacct -ccaccaccacctccaccaccaccaccaccaccaccaccaccaccaccaccacctccacca -ccaccacctgcaccaccacctccacctccaccaccaccaccacctccacctccaccagca -gcagcatcacttgttggggagaccctgtgcaactccatgcacagccctgtccctgccata -g ->ref_chr20:63693349-63693832 -ggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccctatgg -gagtgatgggggcctccacctccaccaccagcaccagcagcaccacctccacctccacct -ccacctccacctccaccaccacctccacctccaccaccacctcctccaccacc------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------accacctccaccaccaccaccaccaccaccacctccacctccacca -cctccacctccaccaccaccacct------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------ccacctccaccaccacc------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------acctcca -cctccaccaccacctccaccaccaccacctccacct------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------------cca -ccaccacctcca------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------ccaccaccaccaccaccaccaccaccaccaccaccacctccacca -ccaccacctgcaccaccacctccacctccaccaccaccaccacctccacctccaccagca -gcagcatcacttgttggggagaccctgtgcaactccatgcacagccctgtccctgccata -g diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ca528d3caf38437128325d25844a1527.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ca528d3caf38437128325d25844a1527.msa deleted file mode 100644 index fe8280cd..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ca528d3caf38437128325d25844a1527.msa +++ /dev/null @@ -1,170 +0,0 @@ ->syndip_1_chr20:55624482-55625807 -agaaagtgaggtcctgtctccctgtctctcatatatatacataactaaaataatatatag -taatatatgttatatattatactatattatataatatactataatatatataatatagta -tatattgtatataatatagtatatataatataatagtatataatatagtatagatagtat -agaatatatagtatatacctagtatactatattatatagtataactattataatatttat -agtatattatactatataatacagtatactgtattatatactataatctactagattata -atatactatataatcagtatactatattatatagtatagtataatatagtattatattat -agtaatatattataaagtattatagtaatatagtataatatactatacattatatagtat -agtatattatatagtatactatatataagtatatataatagtatattgtatatagtaatt -atatatagtatatataatatacaatgtatagtatattatagtatactatacgatactgta -gtatagtatgctatatagtatactatatacgacagtatcatatagtatactacaaaatat -atagtatagcatagtatactatataatatactatattatatatactatattatatatact -acactatattatatatactatattatatatactatactatacataaaatactatatatag -tatattatatatagtatactatatatagtatatatagtatactatatatactatatatag -tatactatatagtatactatatatagtatatatagtatactatatatagtatactatata -tagtatatatatagtatactatatatagtatactatatatagtatatatagtatactata -tatagtatactatatatagtatatatagtatactatatatagtatactatatatagtata -tatagtatactatatatagtatactatatatagtatatatagtatactatatatagtata -tatagtatactatatatagtatatatagtatactatatatactatatatactatatatag -tatactatatatagtatatatagtatactatatatcatatatagtattatatacagtata -ctatatataatatagtatactatactataatatactatttgttataattatctagtatag -tatactatatatactatattatatagtatatagtatatatagtatatttatagtatatat -actatatactatatatactatatactataatatatactatatatactaaataaatataat -atacttatttaaatatatttaaataaatata--aaatatttaaatataattacttaaata -tatatttaaaatatttaataaacatatatttaaatatttatttaatatttaaatattaaa -tatatataattaatataattatatatatattatatactatatattatatatact-----a -tatactatatatagtatactaatataatatactatatatactatatataatatactatat -atagtatatatagtatagtatactataatatactatat---------------------- ----------------tatataatatagtatactatatattgtatactatactatgctata -gtatgctatatactacactatagtatactgtatactatac-----tatacagtatactgt -atactatactatagta-------------tacagtatactatatactattgtatagtata -tagtatactgtatactatagtatagtatactatatactatactatactatagtatactct -atagtatataaagacatatatatagtcttcaaaatgaagatcctgtatcctatatatata -tataacttcaaaagtgagatacatatatatgatgtagaaactttagaatatacaa ->syndip_2_chr20:55624482-55625807 -agaaagtgaggtcctgtctccctgtctctcatatatatacataactaaaataatatatag -taatatatgttatatattatactatattatataatatactataatatatataatatagta -tatattgtatataatatagtatatataatataatagtatataatatagtatagatagtat -agaatatatagtatatacctagtatactatattatatagtataactattataatatttat -agtatattatactatataatacagtatactgtattatatactataatctactagattata -atatactatataatcagtatactatattatatagtatagtataatatagtattatattat -agtaatatattataaagtattatagtaatatagtataatatactatac------------ ------attatatagtatactatatataagtatatataatagtatattgtatatagtaatt -atatatagtatatataatatacaatgtatagtatattatagtatactatacgatactgta -gtatagtatgctatatagtatactatatacgacagtatcatatagtatactacaaaatat -atagtatagcatagtatactatataatat------------------------------- ---actatattatatatactatattatatatactatactatacataaaatactatatatag -tatat------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------tatatatag -tatactatatatagtatatatagtatactatatatcatatatagtattatatacagtata -ctatatataatatagtatactatactataatatactatttgttataattatctagtatag -tatactatatatactatat-------tatatagtatatatagtatatttatagtatatat -actatatactatatatactatataatataatatataatatatatactaaata-----aat -atacttatttaaatatatttaaataaatatattaaatatttaaatataattacttaaata -tatatttaaaatatttaataaacatatatttaaatatttatttaatatttaaatattaaa -tatatataattaatataattatatatatattatatactatatattatatatactatataa -tatactatatatagtatactaatataatatactatatatactatatataatatactatat -atagtatatatagtatagtatactataatatactatatatagtatatatagtatagtata -ctataatatactatatatagtatatagtatactatatattgtatactatactatgctata -gtatgctatatactacactatagtatactgtatactatactatagtatacagtatactat -atactatactatagtatagtatactatagtatagtatactatatactatactatagtata -tagtatactgtatac-----tatagtatactatatactatactatactatagtatactct -atagtatataaagacatatatatagtcttcaaaatgaagatcctgtatcctatatatata -tataacttcaaaagtgagatacatatatatgatgtagaaactttagaatatacaa ->p:HG002_1_chr20:55624482-55625807 -agaaagtgaggtcctgtctccctgtctctcatatatatacataactaaaataatatatag -taatatatgttatatattatactatattatataatatactataatatatataatatagta -tatattgtatataatatagtatatataatataatagtatataatatagtatagatagtat -agaatatatagtatatacctagtatactatattatatagtataactattataatatttat -agtatattatactatataatacagtatactgtattatatactataatctactagattata -atatactatataatcagtatactatattatatagtatagtataatatagtattatattat -agtaatatattataaagtattatagtaatatagtataatatactatac------------ ------attatatagtatactatatataagtatatataatagtatattgtatatagtaatt -atatatagtatatataatatacaatgtatagtatattatagtatactatacgatactgta -gtatagtatgctatatagtatactatatacgacagtatcatatagtatactacaaaatat -atagtatagcatagtatactatataatat------------------------------- ---actatattatatatactatattatatatactatactatacataaaatactatatatag -tatat------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------tatatatag -tatactatatatagtatatatagtatactatatatcatatatagtattatatacagtata -ctatatataatatagtatactatactataatatactatttgttataattatctagtatag -tatactatatatactatat-------tatatagtatatatagtatatttatagtatatat -actatatactatatatactatataatataatatataatatatatactaaata-----aat -atacttatttaaatatatttaaataaatatattaaatatttaaatataattacttaaata -tatatttaaaatatttaataaacatatatttaaatatttatttaatatttaaatattaaa -tatatataattaatataattatatatatattatatactatatattatatatactatataa -tatactatatatagtatactaatataatatactatatatactatatataatatactatat -atagtatatatagtatagtatactataatatactatatatagtatatatagtatagtata -ctataatatactatatatagtatatagtatactatatattgtatactatactatgctata -gtatgctatatactacactatagtatactgtatactatactatagtatacagtatactat -atactatactatagtatagtatactatagtatagtatactatatactatactatagtata -tagtatactgtatac-----tatagtatactatatactatactatactatagtatactct -atagtatataaagacatatatatagtcttcaaaatgaagatcctgtatcctatatatata -tataacttcaaaagtgagatacatatatatgatgtagaaactttagaatatacaa ->p:HG002_2_chr20:55624482-55625807 -agaaagtgaggtcctgtctccctgtctctcatatatatacataactaaaataatatatag -taatatatgttatatattatactatattatataatatactataatatatataatatagta -tatattgtatataatatagtatatataatataatagtatataatatagtatagatagtat -agaatatatagtatatacctagtatactatattatatagtataactattataatatttat -agtatattatactatataatacagtatactgtattatatactataatctactagattata -atatactatataatcagtatactatattatatagtatagtataatatagtattatattat -agtaatatattataaagtattatagtaatatagtataatatactatacattatatagtat -agtatattatatagtatactatatataagtatatataatagtatattgtatatagtaatt -atatatagtatatataatatacaatgtatagtatattatagtatactatacgatactgta -gtatagtatgctatatagtatactatatacgacagtatcatatagtatactacaaaatat -atagtatagcatagtatactatataatatactatattatatatactatattatatatact -acactatattatatatactatattatatatactatactatacataaaatactatatatag -tatattatatatagtatactatatatagtatatatagtatactatatatactatatatag -tatactatatagtatactatatatagtatatatagtatactatatatagtatactatata -tagtatatatatagtatactatatatagtatactatatatagtatatatagtatactata -tatagtatactatatatagtatatatagtatactatatatagtatactatatatagtata -tatagtatactatatatagtatactatatatagtatatatagtatactatatatagtata -tatagtatactatatatagtatatatagtatactatatatactatatatactatatatag -tatactatatatagtatatatagtatactatatatcatatatagtattatatacagtata -ctatatataatatagtatactatactataatatactatttgttataattatctagtatag -tatactatatatactatattatatagtatatagtatatatagtatatttatagtatatat -actatatactatatatactatatactataatatatactatatatactaaataaatataat -atacttatttaaatatatttaaataaatata--aaatatttaaatataattacttaaata -tatatttaaaatatttaataaacatatatttaaatatttatttaatatttaaatattaaa -tatatataattaatataattatatatatattatatactatatattatatatact-----a -tatactatatatagtatactaatataatatactatatatactatatataatatactatat -atagtatatatagtatagtatactataatatactatat---------------------- ----------------tatataatatagtatactatatattgtatactatactatgctata -gtatgctatatactacactatagtatactgtatactatac-----tatacagtatactgt -atactatactatagta-------------tacagtatactatatactattgtatagtata -tagtatactgtatactatagtatagtatactatatactatactatactatagtatactct -atagtatataaagacatatatatagtcttcaaaatgaagatcctgtatcctatatatata -tataacttcaaaagtgagatacatatatatgatgtagaaactttagaatatacaa ->ref_chr20:55624482-55625807 -agaaagtgaggtcctgtctccctgtctctcatatatatacataactaaaataatatatag -taatatatgttatatattatactatattatataatatactataatatatataatatagta -tatattgtatataatatagtatatataatataatagtatataatatagtatagatagtat -agaatatatagtatatacctagtatactatattatatagtataactattataatatttat -agtatattatactatataatacagtatactgtattatatactataatctactagattata -atatactatataatcagtatactatatt-----gtatagtataatatagtattatattat -agtaatatattataaagtattatagtaatatagtataatatactatacattatatagtat -agtatattatatagtatactatatataagtatatttaatagtatattgtatatagtaatt -atatatagtatatataatatacaatgtatagtatattatagtatactatacgatactgta -gtatagtatgctatatagtatactatatacgacagtatcatatagtatactacaaaatat -atagtatagcatagtatactatataatatactatattatatatactatattatatatact -atactatattatatatactatattatatatactatactatacataaaatactatatatag -tatattatatatagtatactatatatagtatataatatata------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------gtatactatatatactatatatag -tatactatatatactatatatagtatactatatatcatatatagtattatatacagtata -ctatatataatatagtatactatactataatatactatttgttataattatctagtatag -tatactatatatactatattatatagtatatagtatatatagta----tatagtatatat -actatatactatatatactatatactatactatataatatatatacta------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------atatattgtatactatactatgctata -gtatgctatatactacactatagtatactgtgtactatactatagtatacagtatactat -atactatactatagtatagtatactatagtatagtatactatatactatagtatagtata -tagtatactgtatactatagtatagtatactatatactatactatactatagtatactct -atagtatataaagacatatatatagtcttcaaaatgaagatcctgtatcctatatatata -tataacttcaaaagtgagatacatatatatgatgtagaaactttagaatatacaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ca89b4aa66038a2241b3c1e4f1a95c17.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ca89b4aa66038a2241b3c1e4f1a95c17.msa deleted file mode 100644 index 46410da2..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ca89b4aa66038a2241b3c1e4f1a95c17.msa +++ /dev/null @@ -1,40 +0,0 @@ ->syndip_1_chr20:63154585-63154995 -gtggatcaggcctgatctcccctagtctcctcctgcaatgcccagattcttgcccccgtc -cttccttctccctcctcccttcctcctccctcctcttc---------------------- -----------------------------------cctccctcctgcttcctccctctgcc -ctccctcctccctcttcctccctcctcctcccctctcctctttcctcctccctctccctt -cctcctcctcccccctttcccaccctcctccccctttccctccctcctcccgactccctc -tccccttctccctcttctca---------------------tcccttcctcctcctccct -ccttcctccctcctccctcctccccacactgtccatttgcaggctgcctggtcct ->syndip_2_chr20:63154585-63154995 -gtggatcaggcctgatctcccctagtctcctcctgcaatgcccagattcttgcccccgtc -cttccttctccctcctcccttcctcctccctcctcttccctccctcctgcttcctccctc -tgccctccctcctccctcttcctccctcctcttccctccctcctgcttcctccctctgcc -ctccctcctccctcttcctccctcctcctcccctctcctctttcctcctccctctccctt -cctcctcctcccccctttcccaccctcctccccctttccctccctcctcccgactccctc -tccccttctccctcttctcatcccttcctcctcctccctcctcccttcctcctcctccct -ccttcctccctcctccctcctccccacactgtccatttgcaggctgcctggtcct ->p:HG002_1_chr20:63154585-63154995 -gtggatcaggcctgatctcccctagtctcctcctgcaatgcccagattcttgcccccgtc -cttccttctccctcctcccttcctcctccctcctcttccctccctcctgcttcctccctc -tgccctccctcctccctcttcctccctcctcttccctccctcctgcttcctccctctgcc -ctccctcctccctcttcctccctcctcctcccctctcctctttcctcctccctctccctt -cctcctcctcccccctttcccaccctcctccccctttccctccctcctcccgactccctc -tccccttctccctcttctcatcccttcctcctcctccctcctcccttcctcctcctccct -ccttcctccctcctccctcctccccacactgtccatttgcaggctgcctggtcct ->p:HG002_2_chr20:63154585-63154995 -gtggatcaggcctgatctcccctagtctcctcctgcaatgcccagattcttgcccccgtc -cttccttctccctcctcccttcctcctccctcctcttc---------------------- -----------------------------------cctccctcctgcttcctccctctgcc -ctccctcctccctcttcctccctcctcctcccctctcctctttcctcctccctctccctt -cctcctcctcccccctttcccaccctcctccccctttccctccctcctcccgactccctc -tccccttctccctcttctca---------------------tcccttcctcctcctccct -ccttcctccctcctccctcctccccacactgtccatttgcaggctgcctggtcct ->ref_chr20:63154585-63154995 -gtggatcaggcctgatctcccctagtctcctcctgcaatgcccagattcttgcccccgtc -cttccttctccctcctcccttcctcctccctcctcttccctccctcctgcttcctccctc -tgccctccctcctccctcttcctccctcct----cctccttcctgcttcctccctctgcc -ctccctcctccctcttcctccctcctcctcccctctcctctttcctcctccctctccctt -cctcctcctcccccctttcccaccctcctccccctttccctccctcctcccgactccctc -tccccttctccctcttctcatcccttcctcctcctccctcctcccttcctcctcctccct -ccttcctccctcctccctcctccccacactgtccatttgcaggctgcctggtcct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_cb73ed8231495bc9552fef4f45c9cd43.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_cb73ed8231495bc9552fef4f45c9cd43.msa deleted file mode 100644 index 7b6165dc..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_cb73ed8231495bc9552fef4f45c9cd43.msa +++ /dev/null @@ -1,145 +0,0 @@ ->syndip_1_chr20:63028676-63029602 -aactgctcccgtgccgagctctgggggagggagtctgttcagagacggtgcagtcctacc -ttttagaaggtacgcctgcctttttaagcagctcagctctcaacaatgcacaagtggctt -gagtagaagagctgctcctgctgggaggcgcaggaggctgagcgaggcccaccctgcagg -ggcgaggccacggtttgtgttatttcccatgatgactccaaacgcacccgagtcccccgg -gcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtccccc -gggcctccgcctctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtccc -ccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtc -ccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcagg -tcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgca -ggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtg -caggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtg -tgcaggtcccccgggcctccgcgtctccgtgtgcaggtcccccgggcctccgcgcctccg -tgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctc -cgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtc -tgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg -cctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccg -cgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctc -cgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc -tccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccggg -cctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccg -ggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccc -cgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcc -cccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggt -cccccgggcctctgcgtctctgtgtgcaggctcaagtttgccaacgtccatgcacgtctc -agcctctcagcctggactggacaactgggcttcgggaattcatttaaattctacccgcta -cacgccttccctggattcagggcggcgtccagtgcattcatcacgcgtgtgctgccgtga -aggtgcggggaccccccccaaaaggcttccttccctgtcctgcgtcctgcccacaaggcg -gtgctgctggcaccaggcct ->syndip_2_chr20:63028676-63029602 -aactgctcccgtgccgagctctgggggagggagtctgttcagagacggtgcagtcctacc -ttttagaaggtacgcctgcctttttaagcagctcagctctcaacaatgcacaagtggctt -gagtagaagagctgctcctgctgggaggcgcaggaggctgagcgaggcccaccctgcagg -ggcgaggccacggtttgtgttatttcccatgatgactccaaacgcacccga--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------gtcccccgggcc -tccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccggg -cctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccg -ggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccc -cgggcctccgcgtctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcc -cccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggt -cccccgggcccctgcgtctctgtgtgcaggctcaagtttgccaacgtccatgcacgtctc -agcctctcagcctggactggacaactgggcttcgggaattcatttaaattctacccgcta -cacgccttccctggattcagggcggcgtccagtgcattcatcacgcgtgtgctgccgtga -aggtgcggggaccccccccaaaaggcttccttccctgtcctgcgtcctgcccacaaggcg -gtgctgctggcaccaggcct ->p:HG002_1_chr20:63028676-63029602 -aactgctcccgtgccgagctctgggggagggagtctgttcagagacggtgcagtcctacc -ttttagaaggtacgcctgcctttttaagcagctcagctctcaacaatgcacaagtggctt -gagtagaagagctgctcctgctgggaggcgcaggaggctgagcgaggcccaccctgcagg -ggcgaggccacggtttgtgttatttcccatgatgactccaaacgcacccga--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------gtcccccgggcc -tccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccggg -cctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccg -ggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccc -cgggcctccgcgtctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcc -cccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggt -cccccgggcccctgcgtctctgtgtgcaggctcaagtttgccaacgtccatgcacgtctc -agcctctcagcctggactggacaactgggcttcgggaattcatttaaattctacccgcta -cacgccttccctggattcagggcggcgtccagtgcattcatcacgcgtgtgctgccgtga -aggtgcggggaccccctccaaaaggcttccttccctgtcctgcgtcctgcccacaaggcg -gtgctgctggcaccaggcct ->p:HG002_2_chr20:63028676-63029602 -aactgctcccatgccgagctctgggggagggagtctgttcagagacggtgcagtcctacc -ttttagaaggtacgcctgcctttttaagcagctcagctctcaacaatgcacaagtggctt -gagtagaagagctgctcctgctgggaggcgcaggaggctgagcgaggcccaccctgcagg -ggcgaggccacggtttgtgttatttcccatgatgactccaaacgcacccgagtcccccgg -gcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtccccc -gggcctccgcctctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtccc -ccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtc -ccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcagg -tcccccgggcctccgcgtctgcgtgtgcaggtcccccgggcctccgcgcctccgtgtgca -ggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtg -caggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtg -tgcaggtcccccgggcctccgcgtctccgtgtgcaggtcccccgggcctccgcgcctccg -tgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctc -cgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtc -tgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg -cctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccg -cgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctc -cgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc -tccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccggg -cctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccg -ggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccc -cgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcc -cccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggt -cccccgggcctctgcgtctctgtgtgcaggctcaagtttgccaacgtccatgcacgtctc -agcctctcagcctggactggacaactcggcttcgggaattcatttaaattctacccgcta -cacgccttccctggattcagggcggcgtccagtgaattcatcacgcgtgtgctgccgtga -aggtgcgggga--ccccccaaaaggcttccttccctgtcctgcgtcctgcccacaaggcg -gtgctgctggcaccaggcct ->ref_chr20:63028676-63029602 -aactgctcccgtgccgagctctgggggagggagtctgttcagagacggtgcagtcctacc -ttttagaaggtacgcctgcctttttaagcagctcagctctcaacaatgcacaagtggctt -gagtagaagagctgctcctgctgggaggcgcaggaggctgagcgaggcccaccctgcagg -ggcgaggccacggtttgtgttatttcccatgatgactccaaacgcacccga--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------gtcccccgggcctccg -cgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctc -cgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc -tccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccggg -cctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccg -ggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccc -cgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcc -cccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggt -cccccgggcctctgcgtctctgtgtgcaggctcaagtttgccaacgtccatgcacgtctc -agcctctcagcctggactggacaactgggcttcgggaattcatttaaattctacccgcta -cacgccttccctggattcagggcggcgtccagtgcattcatcacgcgtgtgctgccgtga -aggtgcggggaccccccccaaaaggcttccttccctgtcctgcgtcctgcccacaaggcg -gtgctgctggcaccaggcct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_cbda939196a2080828ca3d224974df6c.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_cbda939196a2080828ca3d224974df6c.msa deleted file mode 100644 index ff534fc3..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_cbda939196a2080828ca3d224974df6c.msa +++ /dev/null @@ -1,70 +0,0 @@ ->syndip_1_chr20:61561899-61562462 -tgtttctgggcagtgaccatatgatggcagtaatgctgtgtctggaaatcctgaccccag -ggctcccagagagagagagggaccttcgtgtggagaggtggaccccagggctcccggaga -gagagaggggccttcgtgtggagaggtggaccccagggctcccggagagagagaggggcc -tccgtgtggagaggtggaccccagggctcccggagagagggacttccgtgtggagaggtg -gaccccagggctcccggagagagagagggacctccctgagagagagagggacctccgtgt -ggagaggtggaccccagggctcccggagagagagagggacctccctgtggagaggtggac -cccagggctcccagagagagagagggaccttcgtgtggagaggtggaccccagggctccc -ggagagagagagggacctccgtgtggagaggtggaccccagggctcccggagagagagag -ggacctccgtgtggagaggtggaccccagggctcccggagaga----gggacctccgtgt -ggagaggtggaccccagggctcccggagagagagagggacctctgtgtggagaggtggac -cccagggctcccggagagagagagggacctccgtgtggagaggtggaccccagggctccc -ggagagagagggggaccttcgtgtggagaggtggaccccaggactcccggagagagagag -gggcctccgtg ->syndip_2_chr20:61561899-61562462 -tgtttctgggcagtgaccatatgatggcagtaatgctgtgtctggaaatcctgaccccag -ggctcccagagagagagagggaccttcgtgtggagaggtggaccccagggctcccggaga -gagagaggggccttcgtgtggagaggtggaccccagggctcccggagagagagaggggcc -tccgtgtggagaggtggaccccagggctcccggagagagggacctccgtgtggagaggtg -gaccccagggctcccggagagagagagggacctccc---------------------tgt -ggagaggtggaccccagggctcccagagagagagagggaccttcgtgtggagaggtggac -cccagggctccc--ggagagagagggacctccgtgtggagaggtggaccccagggctccc -ggagagagagagggacctctgtgtggagaggtggaccccagggctcccggagagagagag -ggacctccgtgtggagaggtggaccccagggctcccggagagagagggggaccttcgtgt -ggagaggtggaccccaggactcccggagagagagaggggcctccgtg------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------ ->p:HG002_1_chr20:61561899-61562462 -tgtttctgggcagtgaccatatgatggcagtaatgctgtgtctggaaatcctgaccccag -ggctcccagagagagagagggaccttcgtgtggagaggtggaccccagggctcccggaga -gagagaggggccttcgtgtggagaggtggaccccagggctcccggagagagagaggggcc -tccgtgtggagaggtggaccccagggctcccggagagagggacctccgtgtggagaggtg -gaccccagggctcccggagagagagagggacctccc---------------------tgt -ggagaggtggaccccagggctcccagagagagagagggaccttcgtgtggagaggtggac -cccagggctccc--ggagagagagggacctccgtgtggagaggtggaccccagggctccc -ggagagagagagggacctctgtgtggagaggtggaccccagggctcccggagagagagag -ggacctccgtgtggagaggtggaccccagggctcccggagagagagggggaccttcgtgt -ggagaggtggaccccaggactcccggagagagagaggggcctccgtg------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------ ->p:HG002_2_chr20:61561899-61562462 -tgtttctgggcagtgaccatatgatggcagtaatgctgtgtctggaaatcctgaccccag -ggctcccagagagagagagggaccttcgtgtggagaggtggaccccagggctcccggaga -gagagaggggccttcgtgtggagaggtggaccccagggctcccggagagagagaggggcc -tccgtgtggagaggtggaccccagggctcccggagagagggacctccgtgtggagaggtg -gaccccagggctcccggagagagagagggacctccctgagagagagagggacctccctgt -ggagaggtggaccccagggctcccggagagagagagggacctccctgtggagaggtggac -cccagggctcccagagagagagagggaccttcgtgtggagaggtggaccccagggctccc -ggagagagagagggacctccgtgtggagaggtggaccccagggctcccagagagagagag -ggaccttcgtgtggagaggtggaccccagggctcccggagagaga--gggacctccgtgt -ggagaggtggaccccagggctcccggagagagagagggacctctgtgtggagaggtggac -cccagggctcccggagagagagagggacctccgtgtggagaggtggaccccagggctccc -ggagagagagggggaccttcgtgtggagaggtggaccccaggactcccggagagagagag -gggcctccgtg ->ref_chr20:61561899-61562462 -tgtttctgggcagtgaccatatgatggcagtaatgctgtgtctggaaatcctgaccccag -ggctcccagagagagagagggaccttcgtgtggagaggtggaccccagggctcccggaga -gagagaggggccttcgtgtggagaggtggaccccagggctcccggagagagagaggggcc -tccgtgtggagaggtggaccccagggctcccggagagagggacctccgtgtggagaggtg -gaccccagggctcccggagagagagagggacctccc---------------------tgt -ggagaggtggaccccagggctcccagagagagagagggaccttcgtgtggagaggtggac -cccagggctccc--ggagagagagggacctccgtgtggagaggtggaccccagggctccc -ggagagagagagggacctctgtgtggagaggtggaccccagggctcccggagagagagag -ggacctccgtgtggagaggtggaccccagggctcccggagagagagggggaccttcgtgt -ggagaggtggaccccaggactcccggagagagagaggggcctccgtg------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------ diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_cd8f6e8ec2e44115482d60783147d823.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_cd8f6e8ec2e44115482d60783147d823.msa deleted file mode 100644 index 953b3889..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_cd8f6e8ec2e44115482d60783147d823.msa +++ /dev/null @@ -1,150 +0,0 @@ ->syndip_1_chr20:18208929-18210344 -gaatgggggaaggaggagaggagtaggtaaggaaggaatgcacgtcaatctgagtaaagg -gtatataggtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatt -tccaaataaaaaataagcagaaaggaaaagctaatcatctccccctattccagtccccca -ggcatgtatccttccgtagcttctccacacctacacgaacctagacgattccttccacac -cttccccacacccacacgaacctagacgattccttccacaccttccccacacccacacga -acctagatgaattccttccacaccttctccacacccacacgaacctagacgattccttcc -acaccttccccacacccattctccacacccacacgaacctagacgattccttccacacct -ccacacccacacgaacctagatgaattccttccacaccttccccacacccacacaaacct -agacgattccttccacaccttctccacacccacacgaacctagacgaattccttccagac -cttctccacacccacacagacctagacgattccttccacacctccacacccacacgaacc -tagacgaattccttccacaccttgtgcacacccacacgaacctagacgaattccttccac -accttctccacacccacacgaacctagacgaattccttccacaccttctccacacccaca -cgaacctagacgattccttccacactttccccacacccacacgaacctagacg-attcct -tccacac---ctccacacccacacgaacctagatgaattccttccacaccttccccacac -ccacacaaacctagacgattccttccacaccttctccacacccacacaaacctagacaat -tccttccacacacacatgaacctagatgaattccttccacaccttctccacacccacatg -aacctagacgattccttccacaccttctccacacccacacacacctagatgaattccttc -cacaccttccccacacccacacagacctagacgaattccttgcacaccttctccacaccc -acacgaacctagacgaattccttccacaccttctccatacccacacgaacctagacaatt -ccttccacaccttctcacacccacacaaacctagatgaattccttccacaccttctccac -acccacacgaacctaaacgattccttccacaccttctccacacccacacacacctagatg -aattccttccacaccttccccacacccacacagacctagacgaattccttccacaccttc -tccacacccacacgaacctagacgattccttccacaccttctccatacccacacgaacct -agacaattccttccacaccttctcacacccacacaaacctagatgaattccttccacacc -ttccccacacccacacagacctagacgaattccttccacaccttc--------------- ---------------------------tccacacccacacgaacctagacaattccttgca -caccttctcacacccacacaaacctagacgaattccttccacaccttctccacacccaca -caaacctagacgaattccttccacaccttcctcacacccacacgaacctagacgattcct -tccacaccttccccacacccacacagacctagacgaattccttccacaccttctcca ->syndip_2_chr20:18208929-18210344 -gaatgggggaaggaggagaggagtaggtaaggaaggaatgcacgtcaatctgagtaaagg -gtatataggtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatt -tccaaataaaaaataagcagaaaggaaaagctaatcatctccccctattccagtccccca -ggcatgtatccttccgtagcttctccacacctacacgaacctagacgattccttccacac -cttccccacacccacacgaacctagacgattccttccacaccttccccacacccacacga -acctagatgaattccttccacaccttctccacacccacacgaacctagacgattccttcc -acaccttccccacacccattctccacacccacacgaacctagacgattccttccacacct -ccacacccacacgaacctagatgaattccttccacaccttccccacacccacacaaacct -agacgattccttccacaccttctccacacccacacgaacctagacgaattccttccagac -cttctccacacccacacagacctagacgattccttccacacctccacacccacacgaacc -tagacgaattccttccacaccttgtgcacacccacacgaacctagacgaattccttccac -accttctccacacccacacgaacctagacgaattccttccacaccttctccacacccaca -cgaacctagacgattccttccacactttccccacacccacaagaacctagacg-attcct -tccacac---ctccacacccacacgaacctagatgaattccttccacaccttccccacac -ccacacaaacctagacgattccttccacaccttctccacacccacacaaacctagacaat -tccttccacacacacatgaacctagatgaattccttccacaccttctccacacccacatg -aacctagacgattccttccacaccttctccacacccacacacacctagatgaattccttc -cacaccttccccacacccacacagacctagacgaattccttgcacaccttctccacaccc -acacgaacctagacgaattccttccacaccttctccatacccacacgaacctagacaatt -ccttccacaccttctcacacccacacaaacctagatgaattccttccacaccttctccac -acccacacgaacctaaacgattccttccacaccttctccacacccacacacacctagatg -aattccttccacaccttccccacacccacacagacctagacgaattccttccacaccttc -tccacacccacacgaacctagacgattccttccaca------------ccacacgaacct -agacaattccttccacaccttctcacacccacacaaacctagatgaattccttccacacc -ttccccacacccacacagacctagacgaattccttccacaccttc--------------- ---------------------------tccacacccacacgaacctagacaattccttgca -caccttctcacacccacacaaacctagacgaattccttccacaccttctccacacccaca -caaacctagacgaattccttccacaccttcctcacacccacacgaacctagacgattcct -tccacaccttccccacacccacacagacctagacgaattccttccacaccttctcca ->p:HG002_1_chr20:18208929-18210344 -gaatgggggaaggaggagaggagtaggtaaggaaggaatgcacgtcaatctgagtaaagg -gtatataggtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatt -tccaaataaaaaataagcagaaaggaaaagctaatcatctccccctattccagtccccca -ggcatgtatccttccgtagcttctccacacctacacgaacctagacgattccttccacac -cttccccacacccacacgaacctagacgattccttccacaccttccccacacccacacga -acctagatgaattccttccacaccttctccacacccacacgaacctagacgattccttcc -acaccttccccacacccattctccacacccacacgaacctagacgattccttccacacct -ccacacccacacgaacctagatgaattccttccacaccttccccacacccacacaaacct -agacgattccttccacaccttctccacacccacacgaacctagacgaattccttccagac -cttctccacacccacacagacctagacgattccttccacacctccacacccacacgaacc -tagacgaattccttccacaccttgtgcacacccacacgaacctagacgaattccttccac -accttctccacacccacacgaacctagacgaattccttccacaccttctccacacccaca -cgaacctagacgattccttccacaccttccccacacccacacagacctagacgaattcct -tgcacaccttctccacacccacacgaacctagacgaattccttccacaccttctccatac -ccacacgaacctagacaattccttccacaccttctccacacccacacaaacctagacaat -tccttccacacccacacaaacctagatgaattccttccacaccttctccacacccacacg -aacctaaacgattccttccacaccttctccacacccacacacacctagatgaattccttc -cacaccttccccacacccacacagacctagacgaattccttccacaccttctccacaccc -acacgaacctagacg-attccttccacaccttctccatacccacacgaacctagacaatt -ccttccacaccttctcacacccacacaaacctagatgaattccttccacaccttctccac -acccacacgaacctaaacgattccttccacaccttctccacacccacacacacctagatg -aattccttccacaccttccccacacccacacagacctagacgaattccttccacaccttc -tccacacccacacgaacctagacgattccttccaca------------ccacacgaacct -agacaattccttccacaccttcccacacccacacagacctagacgaattccttccacacc -ttctccacacccacacgaacctagacg-attccttccacaccttc--------------- ---------------------------cccacacccacacgaacctagacaattccttgca -caccttctcacacccacacaaacctagacgaattccttccacaccttctccacacccaca -caaacctagacgaattccttccacaccttcctcacacccacacgaacctagacgattcct -tccacaccttccccacacccacacagacctagacgaattccttccacaccttctcca ->p:HG002_2_chr20:18208929-18210344 -gaatgggggaaggaggagaggagtaggtaaggaaggaatgcacgtcaatctgagtaaagg -gtatataggtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatt -tccaaataaaaaataagcagaaaggaaaagctaatcatctccccctattccagtccccca -ggcatgtatccttccgtagcttctccacacctacacgaacctagacgattccttccacac -cttccccacacccacacgaacctagacgattccttccacaccttccccacacccacacga -acctagatgaattccttccacaccttctccacacccacacgaacctagacgattccttcc -acaccttccccacacccattctccacacccacacgaacctagacgattccttccacacct -ccacacccacacgaacctagatgaattccttccacaccttccccacacccacacaaacct -agacgattccttccacaccttctccacacccacacgaacctagacgaattccttccagac -cttctccacacccacacagacctagacgattccttccacacctccacacccacacgaacc -tagacgaattccttccacaccttgtgcacacccacacgaacctagacgaattccttccac -accttctccacacccacacgaacctagacgaattccttccacaccttctccacacccaca -cgaacctagacgattccttccacactttccccacacccacacgaacctagacg-attcct -tccacac---ctccacacccacacgaacctagatgaattccttccacaccttccccacac -ccacacaaacctagacgattccttccacaccttctccacacccacacaaacctagacaat -tccttccacacacacatgaacctagatgaattccttccacaccttctccacacccacatg -aacctagacg------------------------------------------attccttc -cacaccttccccacacccacacagacctagacgaattccttgcacaccttctccacaccc -acacgaacctagacgaattccttccacaccttctccatacccacacgaacctagacaatt -ccttccacaccttctcacacccacacaaacctagatgaattccttccacaccttctccac -acccacacgaacctaaacgattccttccacaccttctccacacccacacacacctagatg -aattccttccacaccttccccacacccacacagacctagacgaattccttccacaccttc -tccacacccacacgaacctagacgattccttccacaccttctccatacccacacgaacct -agacaattccttccacaccttctcacacccacacaaacctagatgaattccttccacacc -ttccccacacccacacagacctagacgaattccttccacaccttctccacacccacacga -acctagacgattccttccacaccttccccacacccacacgaacctagacaattccttgca -caccttctcacacccacacaaacctagacgaattccttccacaccttctccacacccaca -caaacctagacgaattccttccacaccttcctcacacccacacgaacctagacgattcct -tccacaccttccccacacccacacagacctagacgaattccttccacaccttctcca ->ref_chr20:18208929-18210344 -gaatgggggaaggaggagaggagtaggtaaggaaggaatgcacgtcaatctgagtaaagg -gtatataggtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatt -tccaaataaaaaataagcagaaaggaaaagctaatcatctccccctattccagtccccca -ggcatgtatccttccgtagcttctccacacct---------------------------- --------------acacgaacctagacgattccttccacaccttccccacacccacacga -acctagatgaattccttccacaccttctccacacccacacgaacctagacgattccttcc -acaccttccccacacccattctccacacccacacgaacctagacgattccttccacacct -ccacacccacacgaacctagatgaattccttccacaccttccccacacccacacaaacct -agacgattccttccacaccttctccacacccacacgaacctagacgaattccttccagac -cttctccacacccacacagacctagacgattccttccacacctccacacccacacgaacc -tagacgaattccttccacaccttgtgcacacccacacgaacctagacgaattccttccac -accttctccacacccacacgaacctagacgaattccttccacaccttctccacacccaca -cgaacctagacgattccttccacaccttccccacacccacacagacctagacgaattcct -tgcacaccttctccacacccacacgaacctagacgaattccttccacaccttctccatac -ccacacgaacctagacaattccttccacaccttct------------------------- -------cacacccacacaaacctagatgaattccttccacaccttctccacacccacacg -aacctaaacgattccttccacaccttctccacacccacacacacctagatgaattccttc -cacaccttccccacacccacacagacctagacgaattccttccacaccttctccacaccc -acacgaacctagacg-attccttccacaccttctccatacccacacgaacctagacaatt -ccttccacaccttctcacacccacacaaacctagatgaattccttccacaccttc----- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------cccacacccacacagacctagacgaattccttccacacc -ttctccacacccacacgaacctagacg-attccttccacaccttc--------------- ---------------------------cccacacccacacgaacctagacaattccttgca -caccttctcacacccacacaaacctagacgaattccttccacaccttctccacacccaca -caaacctagacgaattccttccacaccttcctcacacccacacgaacctagacgattcct -tccacaccttccccacacccacacagacctagacgaattccttccacaccttctcca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_cd8fd769a12a7d1b4a00cbb1a3d57209.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_cd8fd769a12a7d1b4a00cbb1a3d57209.msa deleted file mode 100644 index c938b7f0..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_cd8fd769a12a7d1b4a00cbb1a3d57209.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:57190046-57190638 -atacacggtgtgtgtcagcacagtgaagaggccagtgaggctggagaagtgagccaggaa -ccagagaggttgagactggagatagtgagcgaggaaccggagggggtgaagctggagaga -gtgagccaggaatcagaggaggtgaggccagagagagtgagcgaggaaccagagggggtg -aggctggagagagtgaccgaggaaccagaggaggtgaggcc----agagtgagtgaggag -cttgaaggggtgaggctggagacagtgagcgaggaaccagagggggtgaggctggagaga -gtgagccaggaaccagaggaggtgaggccaga----gtgagtgaggagcttgaaggggtg -aggctggagacagtgagcgaggaaccagagggggtgaggctggagagcgtgagtgaggag -cccgagggggtgaggctggagagagtgagtgaggagcccaagggggtgaagccgaggtgg -gtatggggctgggtcacctggggtctcccagcccagtgggggatttgggcagggggcgac -gtggccagggttctgtggtgggagacccattctgaatgccgtgtggggaaccaacaa ->syndip_2_chr20:57190046-57190638 -atacacggtgtgtgtcagcacagtgaagaggccagtgaggctggagaagtgagccaggaa -ccagagaggttgagactggagatagtgagcgaggaaccggagggggtgaagctggagaga -gtgagccaggaatcagaggaggtgaggccagagagagtgagcgaggaaccagagggggtg -aggctggagagagtgaccgaggaaccagaggaggtgaggctggagagagtgagccaggaa -ccagaggaggtgaggccag----agtgagtgaggagcttgaaggggtgaggctggagaca -gtgagcgaggaacca------------------------------------gagggggtg -aggctggagagcgtgagtgaggagcccgagggggtgaggctggagagcgtgagtgaggag -cccgagggggtgaggctggagagagtgagtgaggagcccaagggggtgaagccgaggtgg -gtatggggctgggtcacctggggtctcccagcccagtgggggatttgggcagggggcgac -gtggccagggttctgtggtgggagacccattctgaatgccgtgtggggaaccaacaa ->p:HG002_1_chr20:57190046-57190638 -atacacggtgtgtgtcagcacagtgaagaggccagtgaggctggagaagtgagccaggaa -ccagagaggttgagactggagatagtgagcgaggaaccggagggggtgaagctggagaga -gtgagccaggaatcagaggaggtgaggccagagagagtgagcgaggaaccagagggggtg -aggctggagagagtgaccgaggaaccagaggaggtgaggctggagagagtgagccaggaa -ccagaggaggtgaggccag----agtgagtgaggagcttgaaggggtgaggctggagaca -gtgagcgaggaacca------------------------------------gagggggtg -aggctggagagcgtgagtgaggagcccgagggggtgaggctggagagcgtgagtgaggag -cccgagggggtgaggctggagagagtgagtgaggagcccaagggggtgaagccgaggtgg -gtatggggctgggtcacctggggtctcccagcccagtgggggatttgggcagggggcgac -gtggccagggttctgtggtgggagacccattctgaatgccgtgtggggaaccaacaa ->p:HG002_2_chr20:57190046-57190638 -atacacggtgtgtgtcagcacagtgaagaggccagtgaggctggagaagtgagccaggaa -ccagagaggttgagactggagatagtgagcgaggaaccggagggggtgaagctggagaga -gtgagccaggaatcagaggaggtgaggccagagagagtgagcgaggaaccagagggggtg -aggctggagagagtgaccgaggaaccagaggaggtgaggctggagagagtgagccaggaa -ccagaggaggtgaggccag----agtgagtgaggagcttgaaggggtgaggctggagaca -gtgagcgaggaaccagagggggtgaggctggagagcgtgagtgaggagcccgagggggtg -aggctggagagcgtgagtgaggagcccgagggggtgaggctggagagcgtgagtgaggag -cccgagggggtgaggctggagagagtgagtgaggagcccaagggggtgaagccgaggtgg -gtatggggctgggtcacctggggtctcccagcccagtgggggatttgggcagggggcgac -gtggccagggttctgtggtgggagacccattctgaatgccgtgtggggaaccaacaa ->ref_chr20:57190046-57190638 -atacacggtgtgtgtcagcacagtgaagaggccagtgaggctggagaagtgagccaggaa -ccagagaggttgagactggagatagtgagcgaggaaccggagggggtgaagctggagaga -gtgagccaggaatcagaggaggtgaggccagagagagtgagcgaggaaccagagggggtg -aggctggagagagtgaccgaggaaccagaggaggtgaggctggagagagtgagccaggaa -ccagaggaggtgaggccag----agtgagtgaggagcttgaaggggtgaggctggagaca -gtgagcgaggaaccagagggggtgaggctggagagcgtgagtgaggagcccgagggggtg -aggctggagagcgtgagtgaggagcccgagggggtgaggctggagagcgtgagtgaggag -cccgagggggtgaggctggagagagtgagtgaggagcccaagggggtgaagccgaggtgg -gtatggggctgggtcacctggggtctcccagcccagtgggggatttgggcagggggcgac -gtggccagggttctgtggtgggagacccattctgaatgccgtgtggggaaccaacaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_cdc7d6cb5093cc33307e928083c08cc5.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_cdc7d6cb5093cc33307e928083c08cc5.msa deleted file mode 100644 index 83036f1d..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_cdc7d6cb5093cc33307e928083c08cc5.msa +++ /dev/null @@ -1,335 +0,0 @@ ->syndip_1_chr20:38462931-38464783 -agcctgttttgtttggggcaagggttttaacatttatatatatataaatatatatatatt -ttatatatacaaatatatatataaatatatatttatatatatttatatataatatattat -atataaatatatttatatataatatattatatataaatatattatatataaaatattata -tataaatatatatatttatatatataaatatatataaatatatatatatataaaaatacc -agcacatcagtatcaggaataaatgggctgggcagtatatatatatatatatatgtatat -atatatactgtttttcatatatatatactgtcttatatatatatatactgttttacatat -atatactgtttcatatatataatgttttatatatatactgttatatatattatatgtact -gttatatattttttatatatatactgttatatatattttttatatatactgttatatatt -atatatatactgttatatatatattttacatatatactgttatatatatattttatatat -atatactgttatatatatatattttatatatgtatactgttatatatttatattttttat -atgtatactgttatatatatattatatgtatactgttatatatatattttatatgtatac -tgttatatatatatatttcatatatatatactgttatatatattttatatatatatactg -tcatatatatattttatatatatactgtcatatatatattttatatatatatactgtcat -atatatattttatatatatatatactgtcatatatatattttatatatatatactgtcat -atatattttatatatatactgtcatatatatattttatatatatactgtcatatatatat -tttatatatatactgtcatatatatattt--tatatatatactgtcatatatatatttta -tatatatatactgtcatatatatattttatatatatatactgtcatatatatattttata -tatatactgtcatatgtatattttatatatatactgtcatatgtatattt---------- ----------------------tatatatatactgttatatgtatattttatatatatata -ctgttatatatatatttttatatatatactgttatatatatttttttatatatatactgt -tatatatatttttatatatatactgttatatatatattttatatatatactgttatatat -atattttatatatactgttatatatatatattttatatatatactgttatatataatttt -tttcatatatatactgttatatatatattttatatatatatactgttatatatatatttt -atatatatactgttatatatatatattttatatatatactgttattttttatatatatac -tgttatatatatattttatatatatactgttatatatatattatctatatactgttatgt -gtatattttatctatatactgttatgtgtatattttatctatatactgttatgtgtatat -tttacctatatacttttatgtgtatattttatatatatactgttatgtgtatattttata -tatatactgttatgtgtatattttttatatatactgttatgtgtatattttatatatata -tactgttatgtgtatattttatatatatatactgttatgtgtatattttatatatatact -gttatgtgtatattttatatatatactgttatatatagttcatatatatactgttatatg -tatagttcatatatatactgttatatatatagttcatatgtatactgttatatatatagt -tcatatatatactgttatatatatagttcatatatatactgttatatatatatagttcat -atatatactgttatatatagttcatatatatactgttatatatatagttcatatatatac -tgttatatatatagttcatatatatactgttatatatagttcatatatatatactgttct -atatatagttcatatatatatactgttatatatatagttcatatatatatactgttatat -atagttcatatatatatagttcatatatatactgttatatatatagttcatatatatact -gttatatacatagttcatatatatactgttatatatatagttcatatatatatactgtta -tatatatagttcatatatatactgttgtatatagttcatatatatactgttatatatata -gttcatatattactgttatatatatagttcatatatatactgttatatatatatagttca -tatatatactgttatatatagtttatatatatatactgttatatatatagtttatatata -tatactgttatatatatagtttatatatatatactgttatatatatatagtttatatata -tatactgttatatatatagtttatatatatatactgttatatatatatagtttatatata -ctgttatatatatagtttatatatatactgttatatatatagtttatatatatactgtta -tatatatagtttatatatatactgttatatatatagtttatatatatactgttatatata -tagtttatatatatactgttatatatatagtttatatatatactgttatatatatagttt -atatatatatactgt--tatatatagtttatatatactgttatatatatagtttatatac -tgttatatatagtttatatatatatactgttatatatagtttatatatatatactgttat -atatatatagtttatatatatatactgttatatatatatagtttatatatatactgttat -atatatatagtttatatatatactgttgtatatatagtttatatatatactgttatatat -atatttgtgtatatatactgttatataaatatatttgtgtatatatactgttatatatat -attttatgtatatatactgttatatatatattttatgtatatatactgttatatatatat -tttatgtatatatactgttatatatatattttatgtatatatactgttatatatatattt -tatgtatatatactgttatatatattttatgtatatatactgttatatatattttatgta -tatatactgttatatatatattttatgtatatatactgttatatctgtatattttatgtt -tatatactgttatatctgtatattttatgtatatatactgttatatctgtatattttatg -tatatactgttatatatatactgttatatatatactgatatatatactgttatatatata -ctgatatatatatactgttatatatatactgttatatatatatactgttacatatacata -tatatactgttatatatatactgttatatatattgttatatatatacacatatatatata -c--atatatatacatatatatatacatatatatatacatatatatatacacgtatatata -tacatatatatatacacatatatatatatacacacacatatatatatatatatatactgg -ctgtgtgtggtggtgcacacctgtaatcccagcactttgggaggccaaggcaggctgatg -gcttgagctcaggagttcaagaccagctaagcaacatactgagatcccatctctaaaaaa -aatacaaaaaggccaggcacagtggctcacacctgtaatcccagcactttgggaggctga -ggtgggcagatcacgaggtcagcagttcgagaccagcctggccagcatggtgaaacccca -tctctactaaaaatacaaaacattagccggacatggtggcacacacctgtaattccagct -actcaggaagctgaggca ->syndip_2_chr20:38462931-38464783 -agcctgttttgtttggggcaagggttttaacatttatatatatataaatatatatatatt -ttatatatacaaatatatatataaatatatatttatatatatttatatataatatattat -atat-aatatatttatatataatatattatatataaatatattatatataaaatattata -tataaatatatatatttatatatataaatatatataaatatatatatatataaaaatacc -agcacatcagtatcaggaataaatgggctgggcag--tatatatatatatatatgtatat -atatatactgtttttcatatatatatactgtcttatatatatatatactgttttacatat -atatactgtttcatatatataatgttttatatatatactgttatatatattatatgtact -gttatatattttttatatatatactgttatatatattttttatatatactgttatatatt -atatatatactgttatatatatattttacatatatactgttatatatatattttatatat -atatactgttatatatatatattttatatatgtatactgttatatatttatattttttat -atgtatactgttatatatatattatatgtatactgttatatatatattttatatgtatac -tgttatatatatatatttcatatatatatactgttatatatattttatatatatatactg -tcatatatatattttatatatatactgtcatatatatattttatatatatatactgtcat -atatatattt--tatatatatatactgtcatatatatattttatatatatatactgtcat -atatattttatatatatactgtcatatatatattttatatatatactgtcatatatatat -tttatatatatactgtcatatatatattttatatatatatactgtcatatatatatttta -tatatatatactgtcatatatatattt--tatatatatactgtcatatgtatattttata -tatatactgtcatatgtatattttatatatatactgttatatgtatattttatatatata -tactgttatatatatattttatatatatatactgttatatatatattttatatatatata -ctgttatatatatatttttatatatatactgttatatatatttttttatatatatactgt -tatatatatttttatatatatactgttatatatatattttatatatatactgttatatat -atattttatatatactgttatatatatatattttatatatatactgttatatataatttt -tttcatatatatactgttatatatatattttatatatatatactgttatatatatatttt -atatatatactgttatatatatatattttatatatatactgttattttttatatatatac -tgttatatatatattttatatatatactgttatatatatattatctatatactgttatgt -gtatattttatctatatactgttatgtgtatattttatctatatactgttatgtgtatat -tttacctatatacttttatgtgtatattttatatatatactgttatgtgtatattttata -tatatactgttatgtgtatattttttatatatactgttatgtgtatattttatatatata -tactgttatgtgtatattttatatatatatactgttatgtgtatattttatatatatact -gttatgtgtatattttatatatatactgttatatatagttcatatatatactgttatatg -tatagttcatatatatactgttatatatatagttcatatgtatactgttatatatatagt -tcatatatatactgttatatatatagttcatatatatactgttatatatatatagttcat -atatatactgttatatatagttcatatatatactgttatatatatagttcatatatatac -tgttatatatatagttcatatatatactgttatatatagttcatatatatatactgttct -atatatagttcatatatatatactgttatatatatagttcatatatatatactgttatat -atagttcatatatatatagttcatatatatactgttatatatatagttcatatatatact -gttatatacatagttcatatatatactgttatatatatagttcatatatatatactgtta -tatatatagttcatatatatactgttgtatatagttcatatatatactgttatatatata -gttcatatattactgttatatatatagttcatatatatactgttatatatatatagttca -tatatatactgttatatatagtttatatatatatactgttatatatatagtttatatata -tatactgttatatatatagtttatatatatatactgttatatatatatagtttatatata -tatactgttatatatatagtttatatatatatactgt--tatatatatagtttatatata -ctgtta-------------------------tatatatatagtttatatatatactgtta -tatatatagtttatatatatactgttatatatatagtttatatatatactgttatatata -tagtttatatatatactgttatatatatagtttatatatatactgttatatatatagttt -atatatatatactgttatatatatagtttataaatactgttatatatatagtttatatac -tgttatatatagtttatatatatatactgttatatatagtttatatatatatactgttat -atatatatagtttatatatatatactgttatatatatatagtttatatatatactgttat -atatatatagtttatatatatactgttgtatatatagtttatatatatactgttatatat -atatttgtgtatatatactgttatataaatatatttgtgtatatatactgttatatatat -attttatgtatatatactgttatatatatattttatgtatatatactgttatatatatat -tttatgtatatatactgttatatatatattttatgtatatatactgtta----------- -----------------tatatatattttatgtatatatactgttatatatattttatgta -tatatactgttatatatatattttatgtatatatactgttatatctgtatattttatgtt -tatatactgttatatctgtatattttatgtatatatactgttatatctgtatattttatg -tatatactgttatatatatactgttatatatatactgatatatatactgttatatatata -ctgatatatatatactgttatatatatactgttatatatatatactgttacatatacata -tatatactgttatatatatactgttatatatattgttatatatatacacat--------- ----atatatatacatatatatatacatatatatatacatatatatatacacgtatatata -tacatatatatatacacatatatatatatacacacacatatatatatatatatatactgg -ctgtgtgtggtggtgcacacctgtaatcccagcactttgggaggccaaggcaggctgatg -gcttgagctcaggagttcaagaccagctaagcaacatactgagatcccatctctaaaaaa -aatacaaaaaggccaggcacagtggctcacacctgtaatcccagcactttgggaggctga -ggtgggcagatcacgaggtcagcagttcgagaccagcctggccagcatggtgaaacccca -tctctactaaaaatacaaaacattagccggacatggtggcacacacctgtaattccagct -actcaggaagctgaggca ->p:HG002_1_chr20:38462931-38464783 -agcctgttttgtttggggcaagggttttaacatttatatatatataaatatatatatatt -ttatatatacaaatatatatataaatatatatttatatatatttatatataatatattat -atat-aatatatttatatataatatattatatataaatatattatatataaaatattata -tataaatatatatatttatatatataaatatatataaatatatatatatataaaaatacc -agcacatcagtatcaggaataaatgggctgggcag--tatatatatatatatatgtatat -atatatactgtttttcatatatatatactgtcttatatatatatatactgttttacatat -atatactgtttcatatatataatgttttatatatatactgttatatatattatatgtact -gttatatattttttatatatatactgttatatatattttttatatatactgttatatatt -atatatatactgttatatatatattttacatatatactgttatatatatattttatatat -atatactgttatatatatatattttatatatgtatactgttatatatttatattttttat -atgtatactgttatatatatattatatgtatactgttatatatatattttatatgtatac -tgttatatatatatatttcatatatatatactgttatatatattttatatatatatactg -tcatatatatattttatatatatactgtcatatatatattttatatatatatactgtcat -atatatattt--tatatatatatactgtcatatatatattttatatatatatactgtcat -atatattttatatatatactgtcatatatatattttatatatatactgtcatatatatat -tttatatatatactgtcatatatatattttatatatatatactgtcatatatatatttta -tatatatatactgtcatatatatattt--tatatatatactgtcatatgtatattttata -tatatactgtcatatgtatattttatatatatactgttatatgtatattttatatatata -tactgttatatatatattttatatatatatactgttatatatatattttatatatatata -ctgttatatatatatttttatatatatactgttatatatatttttttatatatatactgt -tatatatatttttatatatatactgttatatatatattttatatatatactgttatatat -atattttatatatactgttatatatatatattttatatatatactgttatatataatttt -tttcatatatatactgttatatatatattttatatatatatactgttatatatatatttt -atatatatactgttatatatatatattttatatatatactgttattttttatatatatac -tgttatatatatattttatatatatactgttatatatatattatctatatactgttatgt -gtatattttatctatatactgttatgtgtatattttatctatatactgttatgtgtatat -tttacctatatacttttatgtgtatattttatatatatactgttatgtgtatattttata -tatatactgttatgtgtatattttttatatatactgttatgtgtatattttatatatata -tactgttatgtgtatattttatatatatatactgttatgtgtatattttatatatatact -gttatgtgtatattttatatatatactgttatatatagttcatatatatactgttatatg -tatagttcatatatatactgttatatatatagttcatatgtatactgttatatatatagt -tcatatatatactgttatatatatagttcatatatatactgttatatatatatagttcat -atatatactgttatatatagttcatatatatactgttatatatatagttcatatatatac -tgttatatatatagttcatatatatactgttatatatagttcatatatatatactgttct -atatatagttcatatatatatactgttatatatatagttcatatatatatactgttatat -atagttcatatatatatagttcatatatatactgttatatatatagttcatatatatact -gttatatacatagttcatatatatactgttatatatatagttcatatatatatactgtta -tatatatagttcatatatatactgttgtatatagttcatatatatactgttatatatata -gttcatatattactgttatatatatagttcatatatatactgttatatatatatagttca -tatatatactgttatatatagtttatatatatatactgttatatatatagtttatatata -tatactgttatatatatagtttatatatatatactgttatatatatatagtttatatata -tatactgttatatatatagtttatatatatatactgt--tatatatatagtttatatata -ctgtta-------------------------tatatatatagtttatatatatactgtta -tatatatagtttatatatatactgttatatatatagtttatatatatactgttatatata -tagtttatatatatactgttatatatatagtttatatatatactgttatatatatagttt -atatatatatactgttatatatatagtttataaatactgttatatatatagtttatatac -tgttatatatagtttatatatatatactgttatatatagtttatatatatatactgttat -atatatatagtttatatatatatactgttatatatatatagtttatatatatactgttat -atatatatagtttatatatatactgttgtatatatagtttatatatatactgttatatat -atatttgtgtatatatactgttatataaatatatttgtgtatatatactgttatatatat -attttatgtatatatactgttatatatatattttatgtatatatactgttatatatatat -tttatgtatatatactgttatatatatattttatgtatatatactgtta----------- -----------------tatatatattttatgtatatatactgttatatatattttatgta -tatatactgttatatatatattttatgtatatatactgttatatctgtatattttatgtt -tatatactgttatatctgtatattttatgtatatatactgttatatctgtatattttatg -tatatactgttatatatatactgttatatatatactgatatatatactgttatatatata -ctgatatatatatactgttatatatatactgttatatatatatactgttacatatacata -tatatactgttatatatatactgttatatatattgttatatatatacacat--------- ----atatatatacatatatatatacatatatatatacatatatatatacacgtatatata -tacatatatatatacacatatatatatatacacacacatatatatatatatatatactgg -ctgtgtgtggtggtgcacacctgtaatcccagcactttgggaggccaaggcaggctgatg -gcttgagctcaggagttcaagaccagctaagcaacatactgagatcccatctctaaaaaa -aatacaaaaaggccaggcacagtggctcacacctgtaatcccagcactttgggaggctga -ggtgggcagatcacgaggtcagcagttcgagaccagcctggccagcatggtgaaacccca -tctctactaaaaatacaaaacattagccggacatggtggcacacacctgtaattccagct -actcaggaagctgaggca ->p:HG002_2_chr20:38462931-38464783 -agcctgttttgtttggggcaagggttttaacatttatatatatataaatatatatatatt -ttatatatacaaatatatatataaatatatatttatatatatttatatataatatattat -atataaatatatttatatataatatattatatataaatatattatatataaaatattata -tataaatatatatatttatatatataaatatatataaatatatatatatataaaaatacc -agcacatcagtatcaggaataaatgggctgggcagtatatatatatatatatatgtatat -atatatactgtttttcatatatatatactgtcttatatatatatatactgttttacatat -atatactgtttcatatatataatgttttatatatatactgttatatatattatatgtact -gttatatattttttatatatatactgttatatatattttttatatatactgttatatatt -atatatatactgttatatatatattttacatatatactgttatatatatattttatatat -atatactgttatatatatatattttatatatgtatactgttatatatttatattttttat -atgtatactgttatatatatattatatgtatactgttatatatatattttatatgtatac -tgttatatatatatatttcatatatatatactgttatatatattttatatatatatactg -tcatatatatattttatatatatactgtcatatatatattttatatatatatactgtcat -atatatattttatatatatatatactgtcatatatatattttatatatatatactgtcat -atatattttatatatatactgtcatatatatattttatatatatactgtcatatatatat -tttatatatatactgtcatatatatattt--tatatatatactgtcatatatatatttta -tatatatatactgtcatatatatattttatatatatatactgtcatatatatattttata -tatatactgtcatatgtatattttatatatatactgtcatatgtatattt---------- ----------------------tatatatatactgttatatgtatattttatatatatata -ctgttatatatatatttttatatatatactgttatatatatttttttatatatatactgt -tatatatatttttatatatatactgttatatatatattttatatatatactgttatatat -atattttatatatactgttatatatatatattttatatatatactgttatatataatttt -tttcatatatatactgttatatatatattttatatatatatactgttatatatatatttt -atatatatactgttatatatatatattttatatatatactgttattttttatatatatac -tgttatatatatattttatatatatactgttatatatatattatctatatactgttatgt -gtatattttatctatatactgttatgtgtatattttatctatatactgttatgtgtatat -tttacctatatacttttatgtgtatattttatatatatactgttatgtgtatattttata -tatatactgttatgtgtatattttttatatatactgttatgtgtatattttatatatata -tactgttatgtgtatattttatatatatatactgttatgtgtatattttatatatatact -gttatgtgtatattttatatatatactgttatatatagttcatatatatactgttatatg -tatagttcatatatatactgttatatatatagttcatatgtatactgttatatatatagt -tcatatatatactgttatatatatagttcatatatatactgttatatatatatagttcat -atatatactgttatatatagttcatatatatactgttatatatatagttcatatatatac -tgttatatatatagttcatatatatactgttatatatagttcatatatatatactgttct -atatatagttcatatatatatactgttatatatatagttcatatatatatactgttatat -atagttcatatatatatagttcatatatatactgttatatatatagttcatatatatact -gttatatacatagttcatatatatactgttatatatatagttcatatatatatactgtta -tatatatagttcatatatatactgttgtatatagttcatatatatactgttatatatata -gttcatatattactgttatatatatagttcatatatatactgttatatatatatagttca -tatatatactgttatatatagtttatatatatatactgttatatatatagtttatatata -tatactgttatatatatagtttatatatatatactgttatatatatatagtttatatata -tatactgttatatatatagtttatatatatatactgttatatatatatagtttatatata -ctgttatatatatagtttatatatatactgttatatatatagtttatatatatactgtta -tatatatagtttatatatatactgttatatatatagtttatatatatactgttatatata -tagtttatatatatactgttatatatatagtttatatatatactgttatatatatagttt -atatatatatactgt--tatatatagtttatatatactgttatatatatagtttatatac -tgttatatatagtttatatatatatactgttatatatagtttatatatatatactgttat -atatatatagtttatatatatatactgttatatatatatagtttatatatatactgttat -atatatatagtttatatatatactgttgtatatatagtttatatatatactgttatatat -atatttgtgtatatatactgttatataaatatatttgtgtatatatactgttatatatat -attttatgtatatatactgttatatatatattttatgtatatatactgttatatatatat -tttatgtatatatactgttatatatatattttatgtatatatactgttatatatatattt -tatgtatatatactgttatatatattttatgtatatatactgttatatatattttatgta -tatatactgttatatatatattttatgtatatatactgttatatctgtatattttatgtt -tatatactgttatatctgtatattttatgtatatatactgttatatctgtatattttatg -tatatactgttatatatatactgttatatatatactgatatatatactgttatatatata -ctgatatatatatactgttatatatatactgttatatatatatactgttacatatacata -tatatactgttatatatatactgttatatatattgttatatatatacacatatatatata -c--atatatatacatatatatatacatatatatatacatatatatatacacgtatatata -tacatatatatatacacatatatatatatacacacacatatatatatatatatatactgg -ctgtgtgtggtggtgcacacctgtaatcccagcactttgggaggccaaggcaggctgatg -gcttgagctcaggagttcaagaccagctaagcaacatactgagatcccatctctaaaaaa -aatacaaaaaggccaggcacagtggctcacacctgtaatcccagcactttgggaggctga -ggtgggcagatcacgaggtcagcagttcgagaccagcctggccagcatggtgaaacccca -tctctactaaaaatacaaaacattagccggacatggtggcacacacctgtaattccagct -actcaggaagctgaggca ->ref_chr20:38462931-38464783 -agcctgttttgtttggggcaagggttttaacatttatatatatataaatatatatatatt -ttatatatacaaatatatatataaatatatatttatatatatttatatataatatattat -atataaatatatttatatataatatattatatataaatatattatatataaaatattata -tataaatatatatatttatatatataaatatatataaatatatatatatataaaaatacc -agcacatcagtatcaggaataaatgggctgggcagtatatatatatatatatatgtatat -atatatactgtttttcatatatatatactgtcttatatatatatatactgttttacatat -atatactgtttcatatatataatgttttatatatatactgttatatatattatatgtact -gttatatattttttatatatatactgttatatatattttttatatatactgttatatatt -atatatatactgttatatatatattttacatatatactgttatatatatattttatatat -atatactgttatatatatatattttatatatgtatactgttatatatttatattttttat -atgtatactgttatatatatattatatgtatactgttatatatatattttatatgtatac -tgttatatatatatatttcatatatatatactgttatatatattttatatatatatactg -tcatatatatattttatatatatactgtcatatatatattttatatatatatactgtcat -atatatattttatatatatatatactgtcatatatatattttatatatatatactgtcat -atatattttatatatatactgtcatatatatattttatatatatactgtcatatatatat -tttatatatatactgtcatatatatattt--tatatatatactgtcatatatatatttta -tatatatatactgtcatatatatattttatatatatatactgtcatatatatattttata -tatatactgtcatatgtatattttatatatatactgtcatatgtatattt---------- ----------------------tatatatatactgttatatgtatattttatatatatata -ctgttatatatatatttttatatatatactgttatatatatttttttatatatatactgt -tatatatatttttatatatatactgttatatatatattttatatatatactgttatatat -atatttta---------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -tatatactgttatatagatactgttatatatatactgatatatatactgttatatatata -ctgatatatatatactgttatatatatactgttatatatatatactgttacatatacata -tatatactgttatatatatactgttatatatattgttatatatatacacatatatatata -catatatatatacatatatatatacatatatatatacatatatatatacacgtatatata -tacatatatatatacacatatatatatatacacacacatatatatatatatatatactgg -ctgtgtgtggtggtgcacacctgtaatcccagcactttgggaggccaaggcaggctgatg -gcttgagctcaggagttcaagaccagctaagcaacatactgagatcccatctctaaaaaa -aatacaaaaaggccaggcacagtggctcacacctgtaatcccagcactttgggaggctga -ggtgggcagatcacgaggtcagcagttcgagaccagcctggccagcatggtgaaacccca -tctctactaaaaatacaaaacattagccggacatggtggcacacacctgtaattccagct -actcaggaagctgaggca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ce11c6a832df599630cc716aa0678351.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ce11c6a832df599630cc716aa0678351.msa deleted file mode 100644 index d95e36a9..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ce11c6a832df599630cc716aa0678351.msa +++ /dev/null @@ -1,155 +0,0 @@ ->syndip_1_chr20:14861844-14862854 -tgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggtattatgc -tctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggacattggag -gttttatatataaatatatatatatatatttatatatatatttatatatatatatttata -tatatttatatatatttatatatatatttatatatatat--ttatatatatatttatata -tatatttatatatatatttatatatatatttatatatatatttatatatatttatatata -tttatatatatttttatatatttttatatatataaatatataaaaatatatataaatata -taaaaatatataaaaatatataaatatatataaatatataaatatatataaatatatata -aatatatatttatatataaatatatataaatatatatttatacataaatatatataaata -tatatttatacataaatatataaatatatataatatatataaatatatattatacatata -tatataaatatatattatacataaatatataaatatatataaatatatataaatatatat -ttatacataaatatataaatatatatataaatatatataaatatatataaatatatatat -aaatatatatataaatatatataaatatatatataaatatatatataaatatatataaat -atatataaatatatatataaatatatataaatatatataaatatatatttatatattaat -atataaatatatataaatatatatttatatattaatatataaatatatatatattaatat -atataaatatatataaatatatatttatatattaatatatatatattaatatatatatat -ttatatattaatatatatatttatatattaatatatataaatatattactatgtatattt -atatatatttatataaatatatataaatatatgtaaatatatatataaaaatatatatta -atatataaaaatatatatataaatata---tataaatatatatataaatatatataaata -tatatatataaatatatataaataaatatataaatatatataaatat--atatataaata -tatataaatatatataaatatatataaaaatatatataaatatatatataaatatatata -aatatatatataaatatatatataaatatatatataaatatatataa--atatatatata -aatatatataaatatatatataattatatataaatatatataaatatatataaatatata -tataaatatatataaatatatataaatatatataaatatatatataaatatatataaata -tatatatataaatatatataaatatatatataaatatatataaatatatatataaatata -aatatatataaatata----taaaaatatatatataaatataaatatatataaatatata -tgtataaatatatatataaatataaatatatatatataaatatatatataaatatatata -tataaatatatatataaatatatataaatatatatataaatatatataaatatatatata -tatatttttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcc -cttgccttttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaa -gagagcagaagttgagttggcat ->syndip_2_chr20:14861844-14862854 -tgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggtattatgc -tctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggacattggag -gttttatatataaatatatatatatatatttatatatatatttatatatatatatttata -tatatttatatatatttatatatatatttatatatatat--ttatatata---------- -----------------------------------------------------tttatata -tttatatatatttatatatatttttatatatataaatatataaaa--------------- ------------------------------------------------------------- ----------------------atatataaatatatataaatatataaatatatataaata -tatatttatacataaatatataaatatatataatatatataaatatatattatacatata -tatataaatatatattatacataaatatataaatatatataaatatatataaatatatat -ttatacataaatatataaatatat------atatatataaatatatataa---------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------atatatatttatatattaatatatataaatatattactatgtatattt -atatatatttatataaatatatataaatatatgtaaatatatatataaaaatatatatta -atatataaaaatatatatataaatata-------------tatataaatatatataaata -aatatatataaatatatatataaatatatataaatatatataaatat--atatataaata -tatataaatatatataaatatatatataaatatatatataaatatatataaatatatata -aataaatatataaatatatatataaatatatataaatatatatataaatatatataaata -tatatatataaatatatataaatatatatataaatatatataaatatatatataaatata -tataaatat------atatatataaatatatataaatatatatataaatatatataaata -tat--------atataaatataaatatatataaatatataaaaatatatatataaatata -aatatatataaatatatatgtataaatatatatataaatataaatatatataaatatata -tatataaatatatatataaatatatataaatatatataaaaatatatataa--atatata -tataaatatatatataaatatatataaatatatatataaatatatataaatatatatata -tatatttttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcc -cttgccttttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaa -gagagcagaagttgagttggcat ->p:HG002_1_chr20:14861844-14862854 -tgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggtattatgc -tctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggacattggag -gttttatatataaatatatatatatatatttatatatatatttatatatatatatttata -tatatttatatatatttatatatatatttatatatatat--ttatatata---------- -----------------------------------------------------tttatata -tttatatatatttatatatatttttatatatataaatatataaaa--------------- ------------------------------------------------------------- ----------------------atatataaatatatataaatatataaatatatataaata -tatatttatacataaatatataaatatatataatatatataaatatatattatacatata -tatataaatatatattatacataaatatataaatatatataaatatatataaatatatat -ttatacataaatatataaatatat------atatatataaatatatataa---------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------atatatatttatatattaatatatataaatatattactatgtatattt -atatatatttatataaatatatataaatatatgtaaatatatatataaaaatatatatta -atatataaaaatatatatataaatata-------------tataaatatatatataaata -aatatatataaatatatatataaatatatataaatatatataaatat--atatataaata -tatataaatatatataaatatatatataaatatatatataaatatatataaatatatata -aataaatatataaatatatatataaatatatataaatatatatataa--atatataaata -tatatatataaatatatataaatatatatataaatatatataaatatatatataaatata -tataaatat------atatatataaatatatataaatatatatataaatatatataaata -tat--------atataaatataaatatatataaatatataaaaatatatatataaatata -aatatatataaatatatatgtataaatatatatataaatataaatatatataaatatata -tatataaatatatatataaatatatataaatatatataaaaatatatataa--atatata -tataaatatatatataaatatatataaatatatatataaatatatataaatatatatata -tatatttttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcc -cttgccttttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaa -gagagcagaagttgagttggcat ->p:HG002_2_chr20:14861844-14862854 -tgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggtattatgc -tctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggacattggag -gttttatatataaatatatatatatatatttatatatatatttatatatatatatttata -tatatttatatatatttatatatatatttatatatatataaatatatataaatatataaa -tatatataaatatatatttatacataaatatataaatatatttatatatatttatatata -tttatatatatttttatatatttttatatatataaatatataaaaatatatataaatata -taaaaatatataaaaatatataaatatatataaatatataaatatatataaatatatata -aatatatatttatatataaatatatataaatatatatttatacataaatatatataaata -tatatttatacataaatatataaatatatataatatatataaatatatattatacataaa -tatataaatatatattatacataaatatataaatatatataaatatatataaatatatat -ttatacataaatatataaatatatatataaatatatataaatatatataaatatatatat -aaatatatatataaatatatataaatatatatataaatatatatataaatatatataaat -atatataaatatatatataaatatatataaatatatataaatatatatttatatattaat -atataaatatatataaatatatatttatatattaatatataaatatatatatattaatat -atataaatatatataaatatatatttatatattaatatatatatattaatatatatatat -ttatatattaatatatatatttatatattaatatatataaatatattactatgtatattt -atatatatttatataaatatatataaatatatgtaaatatatatataaaaatatatatta -atatataaa---atatatataaatatatattatacataaatatataaatatatataaata -tatataaatatatatttatacataaatatataaatatatatatatataaatatatataaa -tatatatttatatattaatatatataaatatattactatgtatatttatatatatttata -taaatatatataaatatatgtaaatatatatataaaaatatatatta--atatataaaaa -tatatatataaatatatataaatatatatataaatatatataaatat------atatata -taaatatatataaatatatatataaatatatataaatatatatataaatatatataaata -tatatatataaatatatataaatatatatataaatatatataaatatatatataaatata -aatatatataaatata----taaaaatatatatataaatataaatatatataaatatata -tgtataaatatatatataaatataaatatatatatataaatatatatataaatatatata -tataaatatatatataaatatatataaatatatatataaatatatataaatatatatata -tatatttttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcc -cttgccttttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaa -gagagcagaagttgagttggcat ->ref_chr20:14861844-14862854 -tgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggtattatgc -tctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggacattggag -gttttatatataaatatatatatatatatttatatatatatttatatatatatatttata -tatatttatatatatttatatatatatttatat--------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------atatataaatatatataaatatataaatatatataaata -tatatttatacataaatatataaatatata---------------------------ata -tatataaatatatattatacataaatatataaatatatataaatatatataaatatatat -ttatacataaatatataaatatat------atatatataaatatatataa---------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------atatatatttatatattaatatatataaatatattactatgtatattt -atatatatttatataaatatatataaatatatgtaaatatatatataaaaatatatatta -atatataaaaatatatatataaatata-------------tataaatatatatataaat- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------atatataaata -tatatatataaatatatataaatatatatataaatatatataaatatatatataaatata -tataaatat------atatatataaatatatataaatatatatataaatatatataaata -tat--------atataaatataaatatatataaatatataaaaatatatatataaatata -aatatatataaatatatatgtataaatatatatataaatataaatatatataaatatata -tatataaatatatatataaat--------------------------------atatata -tataaatatatatataaatatatataaatatatatataaatatatataaatatatatata -tatatttttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcc -cttgccttttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaa -gagagcagaagttgagttggcat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ce6ba4dc0f8a352c89d3dfc839c96d2e.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ce6ba4dc0f8a352c89d3dfc839c96d2e.msa deleted file mode 100644 index 7df1d60e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ce6ba4dc0f8a352c89d3dfc839c96d2e.msa +++ /dev/null @@ -1,335 +0,0 @@ ->syndip_1_chr20:64173338-64176430 -gatagagtgggtgtcttttgtgggcttctccccagcctgtggcctggcctagtcagtaga -gatggtcaggggagcaggagggagcccataccccagtgcctgtagttgtgtccatttccc -ctccctgacttctcctcctgcagcatccttccctttagttgtgtccatttcccctccctg -acttctcctcctgcagcatccttccctttagttgtgtccatttcccctccctgacttctc -ctcctgcagcatctttccttgtagttgtgtccatttcccctccctggcttctcctcctgc -agcatctttcc---tagttgtgtccatttcccctccctgacttctcctcctgcagcatcc -ttccctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatctttccttg -tagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccttgtagttgt -gtccatttcccctccctgacttctcctcctgcagcatccttccctgtagttgtgtccatt ------------------------------------------------------------- -----------------------------------------tcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagt -tgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatt -ccccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggc -ttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgta -gcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccattccccct -ccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcc -tgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttc -cctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttg -tgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttc -ccctccctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccctga -cttctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggc------ ------------------------------------------gtctcctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcc---tag -ttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccattcc -ccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctgg ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------ctcctgcagcatctttccctgtagttgtgtc -cattccccctccctggcttctcctgtagcatctttcctagttgtgtccattt-------- ----------------------------------------------cccctccctggcttc -tcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -ttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccc -tggcttctcctgcagcatctttccctgt-------------------------------- -------------------agttgtgtccatttcccctccctggcttctcctgtagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -tccccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccattccccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagca -tctttcctagttgtgtccatttcccctccctgg---cttctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtc -cattccccctccctgacttctcctcctgcagcatctttccctgtagttgtgtccatttcc -cctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctcct -gcagcatctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctt -tcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagca -tctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -tccccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgtagcatctttccctgtagttgtgtccattccccctccctggcgtctcctgcagca -tctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgt -gtccattccccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -gg ->syndip_2_chr20:64173338-64176430 -gatagagtgggtgtcttttgtgggcttctccccagcctgtggcctggcctagtcagtaga -gatggtcaggggagcaggagggagcccataccccagtgcctgtagttgtgtccatttccc -ctccctgacttctcctcctgcagcatccttccctttagttgtgtccatttcccctccctg -acttctcctcctgcagcatctttcc----------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------tagttgtgtccatttcccctccctgacttctcctcctgcagcatctttccttg -tagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccttgtagttgt -gtccatttcccctccctgacttctcctcctgcagcatccttccctgtagttgtgtccatt ------------------------------------------------------------- -----------------------------------------tcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctt -tccctg------------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------tagttgtgtccatttcccctccctggcttctcctgcagcatctttc -cctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttg -tgtccattccccctccctggcttctcctgtagcatctttcc---tagttgtgtccatttc -ccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctgg -cttctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctgg------- --------------------------------------------cttctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctc------------------------------- -----------------ctgtagcatctttccctgtagttgtgtccattccccctccctga -ctt--------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------ctcctgcagcatctttccctgtagttgtgtc -cattccccctccctggcttctcctgtagcatctttcctagttgtgtccattt-------- ----------------------------------------------cccctccctggcttc -tcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgtagcatctttcc---------------- --------------------------------------tagttgtgtccatttcccctccc -tggcttctcctgcagcatctttccctgt-------------------------------- -------------------agttgtgtccatttcccctccctggcttctcctgtagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccat -ttcccctccctgg---cttctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgtagcatctttcc---tagttgtgtccatttcccctccctggcttc -tcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcgtctcctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctgtagcatctttcc---tagttgtgtc -catttcccctccctggcttctcctcctgc------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---agcatctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctt -tcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagca -tctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -tccccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgtagcatctttccctgtagttgtgtccattccccctccctgg-------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------ctcctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -gg ->p:HG002_1_chr20:64173338-64176430 -gatagagtgggtgtcttttgtgggcttctccccagcctgtggcctggcctagtcagtaga -gatggtcaggggagcaggagggagcccataccccagtgcctgtagttgtgtccatttccc -ctccctgacttctcctcctgcagcatccttccctttagttgtgtccatttcccctccctg -acttctcctcctgcagcatctttcc----------------------------------- ------------------------------------------------------------- ---------------tagttgtgtccatttcccctccctgacttctcctcctgcagcatct -ttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccttg -tagttgtgtccatttcccctccctgacttctcctcctgcagcatccttccctgtagttgt -gtccatttcccctccctggctt---ctcctgcagcatctttccctgtagttgtgtccatt ------------------------------------------------------------- -----------------------------------------tcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctt -tccctg------------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------tagttgtgtccatttcccctccctggcttctcctgtagcatctttc -cctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttg -tgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttc -ccctccctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccctga -cttctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggc------ ------------------------------------------gtctcctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcc---tag -ttgtgtccatttcccctccctggcttctc------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------ctcctgcagcatctttccctgtagttgtgtc -cattccccctccctggcttctcctgtagcatctttcctagttgtgtccattt-------- ----------------------------------------------cccctccctggcttc -tcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -ttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccc -tggcttctcctgcagcatctttccctgt-------------------------------- -------------------agttgtgtccatttcccctccctggcttctcctgtagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -tccccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccattccccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagca -tctttcctagttgtgtccatttcccctccctgg---cttctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtc -cattccccctccctgacttctcctcctgc------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------agcatctt -tcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagca -tctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -tccccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgtagcatctttccctgtagttgtgtccattccccctccctgg-------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------ctcctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -gg ->p:HG002_2_chr20:64173338-64176430 -gatagagtgggtgtcttttgtgggcttctccccagcctgtggcctggcctagtcagtaga -gatggtcaggggagcaggagggagcccataccccagtgcctgtagttgtgtccatttccc -ctccctgacttctcctcctgcagcatccttccctttagttgtgtccatttcccctccctg -acttctcctcctgcagcatccttccctttagttgtgtccatttcccctccctgacttctc -ctcctgcagcatctttcc---tagttgtgtccatttcccctccctgacttctcctcctgc -agcatctttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagcatct -ttccttgtagttgtgtccatttcccctccctgacttctcctcctgcagcatctttccctg -tagttgtgtccatttcccctccctgacttctcctcctgcagcatctttccttgtagttgt -gtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatt -ccccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgcagcatccttccctgtagttgtgtccatttcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagt -tgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatt -ccccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggc -ttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgta -gcatctttcctagttgtgtccatttcccctccctggcttctc------------------ ------------------------------------------------------------- --------------------ctcctgcagcatctttccctgtagttgtgtccattccccct -ccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcc -tgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttc -cctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttg -tgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttc -ccctccctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccctga -cttctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggc------ ------------------------------------------gtctcctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcc---tag -ttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccattcc -ccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctgg ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------ctcctgcagcatctttccctgtagttgtgtc -cattccccctccctggcttctcctgtagcatctttcctagttgtgtccattt-------- ----------------------------------------------cccctccctggcttc -tcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -ttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccc -tggcttctcctgcagcatctttccctgt-------------------------------- -------------------agttgtgtccatttcccctccctggcttctcctgtagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -tccccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccattccccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagca -tctttcctagttgtgtccatttcccctccctgg---cttctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtc -cattccccctccctgacttctcctcctgcagcatctttccctgtagttgtgtccatttcc -cctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctcct -gcagcatctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctt -tcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagca -tctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -tccccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgtagcatctttccctgtagttgtgtccattccccctccctggcgtctcctgcagca -tctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgt -gtccattccccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -gg ->ref_chr20:64173338-64176430 -gatagagtgggtgtcttttgtgggcttctccccagcctgtggcctggcctagtcagtaga -gatggtcaggggagcaggagggagcccataccccagtgcctgtagttgtgtccatttccc -ctccctgacttctcctcctgcagcatccttccctttagttgtgtccatttcccctccctg -acttctcctcctgcagcatccttccctt-------------------------------- ------------------------------------------------------------- ---------------tagttgtgtccatttcccctccctgacttctcctcctgcagcatct -ttcc---tagttgtgtccatttcccctccctgacttctcctcctgcagcatctttccttg -tagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccttgtagttgt -gtccatttcccctccctgacttctcctcctgcagcatccttccctgtagttgtgtccatt ------------------------------------------------------------- -----------------------------------------tcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctt -tccctg------------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttg -tgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccattcc -ccctccctggcttctcctgtagcatctttcc---tagttgtgtccatttcccctccctgg -ctt---ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcc -tgtagcatctttcctagttgtgtccatttcccctccctggcttctcctcctgcagcatct -ttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttcc---tag -ttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatttc -ccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctgg -cttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgc -agcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttc -cctgtagttgtgtccattccccctccctgacttctcctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtc -catttcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccc -tggcttctcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttc -tcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatct -ttcc---tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccat -ttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccc -tggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcc -tgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -tccccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccattccccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagca -tctttcctagttgtgtccatttcccctccctgg---cttctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtc -cattccccctccctgacttctcctcctgcagcatctttccctgtagttgtgtccatttcc -cctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctcct -gcagcatctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctt -tcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagca -tctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -tccccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgtagcatctttccctgtagttgtgtccattccccctccctggcgtctc-------- ----------------------------------------ctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgt -gtccattccccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -gg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_cea716cb5fb96bc6d8bf0051a8d70890.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_cea716cb5fb96bc6d8bf0051a8d70890.msa deleted file mode 100644 index af4d665d..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_cea716cb5fb96bc6d8bf0051a8d70890.msa +++ /dev/null @@ -1,190 +0,0 @@ ->syndip_1_chr20:63027966-63029130 -ctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaagaaccaacg -cgggcggggagtggaccggtggggagagggccggtggggagagggccggtggggagagga -ccggtggggagggggccggtggagagggggccggtggggagggggccggtggggagagga -ccggtggggaggggccggtggggagggggccggtggggagaggaccggtggggaggggcc -ggtggggagggggccggtggggagaggaccggtggggaggggccggtggggagggggccg -gcggggagggggccggcggggagggtgccggtggggagtggtctggtggggagggggccg -gtggggagggggcccgcggggaggggccggtggggagggggcctgcggggagggggccgg -cggggagggaccggtggggaggggccggtggggtggggccggtggagagggggccggtgg -ggagggggccggcggggagtggtttggtggggaggaggctggtgaagtagcgtcaggtgc -gggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgcagcttcatc -aggttctcaattagcggagggcgctggcggtggaggagggcattagccgtgcctgctctc -gggctctgcctgccagagtgccctcatgtggcatgagattaaggctcagcctctttcctg -acagcaggttttccatttttcttctccttcctcctctcctggcaacaaagtcctttgctg -ggctggggggtctccactctgatccacttccctccttcctgcctccctcccacgccctgg -aaaccccggcccatgactctttccctgagggggccgcccgcagcctctcccccatggggg -ctttgctctgggcaccccctttcccccggggcgggtggggcagcggccgggactcaggaa -gatggtggcccagtggggctctctccttgggtgtgtgggagcggagtcccctcgctcttc -tgggatagaacgctccgttgagctccccaaactgctcccgtgccgagctctgggggaggg -agtctgttcagagacggtgcagtcctaccttttagaaggtacgcctgcctttttaagcag -ctcagctctcaacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgc -aggaggctgagcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatg -atgactccaaacgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgg -gcctccgcgcctccgtgtgcaggtcccccgggcctccgcctctccgtgtgcaggtccccc -gggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtccc -ccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtc -ccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcagg -tcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgca -ggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtg -caggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctccgtg -tgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtg -tgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctc -cgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcc -tccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg -cctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccg -cgtctgtgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctc -cgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc -tccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtccccc ->syndip_2_chr20:63027966-63029130 -ctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaagaaccaacg -cgggcggggagtggaccggtggggagagggccggtggggagaggaccggtggggag-ggg -ccggtggagagggggccggtggggagggggccggcggggag------------------- -----------tggtttggtggggagggggccggtggggagggggcctgcggggaggggcc -ggtggggag-----------------------------ggggccggtggggagggggccg -gcggggagggggccggcggggagggggccggcggggagtggtctggtggggag------- -----------------------ggggccggtggggagggggccggcggggagggggccgg -cggggaggggccggtggggagtggt-------------ctggtggggagggggcc----- --------------------------ggtggggaggaggctggtgaagtagcgtcaggtgc -gggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgcagcttcatc -aggttctcaattagcggagggcgctggcggtggaggagggcattagccgtgcctgctctc -gggctctgcctgccagagtgccctcatgtggcatgagattaaggctcagcctctttcctg -acagcaggttttccatttttcttctccttcctcctctcctggcaacaaagtcctttgctg -ggctggggggtctccactctgatccacttccctccttcctgcctccctcccacgccctgg -aaaccccggcccatgactctttccctgagggggccgcccgcagcctctcccccatggggg -ctttgctctgggcaccccctttcccccggggcgggtggggcagcggccgggactcaggaa -gatggtggcccagtggggctctctccttgggtgtgtgggagcggagtcccctcgctcttc -tgggatagaacgctccgttgagctccccaaactgctcccgtgccgagctctgggggaggg -agtctgttcagagacggtgcagtcctaccttttagaaggtacgcctgcctttttaagcag -ctcagctctcaacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgc -aggaggctgagcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatg -atgactccaaacgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgg -gcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtccccc ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------- ->p:HG002_1_chr20:63027966-63029130 -ctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaagaaccaacg -cgggcggggagtggaccggtggggagagggccggtggggagaggaccggtggggag-ggg -ccggtggagagggggccggtggggagggggccggcggggag------------------- -----------tggtttggtggggagggggccggtggggagggggcctgcggggaggggcc -ggtggggag-----------------------------ggggccggtggggagggggccg -gcggggagggggccggcggggagggggccggcggggagtggtctggtggggag------- -----------------------ggggccggtggggagggggccggcggggagggggccgg -cggggaggggccggtggggagtggt-------------ctggtggggagggggcc----- --------------------------ggtggggaggaggctggtgaagtagcgtcaggtgc -gggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgcagcttcatc -aggttctcaattagcggagggcgctggcggtggaggagggcattagccgtgcctgctctc -gggctctgcctgccagagtgccctcatgtggcatgagattaaggctcagcctctttcctg -acagcaggttttccatttttcttctccttcctcctctcctggcaacaaagtcctttgctg -ggctggggggtctccactctgatccacttccctccttcctgcctccctcccacgccctgg -aaaccccggcccatgactctttccctgagggggccgcccgcagcctctcccccatggggg -ctttgctctgggcaccccctttcccccggggcgggtggggcagcggccgggactcaggaa -gatggtggcccagtggggctctctccttgggtgtgtgggagcggagtcccctcgctcttc -tgggatagaacgctccgttgagctccccaaactgctcccgtgccgagctctgggggaggg -agtctgttcagagacggtgcagtcctaccttttagaaggtacgcctgcctttttaagcag -ctcagctctcaacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgc -aggaggctgagcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatg -atgactccaaacgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgg -gcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtccccc ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------- ->p:HG002_2_chr20:63027966-63029130 -ctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaagaaccaacg -cgggcggggagtggaccggtggggagagggccggtggggagaggaccggtggggag-ggg -ccggtggagagggggccggtggggagggggccggtggggagggggccggtggggagagga -ccggtggggaggggccggtggggagggggccggtggggagaggaccggtggggaggggcc -ggtggggagggggccggtggggagaggaccggtggggaggggccggtggggagggggccg -gcggggagggggccggcggggagggtgccggtggggagtggtctggtggggagggggccg -gtggggagggggcccgcggggaggggccggtggggagggggcctgcggggagggggccgg -cggggaggggccggtggggaggggccggtggggtggggccggtggggagggggccggtgg -gg-gggggcctgcggggagtggtttggtggggaggaggctggtgaagtagcgtcaggtgc -gggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgcagcttcatc -aggttctcaattagcggagggcgctggcggtggaggagggcattagccgtgcctgctctc -gggctctgcctgccagagtgccctcatgtggcatgagattaaggctcagcctctttcctg -acagcaggttttccatttttcttctccttcctcctctcctggcaacaaagtcctttgctg -ggctggggggtctccactctgatccacttccctccttcctgcctccctcccacgccctgg -aaaccccggcccatgactctttccctgagggggccgcccgcagcctctcccccatggggg -ctttgctctgggcaccccctttcccccggggcgggtggggcagcggccgggactcaggaa -gatggtggcccagtggggctctctccttgggtgtgtgggagcggagtcccctcgctcttc -tgggatagaacgctccgttgagctccccaaactgctcccgtgccgagctctgggggaggg -agtctgttcagagacggtgcagtcctaccttttagaaggtacgcctgcctttttaagcag -ctcagctctcaacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgc -aggaggctgagcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatg -atgactccaaacgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgg -gcctccgcgcctccgtgtgcaggtcccccgggcctccgcctctccgtgtgcaggtccccc -gggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtccc -ccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtc -ccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcagg -tcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgca -ggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtg -caggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctccgtg -tgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtg -tgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctc -cgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcc -tccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg -cctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccg -cgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctc -cgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc -tccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtccccc ->ref_chr20:63027966-63029130 -ctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaagaaccaacg -cgggcggggagtggaccggtggggagagggccggtggggagaggaccggtggggag-ggg -ccggtggagagggggccggtggggagggggccggcggggag------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------tggtttggtggggaggaggctggtgaagtagcgtcaggtgc -gggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgcagcttcatc -aggttctcaattagcggagggcgctggcggtggaggagggcattagccgtgcctgctctc -gggctctgcctgccagagtgccctcatgtggcatgagattaaggctcagcctctttcctg -acagcaggttttccatttttcttctccttcctcctctcctggcaacaaagtcctttgctg -ggctggggggtctccactctgatccacttccctccttcctgcctccctcccacgccctgg -aaaccccggcccatgactctttccctgagggggccgcccgcagcctctcccccatggggg -ctttgctctgggcaccccctttcccccggggcgggtggggcagcggccgggactcaggaa -gatggtggcccagtggggctctctccttgggtgtgtgggagcggagtcccctcgctcttc -tgggatagaacgctccgttgagctccccaaactgctcccgtgccgagctctgggggaggg -agtctgttcagagacggtgcagtcctaccttttagaaggtacgcctgcctttttaagcag -ctcagctctcaacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgc -aggaggctgagcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatg -atgactccaaacgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgg -gcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtccccc -gggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtccc -ccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtc -cccc-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_cf9425969f7f5ed38f54639e08586a04.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_cf9425969f7f5ed38f54639e08586a04.msa deleted file mode 100644 index db141b39..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_cf9425969f7f5ed38f54639e08586a04.msa +++ /dev/null @@ -1,40 +0,0 @@ ->syndip_1_chr20:57190156-57190528 -gctggagagagtgagccaggaatcagaggaggtgaggccagagagagtgagcgaggaacc -agagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggcc----agagt -gagtgaggagcttgaaggggtgaggctggagacagtgagcgaggaaccagagggggtgag -gctggagagagtgagccaggaaccagaggaggtgaggccaga----gtgagtgaggagct -tgaaggggtgaggctggagacagtgagcgaggaaccagagggggtgaggctggagagcgt -gagtgaggagcccgagggggtgaggctggagagagtgagtgaggagcccaagggggtgaa -gccgaggtgggtatggg ->syndip_2_chr20:57190156-57190528 -gctggagagagtgagccaggaatcagaggaggtgaggccagagagagtgagcgaggaacc -agagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggctggagagagt -gagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttgaaggggtgag -gctggagacagtgagcgaggaaccagagggggtgaggctggagagcgtgagtgaggagcc -cgagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggctggagagagt -gagtgaggagcccaagggggtgaagccgaggtgggt------------------------ -------------atggg ->p:HG002_1_chr20:57190156-57190528 -gctggagagagtgagccaggaatcagaggaggtgaggccagagagagtgagcgaggaacc -agagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggctggagagagt -gagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttgaaggggtgag -gctggagacagtgagcgaggaaccagagggggtgaggctggagagcgtgagtgaggagcc -cgagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggctggagagagt -gagtgaggagcccaagggggtgaagccgaggtgggt------------------------ -------------atggg ->p:HG002_2_chr20:57190156-57190528 -gctggagagagtgagccaggaatcagaggaggtgaggccagagagagtgagcgaggaacc -agagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggctggagagagt -gagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttgaaggggtgag -gctggagacagtgagcgaggaaccagagggggtgaggctggagagcgtgagtgaggagcc -cgagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggctggagagcgt -gagtgaggagcccgagggggtgaggctggagagagtgagtgaggagcccaagggggtgaa -gccgaggtgggtatggg ->ref_chr20:57190156-57190528 -gctggagagagtgagccaggaatcagaggaggtgaggccagagagagtgagcgaggaacc -agagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggctggagagagt -gagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttgaaggggtgag -gctggagacagtgagcgaggaaccagagggggtgaggctggagagcgtgagtgaggagcc -cgagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggctggagagcgt -gagtgaggagcccgagggggtgaggctggagagagtgagtgaggagcccaagggggtgaa -gccgaggtgggtatggg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_d3345cc29e9eb9ed11a16e6b9dbbc048.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_d3345cc29e9eb9ed11a16e6b9dbbc048.msa deleted file mode 100644 index 3bf34ac3..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_d3345cc29e9eb9ed11a16e6b9dbbc048.msa +++ /dev/null @@ -1,395 +0,0 @@ ->syndip_1_chr20:64173228-64176540 -cagcctggccaatttccctcccctcctgagcaccgtgggagggtcaggcctcaagcagcc -ctcggaggcagcagtcacagacagaggtgggctgttggacaggtgcggctgatagagtgg -gtgtcttttgtgggcttctccccagcctgtggcctggcctagtcagtagagatggtcagg -ggagcaggagggagcccataccccagtgcctgtagttgtgtccatttcccctccctgact -tctcctcctgcagcatccttccctttagttgtgtccatttcccctccctgacttctcctc -ctgcagcatccttccctttagttgtgtccatttcccctccctgacttctcctcctgcagc -atctttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttc -c---tagttgtgtccatttcccctccctgacttctcctcctgcagcatccttccctgtag -ttgtgtccatttcccctccctgacttctcctcctgcagcatctttccttgtagttgtgtc -catttcccctccctggcttctcctcctgcagcatctttccttgtagttgtgtccatttcc -cctccctgacttctcctcctgcagcatccttccctgtagttgtgtccatttcccctccct -ggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagt -tgtgtccattccccctccctggcttctcctgtagcatctttcc---tagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggctt---ctcctgtagcatctttcc---tagttgtgtccatttcccctccctggcttct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcat -ctttccctgtagttgtgtccatttcccctccctggctt---------------------- -----------------------------ctcctgcagcatctttccctgtagttgtgtcc -attccccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccct -ggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgca -gcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccc-------------------------------------- ------------------------------------------------------------- --------------------------------------------------tccctggcttc -tcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagca -tctttccctgtagttgtgtccattccccctccctgacttctcctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcgtctcct----------------------- ----------------------cctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcc ----tgtagcatctttcc---tagttgtgtccattccccctccctggcttctcctgtagca -tctttccctgtagttgtgtccatttcccctccctgg------ctcctgcagcatctttcc -ctgtagttgtgtccattccccctccctggcttctcctgtagcatctttcctagttgtgtc -catttcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccc -tggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcc -tgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccat -ttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccc -tggctt------------------------------------------------------ ---ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgta -gcatctttccctgtagttgtgtccattccccctccctggcgtctcctcctgcagcatctt -tccctg------------------------------------------------------ -----------------------------------------tagttgtgtccattccccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgcagcatctttccctgtagttgtgtccatttcccctccctggc---ttctcctgta -gcatctttcc---tagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgt -gtccattccccctccctgacttctcctc-------------------------------- ------------------------------------------------------------- --------------------------------------------------------ctgca -gcatctttccctgtagttgtgtccatttcccctccctggcgtctcctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcc---tagt -tgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtcc -attccccctccctggcttctcctgtagcatctttcc------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ----tagttgtgtccatttcccctccctggcttctcctgtagcatctttcc---tagttgt -gtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcc -cctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggc -ttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcc---- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----tgcagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtag -ttgtgtccattccccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccctggcgtc -tcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagca -tctttccctgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttcc -ctgtagttgtgtccattccccctccctggcttctcctcctgcagcatctttccctgtagt -tgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctcttctagcatctttcctgctccctggtagcctcttgggagccacctattt -ct ->syndip_2_chr20:64173228-64176540 -cagcctggccaatttccctcccctcctgagcaccgtgggagggtcaggcctcaagcagcc -ctcggaggcagcagtcacagacagaggtgggctgttggacaggtgcggctgatagagtgg -gtgtcttttgtgggcttctccccagcctgtggcctggcctagtcagtagagatggtcagg -ggagcaggagggagcccataccccagtgcctg---------------------------- --------------------------tagttgtgtccatttcccctccctgacttctcctc -ctgcagcatccttccctttagttgtgtccatttcccctccctgacttctcctcctgcagc -atctttcc---tagttgtgtccatttcccctccctgacttctcctcctgcagcatctttc -cttgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccttgtag -ttgtgtccatttcccctccctgacttctc------------------------------- ------------------------------------------------------------- ----------------ctcctgcagcatccttccctgtagttgtgtccatttcccctccct -ggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagt -tgtgtccattccccctccctggcttctcctgtagcatctttcc---tagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcat -ctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgt -agttgtgtccattccccctccctgacttctcctgcagcatctttccctgtagttgtgtcc -attccccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccct -ggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgca -gcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagca -tctttccctgtagttgtgtccatttcccctccctggctt---ctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctgcagcatctttccctgtagttgtgtccatttcccctccctggcgtctcc -tcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagca -tctttcc---tagttgtgtccatttcccctccctggcttctcctcctgcagcatctttcc -ctgtagttgtgtccattccccctccctggcttctcctgtagcatctttcctagttgtgtc -catttcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccc -tggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcc -tgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttcc------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------tagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgtagcatctttccctgtagttgtgtccattccccctccctgg-------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------cgtctcctcctgcagcatctttccctgtagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccctgg---- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------ctcctcctgcagcatctttccctgtagt -tgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctcttctagcatctttcctgctccctggtagcctcttgggagccacctattt -ct ->p:HG002_1_chr20:64173228-64176540 -cagcctggccaatttccctcccctcctgagcaccgtgggagggtcaggcctcaagcagcc -ctcggaggcagcagtcacagacagaggtgggctgttggacaggtgcggctgatagagtgg -gtgtcttttgtgggcttctccccagcctgtggcctggcctagtcagtagagatggtcagg -ggagcaggagggagcccataccccagtgcctg---------------------------- --------------------------tagttgtgtccatttcccctccctgacttctcctc -ctgcagcatccttccctttagttgtgtccatttcccctccctgacttctcctcctgcagc -atctttcc---tagttgtgtccatttcccctccctgacttctcctcctgcagcatctttc -cttgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccttgtag -ttgtgtccatttcccctccctgacttctc------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------ctcct -gcagcatccttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctt -tccctg------------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------tagttgtgtccatttcccctccc -tggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcc -tgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccat -ttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccc -tgacttctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcgtc -tcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgta -gcatctttcc---tagttgtgtccatttcccctccctggcttctcctcctgcagcatctt -tccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttcctagttgt -gtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgcagcatctttccctgtagttgtgtccatttcccctccctggc---ttctcctgta -gcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt -gtccatttcccctccctggcttctc----------------------------------- ------------------------------------------------------------- --------------------------------------------------------ctgta -gcatctttccctgtagttgtgtccatttcccctccctgg---cttctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagt -tgtgtccattccccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtcc -attccccctccctggcttctcctgcagcatctttcc------------------------ ------------------------------------------------------------- ------------------------------------------------------------- -ctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt -gtccatttcccctccctggcttctcctgtagcatctttcc---tagttgtgtccatttcc -cctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggc -ttctcctgtagcatctttccctgtagttgtgtccattccccctccctgacttctcctcct -gcagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcc -tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgcagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtag -ttgtgtccattccccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccctgg---- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------ctcctcctgcagcatctttccctgtagt -tgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctcttctagcatctttcctgctccctggtagcctcttgggagccacctattt -ct ->p:HG002_2_chr20:64173228-64176540 -cagcctggccaatttccctcccctcctgagcaccgtgggagggtcaggcctcaagcagcc -ctcggaggcagcagtcacagacagaggtgggctgttggacaggtgcggctgatagagtgg -gtgtcttttgtgggcttctccccagcctgtggcctggcctagtcagtagagatggtcagg -ggagcaggagggagcccataccccagtgcctgtagttgtgtccatttcccctccctgact -tctcctcctgcagcatccttccctttagttgtgtccatttcccctccctgacttctcctc -ctgcagcatccttccctttagttgtgtccatttcccctccctgacttctcctcctgcagc -atctttcc---tagttgtgtccatttcccctccctgacttctcctcctgcagcatctttc -cttgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccttgtag -ttgtgtccatttcccctccctgacttctcctcctgcagcatctttccctgtagttgtgtc -catttcccctccctgacttctcctcctgcagcatctttccttgtagttgtgtccatttcc -cctccctggcttctcctcctgcagcatctttccctgtagttgtgtccattccccctccct -ggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcct -gcagcatccttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagt -tgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccct -ggctt---ctcctgtagcatctttcc---tagttgtgtccatttcccctccctggcttct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcat -ctttcc---tagttgtgtccatttcccctccctggcttctc------------------- -----------------------------ctcctgcagcatctttccctgtagttgtgtcc -attccccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccct -ggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgca -gcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccc-------------------------------------- ------------------------------------------------------------- --------------------------------------------------tccctggcttc -tcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagca -tctttccctgtagttgtgtccattccccctccctgacttctcctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcgtctcct----------------------- ----------------------cctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcc ----tgtagcatctttcc---tagttgtgtccattccccctccctggcttctcctgtagca -tctttccctgtagttgtgtccatttcccctccctgg------ctcctgcagcatctttcc -ctgtagttgtgtccattccccctccctggcttctcctgtagcatctttcctagttgtgtc -catttcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccc -tggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcc -tgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccat -ttcccctccctggcttctcctgtagcatctttccctg----------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------tagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgtagcatctttccctgtagttgtgtccattccccctccctggcgtctcctcctgca -gcatctttccctgtagttgtgtccattccccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt -gtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgtagcatctttccctgtagttgtgtccattccccctccctgacttctcctcctgca -gcatctttccctgtagttgtgtccatttcccctccctggcgtctcctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcc---tagt -tgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtcc -attccccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccct -ggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgca -gcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgt -gtccatttcccctccctggcttctcctgcagcatctttcc---tagttgtgtccatttcc -cctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggc -ttctcctgtagcatctttccctgtagttgtgtccattccccctccctggcgtctc----- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------ctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccc---tggcttctcctgtagcatctttccctgtagttgtgtc -cattccccctccctggcgtctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggc--- ------------------------------------------------------------- --------------------------------------ttctcctcctgcagcatctttcc -ctgtagttgtgtccattccccctccctggcttctcctcctgcagcatctttccctgtagt -tgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctcttctagcatctttcctgctccctggtagcctcttgggagccacctattt -ct ->ref_chr20:64173228-64176540 -cagcctggccaatttccctcccctcctgagcaccgtgggagggtcaggcctcaagcagcc -ctcggaggcagcagtcacagacagaggtgggctgttggacaggtgcggctgatagagtgg -gtgtcttttgtgggcttctccccagcctgtggcctggcctagtcagtagagatggtcagg -ggagcaggagggagcccataccccagtgcctgtagttgtgtccatttcccctccctgact -tctcctcctgcagcatccttccctttagttgtgtccatttcccctccctgacttctcctc -ctgcagcatccttccctttagttgtgtccatttcccctccctgacttctcctcctgcagc -atctttcc---tagttgtgtccatttcccctccctgacttctcctcctgcagcatctttc -cttgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccttgtag -ttgtgtccatttcccctccctgacttctc------------------------------- ------------------------------------------------------------- ----------------ctcctgcagcatccttccctgtagttgtgtccatttcccctccct -ggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagt -tgtgtccattccccctccctggcttctcctgtagcatctttcc---tagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggctt---ctcctgtagcatctttcc---tagttgtgtccatttcccctccctggcttct -c----------------------------------------------------------- ------------------------------------------------------------- -----------------------------ctcctgcagcatctttccctgtagttgtgtcc -attccccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccct -ggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgca -gcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccc-------------------------------------- ------------------------------------------------------------- --------------------------------------------------tccctggcttc -tcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagca -tctttccctgtagttgtgtccattccccctccctgacttctcctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcgtctcct----------------------- ----------------------cctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctc- ------------------------------------------------------------- -------------------------------------------ctcctgcagcatctttcc -ctgtagttgtgtccattccccctccctggcttctcctgtagcatctttcctagttgtgtc -catttcccctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccc -tggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcc -tgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccat -ttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccc -tggctt------------------------------------------------------ ---ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgta -gcatctttccctgtagttgtgtccattccccctccctggcgtctcctcctgcagcatctt -tccctg------------------------------------------------------ -----------------------------------------tagttgtgtccattccccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctgcagcatctttccctgtagttgtgtccatttcccctccctggc---ttctcctgta -gcatctttcc---tagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgt -gtccattccccctccctgacttctcctc-------------------------------- ------------------------------------------------------------- --------------------------------------------------------ctgca -gcatctttccctgtagttgtgtccatttcccctccctggcgtctcctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcc---tagt -tgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtcc -attccccctccctggcttctcctgtagcatctttcc------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ----tagttgtgtccatttcccctccctggcttctcctgtagcatctttcc---tagttgt -gtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcc -cctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggc -ttctcctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcc---- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----tgcagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtag -ttgtgtccattccccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccctggcgtc -tc-----------------------------------------------ctcctgcagca -tctttccctgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttcc -ctgtagttgtgtccattccccctccctggcttctcctcctgcagcatctttccctgtagt -tgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctcttctagcatctttcctgctccctggtagcctcttgggagccacctattt -ct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_d43734f99c9c62efa16b6c039f1d8a34.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_d43734f99c9c62efa16b6c039f1d8a34.msa deleted file mode 100644 index ed80cadf..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_d43734f99c9c62efa16b6c039f1d8a34.msa +++ /dev/null @@ -1,185 +0,0 @@ ->syndip_1_chr20:4032019-4033801 -tcggtttttttttggtggagacggggtttcgctgtgttggccgggctgctctccagctcc -taaccgcgagtgatccgccagcctcggcctcccgaggtgccgggattgcagatgaagtct -cgttcactcagtgctcagtggtgtccaggctggagtgcagcggcgtgatctcggctcgct -acaa---ccacctcccagccgcctgccttggcctcccaaagagccgagattgcagcctct -gcccggccgccaccccgtctgggaagtgaggagcgtctctgcttggccacccatcgtctg -ggatatgaggagcccctctgcctggctgcccagtctggaaagt----------------- ------------------------gaggagcgtctctgcccggccgccatcccatctagga -agcgaggagcgcctcttcccggctgccatcccatctaggaagtgaggagcgtctctgccc -ggccgcccatcgtctgagatgtggggagcacctctgccccaccgccctgtctgggatgtg -aggagcgcctctgctgggccgcaaccctgtctgggaggtgaggagcgtctctgccccgcc -gctccgtctgagaagtgaggaaaccctctgcctggcaaccgccccgtctgagaagtgagg -agcccctccgtccggcaaccaccccgtctgggaagtgaggagcgtctccgcccggcagcc -accccgtccgggagggaggtggggggggtcagccccccgcccggccagccgccccgtccg -ggaggtgaggggctcctctgcccggccgcccctactgggaagtgaggagcccctctgccc -ggccagccgccccgtccgggagggaggcgggggggggggtcggccagccgccccgtccgg -gagggaggtgggggggtcagccccccgcccggccggccgccccgtccgggaggtgagggg -cgcctctgcccggccgcccctactgggaagtgaggacccctctgcccggccagccgcccc -gtccgggagggaggtgggggggtcagtcccccgcccggccggctgccccgtccgggaggt -gaggggcgcctctgcccggccgcccctactgggaagtgaggagcccctctgcccggccag -ctgccccgcccgggagggaggtgggggggtcagccccccgcctggccagccgccccatcc -gggagggaggtgggggggtcagccccccgcccggccagccgccccgtccgggagggggga -gggggggtcagccccctgcccggccagccgccccgtccgggagggaggtggg--gggggg -tcagccccccgcccggccagccgccccgtccgggagggaggtggggggatcagccccccg -cctggccagccgccccgtccgggaggtgaggggcgcctctgcccggccacccctactggg -aagtgaggagcccctctgcccggccagccgccccgtccgggagggaggcggggggggggg -tcggccagccgccccgtccgggagggaggtgggggggtcagccccccttccggccggccg -ccctgtccgggaggtgaggggcgcctctgcctggccgcccctactgggaagtgaggaccc -ctctgcccggccagccgccccgtccgggagggaggtgggggggacagccccccgcccggc -cagccgccctatccaggaggtgaggggcgcctctgcccggccgcccctactgggaagtga -ggagcccctctgcccggccagccgccccgtccgggagggtagtgggggggtcagcccccc -gcccggccagccgccccatccgggaggtgaggggcgcttctgcccggccgcccctactgg -gaagtgaggagcccctctgcccggccacgaccccgtctgggaggtgtgcccagcggctca -ttggggatgggccatgatgacaatggcggttttgtggaatagaaaggcgggaagggtggg -gaaaaaattgagaaatcggatggttgccgggtctgtgtggatggaagtagacatgggaga -cttttcattttgttctgtactaagagaaattcttctgccttgggatcctgttgatctgtg -accttatccccaaccctgtgctctctgaagcatg ->syndip_2_chr20:4032019-4033801 -tcggtttttttttggtggagacggggtttcgctgtgttggccgggctgctctccagctcc -taaccgcgagtgatccgccagcctcggcctcccgaggtgccgggattgcagatgaagtct -cgttcactcagtgctcagtggtgtccaggctggagtgcagcggcgtgatctcggctcgct -acaa---ccacctcccagccgcctgccttggcctcccaaagagccgagattgcagcctct -gcccggccgccaccccgtctgggaagtgaggagcgtctctgcttggccacccatcgtctg -ggatatgaggagcccctctgcctggctgcccagtctggaaagtgaggagcgtctctgccc -ggccgccatcccatctaggaagcgaggagcgtctctgcccggccgccatcccatctagga -agcgaggagcgcctcttcccggctgccatcccatctaggaactgaggagcgtctctgccc -ggccgcccatcgtctgagatgtggggagcacctctgccccaccgccctgtctgggatgtg -aggagcgcctctgctgggccgcaaccctgtctgggaggtgaggagcgtctctgccccgcc -gctccgtctgagaagtgaggaaaccctctgcctggcaaccgccccgtctgagaagtgagg -agcccctccgtccggcaaccaccccgtctgggaagtgaggagcgtctccgcccggcagcc -accccgtccgggagggaggt---------------------------------------- ------------------------------------------------------------- -----------------------------gggggggggggtcggccagccgccccgtccgg -gagggaggtgggggggtcagccccccgcccggccggccgccccgtccgggaggtgagggg -cgcctctgcccggccgcccctactgggaagtgaggacccctctgcccggccagccgcccc -gtccgggagggaggtgggggggtcagccccccgcccggccggctgccccgtccgggaggt -gaggggcgcctctgcccggccgcccctactgggaagtgaggagcccctctgcccggccag -ctgccccgcccgggagggaggtgggggggtcagccccccgcctggccagccgccccatcc -gggagggaggtgggggggtcagccccccgcccggccagccgccccgtccgggagggggga -gggggggtcagccccctgcccggccagccgccccgtccgggagggaggtggggggggggg -tcagccccccgcccggccagccgccccgtccgggagggaggtggggggatcagccccccg -cctggccagccgccccgtccgggaggtgaggggcgcctctgcccggccacccctactggg -aagtgaggagcccctctgcccggccagccgccccgtccgggagggaggcggggggggggg -tcggccagccgccccgtccgggagggaggtgggggggtcagccccccttccggccggccg -ccctgtccgggaggtgaggggcgcctctgcctggccgcccctactgggaagtgaggaccc -ctctgcccggccagccgccccgtccgggagggaggtgggggggacagccccccgcccggc -cagccgccctatccaggaggtgaggggcgcctctgcccggccgcccctactgggaagtga -ggagcccctctgcctggccagccgccccgtccgggagggtagtgggggggtcagcccccc -gcccggccagccgccccatccgggaggtgaggggcgcttctgcccggccgcccctactgg -gaagtgaggagcccctctgcccggccacgaccccgtctgggaggtgtgcccagcggctca -ttggggatgggccatgatgacaatggcggttttgtggaatagaaaggcgggaagggtggg -gaaaaaattgagaaatcggatggttgccgggtctgtgtggatggaagtagacatgggaga -cttttcattttgttctgtactaagagaaattcttctgccttgggatcctgttgatctgtg -accttatccccaaccctgtgctctctgaagcatg ->p:HG002_1_chr20:4032019-4033801 -tcggtttttttttggtggagacggggtttcgctgtgttggccgggctgctctccagctcc -taaccgcgagtgatccgccagcctcggcctcccgaggtgccgggattgcagatgaagtct -cgttcactcagtgctcagtggtgtccaggctggagtgcagcggcgtgatctcggctcgct -acaa---ccacctcccagccgcctgccttggcctcccaaagagccgagattgcagcctct -gcccggccgccaccccgtctgggaagtgaggagcgtctctgcttggccacccatcgtctg -ggatatgaggagcccctctgcctggctgcccagtctggaaagtgaggagcgtctctgccc -ggccgccatcccatctaggaagcgaggagcgtctctgcccggccgccatcccatctagga -agcgaggagcgcctcttcccggctgccatcccatctaggaactgaggagcgtctctgccc -ggccgcccatcgtctgagatgtggggagcacctctgccccaccgccctgtctgggatgtg -aggagcgcctctgctgggccgcaaccctgtctgggaggtgaggagcgtctctgccccgcc -gctccgtctgagaagtgaggaaaccctctgcctggcaaccgccccgtctgagaagtgagg -agcccctccgtccggcaaccaccccgtctgggaagtgaggagcgtctccgcccggcagcc -accccgtccgggagggaggt---------------------------------------- ------------------------------------------------------------- -----------------------------gggggggggggtcggccagccgccccgtccgg -gagggaggtgggggggtcagccccccgcccggccggccgccccgtccgggaggtgagggg -cgcctctgcccggccgcccctactgggaagtgaggacccctctgcccggccagccgcccc -gtccgggagggaggtgggggggtcagccccccgcccggccggctgccccgtccgggaggt -gaggggcgcctctgcccggccgcccctactgggaagtgaggagcccctctgcccggccag -ctgccccgcccgggagggaggtgggggggtcagccccccgcctggccagccgccccatcc -gggagggaggtgggggggtcagccccccgcccggccagccgccccgtccgggagggggga -gggggggtcagccccctgcccggccagccgccccgtccgggagggaggtggggggggggg -tcagccccccgcccggccagccgccccgtccgggagggaggtggggggatcagccccccg -cctggccagccgccccgtccgggaggtgaggggcgcctctgcccggccacccctactggg -aagtgaggagcccctctgcccggccagccgccccgtccgggagggaggcggggggggggg -tcggccagccgccccgtccgggagggaggtgggggggtcagccccccttccggccggccg -ccctgtccgggaggtgaggggcgcctctgcctggccgcccctactgggaagtgaggaccc -ctctgcccggccagccgccccgtccgggagggaggtgggggggacagccccccgcccggc -cagccgccctatccaggaggtgaggggcgcctctgcccggccgcccctactgggaagtga -ggagcccctctgcctggccagccgccccgtccgggagggtagtgggggggtcagcccccc -gcccggccagccgccccatccgggaggtgaggggcgcttctgcccggccgcccctactgg -gaagtgaggagcccctctgcccggccacgaccccgtctgggaggtgtgcccagcggctca -ttggggatgggccatgatgacaatggcggttttgtggaatagaaaggcgggaagggtggg -gaaaaaattgagaaatcggatggttgccgggtctgtgtggatggaagtagacatgggaga -cttttcattttgttctgtactaagagaaattcttctgccttgggatcctgttgatctgtg -accttatccccaaccctgtgctctctgaagcatg ->p:HG002_2_chr20:4032019-4033801 -tcggtttttttttggtggagacggggattcgctgtgttggccgggctgctctccagctcc -taaccgcgagtgatccgccagcctcggcctcccgaggtgccgggattgcagatgaagtct -cgttcactcagtgctcaatggtgcccaggctggagtgcagtggcgtgatctccgctcgct -acaacctccacctcccagccgcctgccttggcctcccaaagagccgagattgcagcctct -gcccggccgccaccccgtctgggaagtgaggagcgtctctgcttggccacccatcgtctg -ggatatgaggagcccctctgcctggctgcccagtctggaaagt----------------- ------------------------gaggagcgtctctgcccggccgccatcccatctagga -agcgaggagcgcctcttcccggctgccatcccatctaggaagtgaggagcgtctctgccc -ggccgcccatcgtctgagatgtggggagcacctctgccccaccgccctgtctgggatgtg -aggagcgcctctgctgggccgcaaccctgtctgggaggtgaggagcgtctctgccccgcc -gctccgtctgagaagtgaggaaaccctctgcctggcaaccgccccgtctgagaagtgagg -agcccctccgtccggcaaccaccccgtctgggaagtgaggagcgtctccgcccggcagcc -accccgtccgggagggaggtggggggggtcagccccccgcccggccagccgccccgtccg -ggaggtgaggggctcctctgcccggccgcccctactgggaagtgaggagcccctctgccc -ggccagccgccccgtccgggagggaggcgggggggggggtcggccagccgccccgtccgg -gagggaggtgggggggtcagccccccgcccggccggccgccccgtccgggaggtgagggg -cgcctctgcccggccgcccctactgggaagtgaggacccctctgcccggccagccgcccc -gtccgggagggaggtgggggggtcagtcccccgcccggccggctgccccgtccgggaggt -gaggggcgcctctgcccggccgcccctactgggaagtgaggagcccctctgcccggccag -ctgccccgcccgggagggaggtgggggggtcagccccccgcctggccagccgccccatcc -gggagggaggtgggggggtcagccccccgcccggccagccgccccgtccgggagggggga -gggggggtcagccccctgcccggccagccgccccgtccgggagggaggtggg--gggggg -tcagccccccgcccggccagccgccccgtccgggagggaggtggggggatcagccccccg -cctggccagccgccccgtccgggaggtgaggggcgcctctgcccggccacccctactggg -aagtgaggagcccctctgcccggccagccgccccgtccgggagggaggcggggggggggg -tcggccagccgccccgtccgggagggaggtgggggggtcagccccccttccggccggccg -ccctgtccgggaggtgaggggcgcctctgcctggccgcccctactgggaagtgaggaccc -ctctgcccggccagccgccccgtccgggagggaggtgggggggacagccccccgcccggc -cagccgccctatccaggaggtgaggggcgcctctgcccggccgcccctactgggaagtga -ggagcccctctgcccggccagccgccccgtccgggagggtagtgggggggtcagcccccc -gcccggccagccgccccatccgggaggtgaggggcgcttctgcccggccgcccctactgg -gaagtgaggagcccctctgcccggccacgaccccgtctgggaggtgtgcccagcggctca -ttggggatgggccatgatgacaatggcggttttgtggaatagaaaggcgggaagggtggg -gaaaaaattgagaaatcggatggttgccgggtctgtgtggatggaagtagacatgggaga -cttttcattttgttctgtactaagagaaattcttctgccttgggatcctgttgatctgtg -accttatccccaaccctgtgctctctgaagcatg ->ref_chr20:4032019-4033801 -tcggtttttttttggtggagacggggtttcgctgtgttggccgggctgctctccagctcc -taaccgcgagtgatccgccagcctcggcctcccgaggtgccgggattgcagatgaagtct -cgttcactcagtgctcagtggtgtccaggctggagtgcagcggcgtgatctcggctcgct -acaa---ccacctcccagccgcctgccttggcctcccaaagagccgagattgcagcctct -gcccggccgccaccccgtctgggaagtgaggagcgtctctgcttggccacccatcgtctg -ggatatgaggagcccctctgcctggctgcccagtctggaaagtgaggagcgtctctgccc -ggccgccatcccatctaggaagcgaggagcgtctctgcccggccgccatcccatctagga -agcgaggagcgcctcttcccggctgccatcccatctaggaactgaggagcgtctctgccc -ggccgcccatcgtctgagatgtggggagcacctctgccccaccgccctgtctgggatgtg -aggagcgcctctgctgggccgcaaccctgtctgggaggtgaggagcgtctctgccccgcc -gctccgtctgagaagtgaggaaaccctctgcctggcaaccgccccgtctgagaagtgagg -agcccctccgtccggcaaccaccccgtctgggaagtgaggagcgtctccgcccggcagcc -accccgtccgggagggaggt---------------------------------------- ------------------------------------------------------------- -----------------------------gggggggggggtcggccagccgccccgtccgg -gagggaggtgggggggtcagccccccgcccggccggccgccccgtccgggaggtgagggg -cgcctctgcccggccgcccctactgggaagtgaggacccctctgcccggccagccgcccc -gtccgggagggaggtgggggggtcagccccccgcccggccggctgccccgtccgggaggt -gaggggcgcctctgcccggccgcccctactgggaagtgaggagcccctctgcccggccag -ctgccccgcccgggagggaggtgggggggtcagccccccgcctggccagccgccccatcc -gggagggaggtgggggggtcagccccccgcccggccagccgccccgtccgggagggggga -gggggggtcagccccctgcccggccagccgccccgtccgggagggaggtggg-------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------gggggggtcagccccctttccggccg--cc -gcctgtccgggaggtgaggggcgcctctgcctggccgcccctactgggaagtgaggaccc -ctctgcccggccagccgccccgtccgggagggaggtgggggggacagccccccgcccggc -cagccgccctatccaggaggtgaggggcgcctctgcccggccgcccctactgggaagtga -ggagcccctctgcctggccagccgccccgtccgggagggtagtgggggggtcagcccccc -gcccggccagccgccccatccgggaggtgaggggcgcttctgcccggccgcccctactgg -gaagtgaggagcccctctgcccggccacgaccccgtctgggaggtgtgcccagcggctca -ttggggatgggccatgatgacaatggcggttttgtggaatagaaaggcgggaagggtggg -gaaaaaattgagaaatcggatggttgccgggtctgtgtggatggaagtagacatgggaga -cttttcattttgttctgtactaagagaaattcttctgccttgggatcctgttgatctgtg -accttatccccaaccctgtgctctctgaagcatg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_d44674bef5ffc7c0270aa221533f0c99.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_d44674bef5ffc7c0270aa221533f0c99.msa deleted file mode 100644 index ca76fc37..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_d44674bef5ffc7c0270aa221533f0c99.msa +++ /dev/null @@ -1,165 +0,0 @@ ->syndip_1_chr20:18209097-18210727 -tccagtcccccaggcatgtatccttccgtagcttctccacacctacacgaacctagacga -ttccttccacaccttccccacacccacacgaacctagacgattccttccacaccttcccc -acacccacacgaacctagatgaattccttccacaccttctccacacccacacgaacctag -acgattccttccacaccttccccacacccattctccacacccacacgaacctagacgatt -ccttccacacctccacacccacacgaacctagatgaattccttccacaccttccccacac -ccacacaaacctagacgattccttccacaccttctccacacccacacgaacctagacgaa -ttccttccagaccttctccacacccacacagacctagacgattccttccacacctccaca -cccacacgaacctagacgaattccttccacaccttctccacacccacacgaacctagacg -aattccttccacaccttctccacacccacacgaacctagacgaattccttccacaccttc -tccacacccacacgaacctagacgattccttccacactttccccacacccacacgaacct -agacg-attccttccacac---ctccacacccacacgaacctagatgaattccttccaca -ccttccccacacccacacaaacctagacgattccttccacaccttctccacacccacaca -aacctagacaattccttccacacacacatgaacctagatgaattccttccacaccttctc -cacacccacatgaacctagacgattccttccacaccttctccacacccacacacacctag -atgaattccttccacaccttccccacacccacacagacctagacgaattccttccacacc -ttctccacacccacacgaacctagacgattccttccacaccttctccatacccacacgaa -cctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttccac -accttctccacacccacacgaacctaaacgattccttccacaccttctccacacccacac -acacctagatgaattccttccacaccttccccacacccacacagacctagacgaattcct -tccacaccttctccacacccacacgaacctagacgattccttccacaccttctccatacc -cacacgaacctagacaattccttccacaccttctcacacccacacaaacctagatgaatt -ccttccacaccttccccacacccacacagacctagacgaattccttccacaccttctcca -cacccacacgaacctagacaattccttccacaccttctcacacccacacaaacctagacg -aattccttccacaccttctccacacccacacaaacctagatgaattccttccacaccttc -ctcacacccacacgaacctagacgattccttccacaccttccccacacccacacagacct -agacgaattccttccacaccttctccacacccacacgaacctagacgattccttccacac -cttccccacacccacacgaacctagacaattccttccacaccttctcacacccacacaaa -cctagatgaattccttccacaccttctccacacccacacaaacctagacgaattccttcc -acaccttcctcacacccacacgaacctagacgattccttccacaccttccccacacccac -acagacctagacgaattccttccacaccttcctaacacccacacgaacctagagaattcc -ttccacaccttcacacccacacaaacctagacgaattccttccacaccttctccacaccc -acacaaacctagacaaattcttatacacttaaaatgggattttgttgttt ->syndip_2_chr20:18209097-18210727 -tccagtcccccaggcatgtatccttccgtagcttctccacacctacacgaacctagacga -ttccttccacaccttccccacacccacacgaacctagacgattccttccacaccttcccc -acacccacacgaacctagatgaattccttccacaccttctccacacccacacgaacctag -acgattccttccacaccttccccacacccattctccacacccacacgaacctagacgatt -ccttccacacctccacacccacacgaacctagatgaattccttccacaccttccccacac -ccacacaaacctagacgattccttccacaccttctccacacccacacgaacctagacgaa -ttccttccagaccttctccacacccacacagacctagacgattccttccacacctccaca -cccacacgaacctagacgaattccttccacaccttctccacacccacacgaacctagacg -aattccttccacaccttctccacacccacacgaacctagacgaattccttccacaccttc -tccacacccacacgaacctagacgattccttccacactttccccacacccacaagaacct -agacg-attccttccacac---ctccacacccacacgaacctagatgaattccttccaca -ccttccccacacccacacaaacctagacgattccttccacaccttctccacacccacaca -aacctagacaattccttccacacacacatgaacctagatgaattccttccacaccttctc -cacacccacatgaacctagacgattccttccacaccttctccacacccacacacacctag -atgaattccttccacaccttccccacacccacacagacctagacgaattccttccacaca -ttctccacacccacacgaacctagacgattccttccacaccttctccatacccacacgaa -cctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttccac -accttctccacacccacacgaacctaaacgattccttccacaccttctccacacccacac -acacctagatgaattccttccacaccttccccacacccacacagacctagacgaattcct -tccacaccttctccacacccacacgaacctagacgattccttccaca------------c -cacacgaacctagacaattccttccacaccttctcacacccacacaaacctagatgaatt -ccttccacaccttccccacacccacacagacctagacgaattccttccacaccttctcca -cacccacacgaacctagacaattccttccacaccttctcacacccacacaaacctagacg -aattccttccacaccttctccacacccacacaaacctagacgaattccttccacaccttc -ctcacacccacacgaacctagacgattccttccacaccttccccacacccacacagacct -agacgaattccttccacaccttctccacacccacacgaacctagacgattccttccacac -cttccccacacccacacgaacctagacaattccttccacaccttctcacacccacacaaa -cctagatgaattccttccacaccttctccacacccacacaaacctagacgaattccttcc -acaccttcctcacacccacacgaacctagacgattccttccacaccttccccacacccac -acagacctagacgaattccttccacaccttcctaacacccacacgaacctagagaattcc -ttccacaccttcacacccacacaaacctagacgaattccttccacaccttctccacaccc -acacaaacctagacaaattcttatacacttaaaatgggattttgttgttt ->p:HG002_1_chr20:18209097-18210727 -tccagtcccccaggcatgtatccttccgtagcttctccacacctacacgaacctagacga -ttccttccacaccttccccacacccacacgaacctagacgattccttccacaccttcccc -acacccacacgaacctagatgaattccttccacaccttctccacacccacacgaacctag -acgattccttccacaccttccccacacccattctccacacccacacgaacctagacgatt -ccttccacacctccacacccacacgaacctagatgaattccttccacaccttccccacac -ccacacaaacctagacgattccttccacaccttctccacacccacacgaacctagacgaa -ttccttccagaccttctccacacccacacagacctagacgattccttccacacctccaca -cccacacgaacctagacgaattccttccacaccttctccacacccacacgaacctagacg -aattccttccacaccttctccacacccacacgaacctagacgaattccttccacaccttc -tccacacccacacgaacctagacgattccttccacactttccccacacccacaagaacct -agacg-attccttccacac---ctccacacccacacgaacctagatgaattccttccaca -ccttccccacacccacacaaacctagacgattccttccacaccttctccacacccacaca -aacctagacaattccttccacacacacatgaacctagatgaattccttccacaccttctc -cacacccacatgaacctagacgattccttccacaccttctccacacccacacacacctag -atgaattccttccacaccttccccacacccacacagacctagacgaattccttccacaca -ttctccacacccacacgaacctagacgattccttccacaccttctccatacccacacgaa -cctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttccac -accttctccacacccacacgaacctaaacgattccttccacaccttctccacacccacac -acacctagatgaattccttccacaccttccccacacccacacagacctagacgaattcct -tccacaccttctccacacccacacgaacctagacgattccttccaca------------c -cacacgaacctagacaattccttccacaccttctcacacccacacaaacctagatgaatt -ccttccacaccttccccacacccacacagacctagacgaattccttccacaccttctcca -cacccacacgaacctagacaattccttccacaccttctcacacccacacaaacctagacg -aattccttccacaccttctccacacccacacaaacctagacgaattccttccacaccttc -ctcacacccacacgaacctagacgattccttccacaccttccccacacccacacagacct -agacgaattccttccacaccttctccacacccacacgaacctagacgattccttccacac -cttccccacacccacacgaacctagacaattccttccacaccttctcacacccacacaaa -cctagatgaattccttccacaccttctccacacccacacaaacctagacgaattccttcc -acaccttcctcacacccacacgaacctagacgattccttccacaccttccccacacccac -acagacctagacgaattccttccacaccttcctaacacccacacgaacctagagaattcc -ttccacaccttcacacccacacaaacctagacgaattccttccacaccttctccacaccc -acacaaacctagacaaattcttatacacttaaaatgggattttgttgttt ->p:HG002_2_chr20:18209097-18210727 -tccagtcccccaggcatgtatccttccgtagcttctccacacctacacgaacctagacga -ttccttccacaccttccccacacccacacgaacctagacgattccttccacaccttcccc -acacccacacgaacctagatgaattccttccacaccttctccacacccacacgaacctag -acgattccttccacaccttccccacacccattctccacacccacacgaacctagacgatt -ccttccacacctccacacccacacgaacctagatgaattccttccacaccttccccacac -ccacacaaacctagacgattccttccacaccttctccacacccacacgaacctagacgaa -ttccttccagaccttctccacacccacacagacctagacgattccttccacacctccaca -cccacacgaacctagacgaattccttccacaccttctccacacccacacgaacctagacg -aattccttccacaccttctccacacccacacgaacctagacgaattccttccacaccttc -tccacacccacacgaacctagacgattccttccacactttccccacacccacacgaacct -agacg-attccttccacac---ctccacacccacacgaacctagatgaattccttccaca -ccttccccacacccacacaaacctagacgattccttccacaccttctccacacccacaca -aacctagacaattccttccacacacacatgaacctagatgaattccttccacaccttctc -cacacccacatgaacctagacgattccttccacaccttctccacacccacacacacctag -atgaattccttccacaccttccccacacccacacagacctagacgaattccttccacacc -ttctccacacccacacgaacctagacgattccttccacaccttctccatacccacacgaa -cctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttccac -accttctccacacccacacgaacctaaacgattccttccacaccttctccacacccacac -acacctagatgaattccttccacaccttccccacacccacacagacctagacgaattcct -tccacaccttctccacacccacacgaacctagacgattccttccacaccttctccatacc -cacacgaacctagacaattccttccacaccttctcacacccacacaaacctagatgaatt -ccttccacaccttccccacacccacacagacctagacgaattccttccacaccttctcca -cacccacacgaacctagacaattccttccacaccttctcacacccacacaaacctagacg -aattccttccacaccttctccacacccacacaaacctagatgaattccttccacaccttc -ctcacacccacacgaacctagacgattccttccacaccttccccacacccacacagacct -agacgaattccttccacaccttctccacacccacacgaacctagacgattccttccacac -cttccccacacccacacgaacctagacaattccttccacaccttctcacacccacacaaa -cctagatgaattccttccacaccttctccacacccacacaaacctagacgaattccttcc -acaccttcctcacacccacacgaacctagacgattccttccacaccttccccacacccac -acagacctagacgaattccttccacaccttcctaacacccacacgaacctagagaattcc -ttccacaccttcacacccacacaaacctagacgaattccttccacaccttctccacaccc -acacaaacctagacaaattcttatacacttaaaatgggattttgttgttt ->ref_chr20:18209097-18210727 -tccagtcccccaggcatgtatccttccgtagcttctccacacct---------------- --------------------------acacgaacctagacgattccttccacaccttcccc -acacccacacgaacctagatgaattccttccacaccttctccacacccacacgaacctag -acgattccttccacaccttccccacacccattctccacacccacacgaacctagacgatt -ccttccacacctccacacccacacgaacctagatgaattccttccacaccttccccacac -ccacacaaacctagacgattccttccacaccttctccacacccacacgaacctagacgaa -ttccttccagaccttctccacacccacacagacctagacgattccttccacacctccaca -cccacacgaacctagacgaattccttccacaccttgtgcacacccacacgaacctagacg -aattccttccacaccttctccacacccacacgaacctagacgaattccttccacaccttc -tccacacccacacgaacctagacgattccttccacaccttccccacacccacacagacct -agacgaattccttgcacaccttctccacacccacacgaacctagacgaattccttccaca -ccttctccatacccacacgaacctagacaattccttccacaccttct------------- -------------------cacacccacacaaacctagatgaattccttccacaccttctc -cacacccacacgaacctaaacgattccttccacaccttctccacacccacacacacctag -atgaattccttccacaccttccccacacccacacagacctagacgaattccttccacacc -ttctccacacccacacgaacctagacgattccttccacaccttctccatacccacacgaa -cctagacaattccttccacaccttctcacacccacacaa--------------------- ------------------------------------------------------------- ---acctagatgaattccttccacaccttccccacacccacacagacctagacgaattcct -tccacaccttctccacacccacacgaacctagacg------------------------- ------------------------------------------------------------- ----------------------------------------attccttccacaccttcccca -cacccacacgaacctagacaattccttgcacaccttctcacacccacacaaacctagacg -aattccttccacaccttctccacacccacacaaacctagacgaattccttccacaccttc -ctcacacccacacgaacctagacgattccttccacaccttccccacacccacacagacct -agacgaattccttccacaccttctccacacccacacgaacctagacgattccttccacac -cttccccacacccacacgaacctagacaattccttccacaccttctcacacccacacaaa -cctagatgaattccttccacaccttctccacacccacacaaacctagacgaattccttcc -acaccttcctcacacccacacgaacctagatgattccttccacaccttccccacacccac -acagacctagacgaattccttccacaccttcctaacacccacacgaacctagagaattcc -ttccacaccttcacacccacacaaacctagacgaattccttccacaccttctccacaccc -acacaaacctagacaaattcttatacacttaaaatgggattttgttgttt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_d4b126e5900cc00f6c75e82b4be27559.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_d4b126e5900cc00f6c75e82b4be27559.msa deleted file mode 100644 index 7f48c7be..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_d4b126e5900cc00f6c75e82b4be27559.msa +++ /dev/null @@ -1,40 +0,0 @@ ->syndip_1_chr20:34235798-34236081 -aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaggaaggaaggaagg -aaggaaggaaaggaaggaaggaaggaaggaaggaaggaaggaaggaagcgggagggaggg -aagaaggaaggaaggaggagggagggaagaatgaaggaaggaaggaaggaaggaaggaag -gaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggagggagggaagaa -ggaaggaggagggagggagggaagcaggaaagaaggaaggaaggagaaagagagaaagag -agagagaagaagaaagagaaagaaacagaaaaggaaggaaggagagagagaaagaaagag -aaaga ->syndip_2_chr20:34235798-34236081 -aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaggaaggaaggaagg -aaggaaggaaaggaaggaaggaaggaaggaaggaaggaaggaaggaagcgggagggaggg -aagaaggaaggaaggaggagggagggaagaatgaaggaaggaaggaaggaaggaaggaag -gaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggagggagggaagaa -ggaaggaggagggagggagggaagcaggaaagaaggaaggaaggagaaagagagaaagag -agagagaagaagaaagagaaagaaacagaaaaggaaggaaggagagagagaaagaaagag -aaaga ->p:HG002_1_chr20:34235798-34236081 -aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaggaaggaaggaagg -aaggaaggaaaggaaggaaggaaggaaggaaggaaggaaggaaaggaa-ggaaggaagga -aggaaggaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggaaggaag -gaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggagggagggaagaa -ggaaggaggagggagggagggaagaaggaaagaaggaaggaaggagaaagagagaaagag -agagagaagaagaaagagaaagaaacagaaaaggaaggaaggagagagagaaagaaagag -aaaga ->p:HG002_2_chr20:34235798-34236081 -aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaggaaggaaggaagg -aaggaaggaaaggaaggaaggaaggaaggaaggaaggaaggaaaggaa-ggaaggaagga -aggaaggaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggaaggaag -gaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggagggagggaagaa -ggaaggaggagggagggagggaagaaggaaagaaggaaggaaggagaaagagagaaagag -agagagaagaagaaagagaaagaaacagaaaaggaaggaaggagagagagaaagaaagag -aaaga ->ref_chr20:34235798-34236081 -aaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaggaaggaaggaagg -aaggaaggaaaggaaggaaggaaggaaggaaggaaggaaggaaaggaa------------ --------------------------------------------ggaaggaaggaaggaag -gaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggagggagggaaga- --------------------------aggaaagaaggaaggaaggagaaagagagaaagag -agagagaagaagaaagagaaagaaacagaaaaggaaggaaggagagagagaaagaaagag -aaaga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_d68e9f67e20c4afd7f0f9e6fada0a063.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_d68e9f67e20c4afd7f0f9e6fada0a063.msa deleted file mode 100644 index 60e6926f..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_d68e9f67e20c4afd7f0f9e6fada0a063.msa +++ /dev/null @@ -1,110 +0,0 @@ ->syndip_1_chr20:55944172-55945275 -atggcaccactgcattccagctgggcaacagagagagactctttcttaaatatatatatt -ttatatatatatagatacacacacacacacacacacacacac------------------ -----------------atatatatatatatatatatatatatatatatatgcatgcatgc -cagatgcagtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatca -tctgaggtcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaa -aatacaaaattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctg -aggcaggagaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccac -tgcactccagcctggatgacagagcgagactccattaaaaaaatatatctatatctatag -atatctatagatatatatctagatatagatctatgagtatatatctatagatatctagat -atatatttatagatagatatatctatagatatctatatatttctatcgatagagatatct -atagatatctatcaatatatctatagatttctagagatatgtatctagatataaatctat -agacatagatatagatatatagatatttaactgccaatgtcctaaacactttatactcaa -cacattttttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtc -tagatagtatctatctagatatctgtgtagatgtctagatatctatctagatat-----t -atctatctagatatctgtcgctatctagatatctatctagatatctgtcgctatctagat -atctatctagatatctgtcgctatctagatatctatctagatagtatctgtcgctatcta -gatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgc -tatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatc -tgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagat -agtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctat -ctagatagtatctgtcgctatctagatatctatctagatagt ->syndip_2_chr20:55944172-55945275 -atggcaccactgcattccagctgggcaacagagagagactctttcttaaatatatatatt -ttatatatatatagatacacacacacacacacacacacacacacacacacacacacacac -acatatatatatatatatatatatatatatatatatatatatatatatatgcatgcatgc -cagatgcagtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatca -tctgaggtcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaa -aatacaaaattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctg -aggcaggagaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccac -tgcactccagcctggatgacagagcgagactccattaaaaaaatatatctatatctatag -atatctatagatatatatctagatatagatctatgagtatatatctatagatatctagat -atatatttatagatagatatatctatagatatctatatatttctatcgatagagatatct -atagatatctatcaatatatctatagatttctagagatatgtatctagatataaatctat -agacatagatatagatatatagatatttaactgccaatgtcctaaacactttatactcaa -cacattttttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtc -tagatagtatctatctagatatcggtctagat-----agtatctatctagatatctgtgt -agatgtctagatatctatctagatat---tatctatctagatatctgtcgctatctagat -atctatctagatatctgtcgctatctagatatctatctaga---tatctgtcgctatcta -gatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgc -tatctagatatctatctagatagt------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------- ->p:HG002_1_chr20:55944172-55945275 -atggcaccactgcattccagctgggcaacagagagagactctttcttaaatatatatatt -ttatatatatatagatacacacacacacacacacacacacacacacacacacacacacac -acatatatatatatatatatatatatatatatatatatatatatatatatgcatgcatgc -cagatgcagtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatca -tctgaggtcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaa -aatacaaaattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctg -aggcaggagaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccac -tgcactccagcctggatgacagagcgagactccattaaaaaaatatatctatatctatag -atatctatagatatatatctagatatagatctatgagtatatatctatagatatctagat -atatatttatagatagatatatctatagatatctatatatttctatcgatagagatatct -atagatatctatcaatatatctatagatttctagagatatgtatctagatataaatctat -agacatagatatagatatatagatatttaactgccaatgtcctaaacactttatactcaa -cacattttttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtc -tagatagtatctatctagatatctgtgtagatgtctagatatctatctagatat-----t -atctatctagatatctgtcgctatctagatatctatctagatatctgtcgctatctagat -atctatctagatatctgtcgctatctagatatctatctaga---tatctgtcgctatcta -gatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgc -tatctagatatctatctagatagt------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------- ->p:HG002_2_chr20:55944172-55945275 -atggcaccactgcattccagctgggcaacagagagagactctttcttaaatatatatatt -ttatatatatatagatacacacacacacacacacacacacac------------------ -----------------atatatatatatatatatatatatatatatatatgcatgcatgc -cagatgcagtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatca -tctgaggtcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaa -aatacaaaattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctg -aggcaggagaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccac -tgcactccagcctggatgacagagcgagactccattaaaaaaatatatctatatctatag -atatctatagatatatatctagatatagatctatgagtatatatctatagatatctagat -atatatttatagatagatatatctatagatatctatatatttctatcgatagagatatct -atagatatctatcaatatatctatagatttctagagatatgtatctagatataaatctat -agacatagatatagatatatagatatttaactgccaatgtcctaaacactttatactcaa -cacattttttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtc -tagatagtatctatctagatatctgtgtagatgtctagatatctatctagatat-----t -atctatctagatatctgtcgctatctagatatctatctagatatctgtcgctatctagat -atctatctagatatctgtcgctatctagatatctatctagatagtatctgtcgctatcta -gatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgc -tatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatc -tgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagat -agtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctat -ctagatagtatctgtcgctatctagatatctatctagatagt ->ref_chr20:55944172-55945275 -atggcaccactgcattccagctgggcaacagagagagactctttcttaaatatatatatt -ttatatatatatagatacacacacacacacacacacacacac------------------ -----------------atatatatatatatatatatatatatatatatatgcatgcatgc -cagatgcagtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatca -tctgaggtcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaa -aatacaaaattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctg -aggcaggagaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccac -tgcactccagcctggatgacagagcgagactccattaaaaaaatatatctatatctatag -atatctatagatatatatctagatatagatctatgagtatatatctatagatatctagat -atatatttatagatagatatatctatagatatctatatatttctatcgatagagatatct -atagatatctatcaatatatctatagatttctagagatatgtatctagatataaatctat -agacatagatatagatatatagatatttaactgccaatgtcctaaacactttatactcaa -cacattttttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtc -tagatagtatctatctagatatctgtgtagatgtctagatatctatctagatat-----t -atctatctagatatctgtcgctatctagatatctatctagatatctgtcgctatctagat -atctatctagatatctgtcgctatctagatatctatctagatagtatctgtcgctatcta -gatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgc -tatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatc -tgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagat -agt--------------------------------------------------------- ------------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_d7b1e6c08fc312747c7f2a51cab521a5.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_d7b1e6c08fc312747c7f2a51cab521a5.msa deleted file mode 100644 index 1a1c8ecb..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_d7b1e6c08fc312747c7f2a51cab521a5.msa +++ /dev/null @@ -1,295 +0,0 @@ ->syndip_1_chr20:64131804-64133955 -cctcccctgtcccagacttctcctggcctctctcatgtcctatgagaccccctcactgtc -cactctcatggcctgtagagaccccctcactgtcaactctcatgtcctatagagaccccc -tcactgtcaactctcatgtcctatgagaccccctcactgtccactctcatggcctgtaga -gaccccctcactgtccaccctcatgtcctata---------------------------- -----gagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccc -tcatgtcctatg-agaccccctcactgtccaccctcatggcctatagagaccccctcact -gtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccc -cctcactgtccactctcatgtcctatagagaccccctcactgtccaccctcatgtcctat -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcat -ggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtcc -actctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctc -actgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagag -accccctcactgtccaccctcatgtcctatgagaccccctcactgtccactctcatgtcc -tat-gagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccc -tcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcact -gtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctat-gagacc -ccctcactgtccactctcatgtcctat-gagaccccctcactgtccactctcatggcctg -tagagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtccaccctc -gtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccc -tcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtag -agaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccactctcatg -tcctatagagacccctcactgtccaccctcatggcctatagagaccccctcactgtccac -cctcatggcctgtagagaccccctcactgtccaccctcgtgtcctatagagaccccctca -ctgtccaccctcatgtcctatgagaccccctcactgtccactctcatgtcctatgagacc -ccctcactgtccactctcatggcctgtagagaccccctcactgtccaccctcatgtccta -tgagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtccaccctcg -tgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtc -caccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccct -cactgtccaccctcatggcctgtagagaccccctcactgtccaccctcgtgtcctataga -gaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgt -cctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccacc -ctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcac -tgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctat-gagac -cccctcactgtccaccctcgtgtcctatagagaccccctcactgtcaactctcatgtcct -atagagaccccctcactgtccaccctcgtgtcctat-gagaccccctcactgtccaccct -catgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactg -tccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctat-gagaccc -cctcactgtccaccctcgtgtcctatagagaccccctcactgtcaactctcatgtcctat -agagaccccctcactgtccaccctcgtgtcctatagagaccccctcactctccaccctca -tgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtc -caccctcatgtcctat-gagaccccctcactgtccaccctcatggcctatagagaccccc -tcactgtccaccctcatgtccta-tgagaccccctcactgtccaccctcatgtcctatag -agaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatg -tcctatagagaccccctcactctccaccctcatggcctatagagaccccctcactgtcca -ccctcgtgtcctatagagaccccctcactctccaccctcatggcctatagagaccccctc -actgtccaccctcatggcctatagagaccccctcactgtccactctcatgtccta-tgag -accccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtc -ctatgagaccccctcactgtccactctcatgtcctatgagaccccctcactgtccaccct -catggcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgt -ccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctat-gagacccc -ctcactgtccaccctcatgtcctatagagaccccctcactgtccactctcatgtcctat- -gagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatg -gcctatagagaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtcca -ccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctc -actgtccaccctcatgtcctatagagaccccctcactgtccactctcatggcctgtagag -accccctcactgtccacccatatggcctgtagagaccccctcactgtccaccctcaggac -cctctgcatttgctccttgggttccc ->syndip_2_chr20:64131804-64133955 -cctcccctgtcccagacttctcctggcctctctcatgtcctatgagaccccctcactgtc -cactctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccc -tcactgtccaccctcatggcctatgagaccccctcactgtccaccctcgtgtcctataga -gaccccctcactgtccaccctcatgtcctatagagacccctcactgtccaccctcatggc -ctatgagaccccctcactgtccactctcatgtcctatagagaccccctcactgtccaccc -tcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagaga-cccctcact -gtccaccctcatggcctatgagaccccctcactgtccaccctcatggcctatagagaccc -cctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctat -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcat -gtcctat-gagaccccctcactgtccactctcatgtcctatagagaccccctcactgtcc -accctcgtgtcctatagagaccccctcactgtccaccctcgtgtcctatgagaccccctc -actgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagag -accccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc -tcgtgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcact -gtccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagacc -ccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtccta -tagagaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctc -atggcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatgtcctatgagaccccctcactgtccaccctcgtgtcctatagagaccccc -tcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctat-g -agaccccctcactgtccaccctcatgtcctatagagac---------------------- ------------cccctcactgtccaccctcatggcctatagagaccccctcactgtccac -cctcatggcctgtagagaccccctcactgtccaccctcatggcctatagagaccccctca -ctgtccacc---------------------------------ctcgtgtcctatgagacc -ccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatggccta -t----------------------------------gagaccccctcactgtccaccctcg -tgtcctat-gagaccccctcactgtccaccctcatggcctatagagaccccctcactgtc -caccctcatggcctatgagaccccctcactgtccaccctcatggcctgtagagaccccct -cactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctataga -gaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgt -cctatgagaccccctcactgtccactctcatgtcctatagaga-cccctcactgtccacc -ctcatggcctatagagaccccctcactgtccaccctcatggcctatagagaccccctcac -tgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagagac -cccctcactgtccaccctcatgtcctgtagagaccccctcactgtccaccctcatggcct -gtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccct -catgtcctatagagaccccctcactgtccaccctcatggcctatagagaccccctcactg -tccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccc -cctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctat --gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctca -tgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtc -caccctcgtgtcctatagagaccccctcactgtccaccctcatggcctatagagaccccc -tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatag -agaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatg -tcctat-gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtcca -ccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctc -actgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctgtagag -accccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatggc -ctat---------------------------------gagaccccctcactgtccaccct -catggcctgtagagaccccctcactgtccaccctcatgtcctatagagacccctcactgt -ccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagacccc -ctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatg -tcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtcca -ccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctc -actgtccaccctcgtgtcctatagagaccccctcactgtccacccatatggcctgtagag -accccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcaggac -cctctgcatttgctccttgggttccc ->p:HG002_1_chr20:64131804-64133955 -cctcccctgtcccagacttctcctggcctctctcatgtcctatgagaccccctcactgtc -cactctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccc -tcactgtccaccctcatggcctatgagaccccctcactgtccaccctcgtgtcctataga -gaccccctcactgtccaccctcatgtcctatagagacccctcactgtccaccctcatggc -ctatgagaccccctcactgtccactctcatgtcctatagagaccccctcactgtccaccc -tcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagaga-cccctcact -gtccaccctcatggcctatgagaccccctcactgtccaccctcatggcctatagagaccc -cctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctat -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcat -gtcctat-gagaccccctcactgtccactctcatgtcctatagagaccccctcactgtcc -accctcgtgtcctatagagaccccctcactgtccaccctcgtgtcctatgagaccccctc -actgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagag -accccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc -tcgtgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcact -gtccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagacc -ccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtccta -tagagaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctc -atggcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatgtcctatgagaccccctcactgtccaccctcgtgtcctatagagaccccc -tcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctat-g -agaccccctcactgtccaccctcatgtcctatagagac---------------------- ------------cccctcactgtccaccctcatggcctatagagaccccctcactgtccac -cctcatggcctgtagagaccccctcactgtccaccctcatggcctatagagaccccctca -ctgtccacc---------------------------------ctcgtgtcctatgagacc -ccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatggccta -t----------------------------------gagaccccctcactgtccaccctcg -tgtcctat-gagaccccctcactgtccaccctcatggcctatagagaccccctcactgtc -caccctcatggcctatgagaccccctcactgtccaccctcatggcctgtagagaccccct -cactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctataga -gaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgt -cctatgagaccccctcactgtccactctcatgtcctatagaga-cccctcactgtccacc -ctcatggcctatagagaccccctcactgtccaccctcatggcctatagagaccccctcac -tgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagagac -cccctcactgtccaccctcatgtcctgtagagaccccctcactgtccaccctcatggcct -gtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccct -catgtcctatagagaccccctcactgtccaccctcatggcctatagagaccccctcactg -tccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccc -cctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctat --gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctca -tgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtc -caccctcgtgtcctatagagaccccctcactgtccaccctcatggcctatagagaccccc -tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatag -agaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatg -tcctat-gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtcca -ccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctc -actgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctgtagag -accccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatggc -ctat---------------------------------gagaccccctcactgtccaccct -catggcctgtagagaccccctcactgtccaccctcatgtcctatagagacccctcactgt -ccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagacccc -ctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatg -tcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtcca -ccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctc -actgtccaccctcgtgtcctatagagaccccctcactgtccacccatatggcctgtagag -accccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcaggac -cctctgcatttgctccttgggttccc ->p:HG002_2_chr20:64131804-64133955 -cctcccctgtcccagacttctcctggcctctctcatgtcctatgagaccccctcactgtc -cactctcatggcctgtagagaccccctcactgtcaactctcatgtcctatagagaccccc -tcactgtcaactctcatgtcctatgagaccccctcactgtccactctcatggcctgtaga -gaccccctcactgtccaccctcatgtcctata---------------------------- -----gagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccc -tcatgtcctatg-agaccccctcactgtccaccctcatggcctatagagaccccctcact -gtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccc -cctcactgtccactctcatgtcctatagagaccccctcactgtccaccctcatgtcctat -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcat -ggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtcc -actctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctc -actgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagag -accccctcactgtccaccctcatgtcctatgagaccccctcactgtccactctcatgtcc -tat-gagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccc -tcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcact -gtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctat-gagacc -ccctcactgtccactctcatgtcctat-gagaccccctcactgtccactctcatggcctg -tagagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtccaccctc -gtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccc -tcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtag -agaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccactctcatg -tcctatagagacccctcactgtccaccctcatggcctatagagaccccctcactgtccac -cctcatggcctgtagagaccccctcactgtccaccctcgtgtcctatagagaccccctca -ctgtccaccctcatgtcctatgagaccccctcactgtccactctcatgtcctatgagacc -ccctcactgtccactctcatggcctgtagagaccccctcactgtccaccctcatgtccta -tgagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtccaccctcg -tgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtc -caccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccct -cactgtccaccctcatggcctgtagagaccccctcactgtccaccctcgtgtcctataga -gaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgt -cctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccacc -ctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcac -tgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctat-gagac -cccctcactgtccaccctcgtgtcctatagagaccccctcactgtcaactctcatgtcct -atagagaccccctcactgtccaccctcgtgtcctat-gagaccccctcactgtccaccct -catgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactg -tccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctat-gagaccc -cctcactgtccaccctcgtgtcctatagagaccccctcactgtcaactctcatgtcctat -agagaccccctcactgtccaccctcgtgtcctatagagaccccctcactctccaccctca -tgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtc -caccctcatgtcctat-gagaccccctcactgtccaccctcatggcctatagagaccccc -tcactgtccaccctcatgtccta-tgagaccccctcactgtccaccctcatgtcctatag -agaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatg -tcctatagagaccccctcactctccaccctcatggcctatagagaccccctcactgtcca -ccctcgtgtcctatagagaccccctcactctccaccctcatggcctatagagaccccctc -actgtccaccctcatggcctatagagaccccctcactgtccactctcatgtccta-tgag -accccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtc -ctatgagaccccctcactgtccactctcatgtcctatgagaccccctcactgtccaccct -catggcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgt -ccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctat-gagacccc -ctcactgtccaccctcatgtcctatagagaccccctcactgtccactctcatgtcctat- -gagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatg -gcctatagagaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtcca -ccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctc -actgtccaccctcatgtcctatagagaccccctcactgtccactctcatggcctgtagag -accccctcactgtccacccatatggcctgtagagaccccctcactgtccaccctcaggac -cctctgcatttgctccttgggttccc ->ref_chr20:64131804-64133955 -cctcccctgtcccagacttctcctggcctctctcatgt---------------------- ------------------------------------------------------------- --------------------cctatgagaccccctcactgtccaccctcatgtcctgtaga -gaccccctcactgtccactctcatggcctata---------------------------- -----gagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccc -tcatgtcctata------------------------------------------------ --------------------gagaccccctcactgtccaccctcatgtcctatagagaccc -cctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctat -gagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcat -gtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtcc -accctcatgtcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctc -actgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagag -accccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcc -tat--------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------agagaccccctcactgtccactctcatgtcctatagagaccccctcactgt -ccaccctcatggcctatgagaccccctcactgtccactctcatggcctatagagaccccc -tcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatggcctgtag -agaccccctcactgtccaccctca------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -tgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtc -caccctcatggcctatgagaccccctcactgtccaccctcatgtcctat-gagaccccct -cactgtccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctataga -gaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccgccctcatgt -cctatgagaccccctcactgtccaccctcatgtcctatagaga----------------- ----------------------------------------------------ccccctcac -tgtccaccctcatggcctgtagagaccccctcactgtccgccctcatgtcctat-gagac -cccctcactgtccaccctcatgtcctgtagagaccccctcactgtccaccctcatgtcct -atagagaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccct -catgtcctat-gagaccccctcactgtccaccctcatgtcctatgaga--cccctcactg -tccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctat-gagaccc -cctcactgtccactctcatgtcctatgaga------------------------------ -----------------------------------------cccctcactgtccaccctca -tgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtc -aactctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatagagaccccc -tcactgtccaccctcatgtccaa-agagaccccctcactgtccaccctcatggcctgtag -agaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatg -gcctatagagaccccctcactgtccaccctcatgtcc-aaagagaccccctcactgtcca -ccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctc -actgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtccaa-agag -accccctcactgtccaccctcatggcctgta----------------------------- --------------------------------------gagaccccctcactgtccaccca -tatggcctgtagagaccccctcactgtccaccctcatgtcctata--------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------gagaccccctcactgtcca -ccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctc -actgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagag -accccctcactgtccacccatatggcctgtagagaccccctcactgtccaccctcaggac -cctctgcatttgctccttgggttccc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_d7c982150b9084cabc20a2d51cc2fab7.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_d7c982150b9084cabc20a2d51cc2fab7.msa deleted file mode 100644 index 58ba55a3..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_d7c982150b9084cabc20a2d51cc2fab7.msa +++ /dev/null @@ -1,240 +0,0 @@ ->syndip_1_chr20:20356430-20357910 -ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag -tgtgaggggagatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcaca -ctgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacactg -tgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactga -ggggaggtggtcaca--ctgaggggaggtggtcatagtgtgaggggaggtggtcacactg -tgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactga -ggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactggg -gaggtggtcacactgtgaggggaggtggtcacactgtgaggggaggtggtcacactgaga -ggaggtggtcacactgaggggaagtggtcacactgagaggaggtggtcacactg------ ------------------------------------------------------------- ------------------------------------------------------------- ------------aggggaggtggtcatactg------------------------------ ------------------------------tgaggggaggtggtcatactgtgagtgagga -ggtagtcacactgaggggagggggtcatactgcgagtggaggtagtcacactgtgaaggg -tggtagtcacactgagaggaggtggtcacactgaggggaagtggtcacactgaggggagg -tggtcatactgtgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggag -gtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacact----gaggg -gaggtggtcacactgaggggaggtggtcacagtgtgagaggaggtggtcacactgagggg -aggtggtcacagtgtga--ggggagatggtcacactgaggggaggtggtcacagtgtgag -gggaggtggtcacactgaggggaggtggtcac-------------------agtgtgagg -ggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcaca--------- -------------gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgagg -ggagatggtcacactgaggggaggtggtcacagtgtga--ggggaggtggtcacactgag -g---------------------ggaggtggtcacagtgtgcggggaggtggtcatactga -ggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatactgtgag -tgaggaggtagtcacactgaggggaagtggtcaca-----------------------ct -gaggggaggtggtcacactgaggggagggggtcatactgcgagtggaggtagtcacactg -tga--agggtggtagtcacactgagaggaggtggtcacactgaggggaagtggtcacact -gaggggaggtggtcatactgtga--ggggaagtggtcacactgaggggaggtggtcatag -tgtgaggggaggtggtcacac--tgaggggaggtggtcacactgaggggaggtggtcaca -gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtcat -actgaggggaggtggtcacagtgtgaggggaggtggtcaca------------------- ---ctgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtca- -----------------------------------------------------------ca -ctgaggggaggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcatag -tgtgaggggaggtggtcacactgaggggaggtggtcaca--ctgaggagaggtggtcata -gtgtgaggggaggtggtcacac--tgaggggaggtggtcacactgaggggaggtggtcat -agtgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtca -cactgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcac -agtg--------------------------------------tgaggggaggtggtcaca -ctgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacac -tgaggggaggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtcaca -ttgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacac -tgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagt -gtgcggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtg -tgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtca ->syndip_2_chr20:20356430-20357910 -ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag -tgtgaggggagatggtcacactgaggggaggtggtcacagtg------------------ --tgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacactg -tgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactga -ggggaggtggtcatagtgtgaggggaggtggtcacact----ggggaggtggtcacactg -tgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactga -ggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactggg -gaggtggtcacactgtgaggggaggtggtcacac--tgagaggaggtggtcacactgagg -ggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggg -gaggtggtcacactggggaggtggtcacactgtgaggggaggtggtcacactgtgagggg -aggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgagaggagg -tggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggaa -gtggtcacactgaggggaggtggtcacactgaggggaggtggtcatactgtgagtgagga -ggtagtcacactgaggggagggggtcatactgcgagtggaggtagtcacactgtgaaggg -tggtagtcacactgagaggaggtggtcacactgaggggaagtggtcacactgaggggagg -tggtcatactgtgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggag -gtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacact----gaggg -gaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtcatactgagggg -aggtggtcacagtgtga--ggggaggtggtcacactgaggggaggtggtcacagtgtgag -gggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtgtgagg -ggaggtggtcacactgaggggaggtggtcacactgagaggaggtggtcacactgagggga -ggtggtcatactgtgagtgaggaagtagtcacactgaggggaagtggtcaca--ctgagg -ggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcacactgag -gggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcacactga -gaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatactgtga- --ggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactgt -gaggggaggtggtcacactgagaggaggtggtcacactg--aggggaggtggtcatactg -tgagtgaggaggtagtcacactgaggggaagtggtcacactgaggggaggtggtcacact -gaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggagggggtcatac -tgcgagtggaggtagtcacactgtgaagggtggtagtcacactgagaggaggtggtcaca ---ctgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcac -actgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcaca -gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtca- -----------------------------------------------------------ta -ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag -tgtgcggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcata ---ctgaggggaggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcac -actgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtca -cactgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcac -actgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcaca -ctgaggggaggtggtcatagtgtgaggggaggtggtgacactgaggggaggtggtcacac -tgaggggaggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtcaca -ttgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacac -tgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagt -gtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtg -tgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtca ->p:HG002_1_chr20:20356430-20357910 -ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag -tgtgaggggagatggtcacactgaggggaggtggtcacagtg------------------ --tgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacactg -tgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactga -ggggaggtggtcatagtgtgaggggaggtggtcacact----ggggaggtggtcacactg -tgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactga -ggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactggg -gaggtggtcacactgtgaggggaggtggtcacac--tgagaggaggtggtcacactgagg -ggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggg -gaggtggtcacactggggaggtggtcacactgtgaggggaggtggtcacactgtgagggg -aggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgagaggagg -tggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggaa -gtggtcacactgaggggaggtggtcacactgaggggaggtggtcatactgtgagtgagga -ggtagtcacactgaggggagggggtcatactgcgagtggaggtagtcacactgtgaaggg -tggtagtcacactgagaggaggtggtcacactgaggggaagtggtcacactgaggggagg -tggtcatactgtgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggag -gtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacact----gaggg -gaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacactgagggg -aggtggtcacagtgtga--ggggaggtggtcacactgaggggaggtggtcacagtgtgag -gggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtgtgagg -ggaggtggtcacactgaggggaggtggtcacactgagaggaggtggtcacactgagggga -ggtggtcatactgtgagtgaggaagtagtcacactgaggggaagtggtcaca--ctgagg -ggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcacactgag -gggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcacactga -gaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatactgtga- --ggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactgt -gaggggaggtggtcacactgagaggaggtggtcacactg--aggggaggtggtcatactg -tgtgcggggaggtggtcatactgaggggaggtggtcacactgaggggaggtggtcacact -gaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggagggggtcatac -tgcgagtggaggtagtcacactgtgaagggtggtagtcacactgagaggaggtggtcaca ---ctgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcac -actgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcaca -gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtca- -----------------------------------------------------------ta -ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag -tgtgcggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcata ---ctgaggggaggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcac -actgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtca -cactgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcac -actgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcaca -ctgaggggaggtggtcatagtgtgaggggaggtggtgacactgaggggaggtggtcacac -tgaggggaggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtcaca -ttgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacac -tgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagt -gtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtg -tgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtca ->p:HG002_2_chr20:20356430-20357910 -ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag -tgtgaggggagatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcaca -ctgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacactg -tgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactga -ggggaggtggtcatagtgtgaggggaggtggtcacact----ggggaggtggtcacactg -tgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactga -ggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactggg -gaggtggtcacactgtgaggggaggtggtcacac--tgagaggaggtggtcacactgagg -ggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg------ ------------------------------------------------------------- ------------------------------------------------------------- ------------aggggaggtggtcacagtg------------------------------ ------------------------------tgaggggaggtggtcatactgtgagtgagga -ggtagtcacactgaggggagggggtcatactgcgagtggaggtagtcacactgtgaaggg -tggtagtcacactgaggggaggtggtcacactggggaggtggtcacactgtgaggggagg -tggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca--ctgaggggaa -gtggtcacactgagaggaggtggtcaca--ctgaggggaggtggtcatactgtgagtgag -gaggtagtcacactgaggggaagtggtcaca--ctgaggggaggtggtcacactgagggg -aggtggtcatactgtgagtgaggaggtagtcacactgaggggagggggtcatactgcgag -tggaggtagtcacactgtgaagggtggtagtc-------------------acactgaga -ggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcata--------- -------------ctgtgaggggaagtggtcacactgaggggaggtggtcatagtgtgagg -ggaggtggtcacactgaggggaggtggtcacagtgtga--ggggaggtggtcacactgag -g---------------------ggaggtggtcacagtgtgcggggaggtggtcatactga -ggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatactgtgag -tgaggaggta-------------------------------------------------- ------------gtcacactgaggggagggggtcatactgcgagtggaggtagtcacactg -tga--agggtggtagtcacactgagaggaggtggtcacactgaggggaagtggtcacact -gaggggaggtggtcatactgtga--ggggaagtggtcacactgaggggaggtggtcatag -tg---------------------tgaggggaggtggtcacactgaggggaggtggtcaca -gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgaggggaggtggtcacag -tgtgaggggaggtggtcaca--ctgaggggaggtggtcaca------------------- -gtgtacggggaggtggtcatactgaggggaggtggtcacagtgtgaggggaggtggtcac -actgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcaca -ctgaggggaggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcatag -tgtgaggggaggtggtcacactgaggggaggtggtcaca--ctgaggagaggtggtcata -gtgtgaggggaggtggtcacac--tgaggggaggtggtcacactgaggggaggtggtcat -agtgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtca -cactgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcac -agtg--------------------------------------tgaggggaggtggtcaca -ctgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacac -tgaggggaggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtcaca -ttgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacac -tgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagt -gtgcggggaggtggtcacactgcggggaggtggtcatactgaggggaggtggtcacagtg -tgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtca ->ref_chr20:20356430-20357910 -ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag -tgtgaggggagatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcaca -ctgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacactg -tgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactga -ggggaggtggtcatagtgtgaggggaggtggtcacact----ggggaggtggtcacactg -tgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactga -ggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactggg -gaggtggtcacactgtgaggggaggtggtcacac--tgagaggaggtggtcacactgagg -ggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------tgaggggaggtggtcacactggggaggtggtcacactgtgaggggagg -tggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca--ctgaggggaa -gtggtcacactgagaggaggtggtcaca--ctgaggggaggtggtcatactgtgagtgag -gaggtagtcacactgaggggaagtggtcaca--ctgaggggaggtggtcacactgagggg -aggtggtcatactgtgagtgaggaggtagtcacactgaggggagggggtcatactgcgag -tggaggtagtcacactgtgaagggtggtagtc-------------------acactgaga -ggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcata--------- -------------ctgtgaggggaagtggtcacactgaggggaggtggtcatagtgtgagg -ggaggtggtcacactgaggggaggtggtcacagtgtga--ggggaggtggtcacactgag -g---------------------ggaggtggtcacagtgtgcggggaggtggtcatactga -ggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatactgtgag -tgaggaggta-------------------------------------------------- ------------gtcacactgaggggagggggtcatactgcgagtggaggtagtcacactg -tga--agggtggtagtcacactgagaggaggtggtcacactgaggggaagtggtcacact -gaggggaggtggtcatactgtga--ggggaagtggtcacactgaggggaggtggtcatag -tg---------------------tgaggggaggtggtcacactgaggggaggtggtcaca -gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtcat -actgaggggaggtggtcacagtgtgaggggaggtggtcaca------------------- -gtgtgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtca- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------ diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_d93f34869d950b81a7a321257e52324e.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_d93f34869d950b81a7a321257e52324e.msa deleted file mode 100644 index b91bd251..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_d93f34869d950b81a7a321257e52324e.msa +++ /dev/null @@ -1,175 +0,0 @@ ->syndip_1_chr20:20337200-20337707 -agggtttaggaaggcctcactagacctgttaggatggatgcatggatggatggatggatg -gacagaatgggtgggtggatggatggatggatggatggatggatggatagatgggtgggt -ggatggatggatggatagatgggtggatggatagatgggtggatggataaatggatggat -ggatggatggatagatgggtgggtggatggatggatggatggatggatggatggatggat -ggatagatggatagatgggtgggtggatggatggatggatggatggatggatggatggat -ggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggat -ggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggat -ggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt -ggatggatggatggatagatgggtgggtggatggatggatggatagatgggtggatggat -aaatggatggatggatggatggatagatgtgtgggtggatggatggatggatggatggat -ggatggatggatggatagatggatagatgggtgggtggatggatggatggatggatggat -ggatggatggatggatagatgggtggatggatggatagatgggtgggtggatggatggat -ggatagatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt -ggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt -gggtggatggatggatggatagatgggtgggtggatggatggatggatagatggatagat -gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggt -gggtggatggatggatggatagatgggtgggtggatggatggatggatagatggatagat -gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatggatggat -ggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggat -ggatggatggatggatggatggatggatagatggatagatgggtgggtggatggatggat -ggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggat -ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat -ggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat -ggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggat -ggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat -ggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggt -gggtggatggatggatggatggatggatggatggatggatggatagatggatagatgggt -gggtggatggatggatggatagatgggtgggtggatggatggatggatagatggatagat -gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat -agatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagat -ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat -agatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggat -ggatagatgggtgggtgggtggatggatggatggatggatggatagaataaaaagaaagc -taggacatggttc ->syndip_2_chr20:20337200-20337707 -agggtttaggaaggcctcactagacctgttaggatggatgcatggatggatggatggatg -gacagaatgggtgggtggatggatggatggatggatggatggatggatggatagatgggt -gggtggatggatggatggatagatgggtggatggataaatggatgg----atggatggat -ggatagatgggtgggtggatggatggatggatggatggatggatggatggatggatagat -ggatagatgggtgggtggatggatggatggatggatggatggatggatggatggatggat -ggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggat -ggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggat -ggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt -ggatggatggatggatagatgggtgggtggatggatggatggatagatgggtggatggat -aaatggatggatggatggatggatagatgggtgggtggatggatggatggatggatggat -ggatagatggataga----------------tgggtgggtggatggatggatggatggat -ggatggatggatggatagatgggtggatggatggatagatgggtgggtggatggatggat -ggatagatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt -ggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt -gggtggatggatggatggatagatgggtgggtggatggatggatggatagatggatagat -gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggt -gggtggatggatggatggatagatgggtgggtggatggatggatggatagatggatagat -gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatggatggat -agatggatagatgggtgggtggatggatggatggatagatgggtggg----tggatggat -ggatggatggatggatggatggatggatagatggatagatgggtgggtggatggatggat -ggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggat -ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat -ggatggatggatagatgggtgggtggatggatggatggata------------------- --gatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggat -ggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat -ggatggatagatg------------ggtgggtgggtggatggatggatagatgggtgggt -ggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt -gggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggt -gggtggatggatggatggatggatggatagaataaaaag--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------aaagc -taggacatggttc ->p:HG002_1_chr20:20337200-20337707 -agggtttaggaaggcctcactagacctgttaggatggatgcatggatggatggatggatg -gacagaatgggtgggtggatggatggatggatggatggatggatggatggatagatgggt -gggtggatggatggatggatagatgggtggatggataaatggatgg----atggatggat -ggatagatgggtgggtggatggatggatggatggatggatggatggatggatggatagat -ggatagatgggtgggtggatggatggatggatggatggatggatggatggatggatggat -ggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggat -ggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggat -ggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt -ggatggatggatggatagatgggtgggtggatggatggatggatagatgggtggatggat -aaatggatggatggatggatggatagatgggtgggtggatggatggatggatggatggat -ggatagatggataga----------------tgggtgggtggatggatggatggatggat -ggatggatggatggatagatgggtggatggatggatagatgggtgggtggatggatggat -ggatagatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt -ggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt -gggtggatggatggatggatagatgggtgggtggatggatggatggatagatggatagat -gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggt -gggtggatggatggatggatagatgggtgggtggatggatggatggatagatggatagat -gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatggatggat -agatggatagatgggtgggtggatggatggatggatagatgggtggg----tggatggat -ggatggatggatggatggatggatggatagatggatagatgggtgggtggatggatggat -ggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggat -ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat -ggatggatggatagatgggtgggtggatggatggatggata------------------- --gatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggat -ggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat -ggatggatagatg------------ggtgggtgggtggatggatggatagatgggtgggt -ggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt -gggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggt -gggtggatggatggatggatggatggatagaataaaaag--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------aaagc -taggacatggttc ->p:HG002_2_chr20:20337200-20337707 -agggtttaggaaggcctcactagacctgttaggatggatgcatggatggatggatggatg -gacagaatgggtgggtggatggatggatggatggatggatggatggatagatgggtgggt -ggatggatggatggatagatgggtggatggatagatgggtggatggataaatggatggat -ggatggatggatagatgggtgggtggatggatggatggatggatggatggatggatggat -ggatagatggatagatgggtgggtggatggatggatggatggatggatggatggatggat -ggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggat -ggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggat -ggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt -ggatggatggatggatagatgggtgggtggatggatggatggatagatgggtggatggat -aaatggatggatggatggatggatagatgtgtgggtggatggatggatggatggatggat -ggatggatggatggatagatggatagatgggtgggtggatggatggatggatggatggat -ggatggatggatggatagatgggtggatggatggatagatgggtgggtggatggatggat -ggatagatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt -ggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt -gggtggatggatggatggatagatgggtgggtggatggatggatggatagatggatagat -gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggt -gggtggatggatggatggatagatgggtgggtggatggatggatggatagatggatagat -gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatggatggat -ggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggat -ggatggatggatggatggatggatggatagatggatagatgggtgggtggatggatggat -ggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggat -ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat -ggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat -ggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggat -ggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat -ggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggt -gggtggatggatggatggatggatggatggatggatggatggatagatggatagatgggt -gggtggatggatggatggatagatgggtgggtggatggatggatggatagatggatagat -gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat -agatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagat -ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat -agatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggat -ggatagatgggtgggtgggtggatggatggatggatggatggatagaataaaaagaaagc -taggacatggttc ->ref_chr20:20337200-20337707 -agggtttaggaaggcctcactagacctgttaggatggatgcatggatggatggatggatg -gacagaatgggtgggtggatggatggatggatagatggatggatggatggatggatggat -ggatggatggatggatggatagatgggtgggtgg----gtggatgg----atggatggat -ggatggatggatggatggatggatggatagatgggtgggtggatggatggatggatagat -ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat -agatgggtggatggataaatggatggatggatggatggatagatgggtgggtggatggat -ggatggatggatggatggatggatggatagat------------------gtgggtggat -ggatggatggatagatgggtgggtgggtggatggatggatggatggatagatgggtgggt -gggtggatggatggatggatggatagaataaaaaagaaa--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------------gc -taggacatggttc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_dc6a104deccad1208b50e281e8d4debe.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_dc6a104deccad1208b50e281e8d4debe.msa deleted file mode 100644 index 605854b6..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_dc6a104deccad1208b50e281e8d4debe.msa +++ /dev/null @@ -1,245 +0,0 @@ ->syndip_1_chr20:63491589-63493064 -tcagatttgtttatggtttctcttcttggtgggatggatggatggatggacggatggatg -gggaggtgggtggatggatggatggatgtatgaatggggtggtagatggatggggaggtg -gatggacagaaggatgggtggggagatggatgagtagggagatggatggatggattggtg -gatggatggatggatggatggatgaggaggtagatgagtggatggacagaaggatggatg -ggtaggaaggtgggtggatgaatggatggatggggaggtggatggatagatggatggatg -gatggatggatggatggatggatggatggggggatagatggatggatggatggatggatg -gacggacg----gatggggaggtggatggatggatggatggatggatggatggatggatg -aggagatgaatggatggatgagatggatggatggatgatggagggaaggatggctgggtg -gggagatggatggatagagaggtggatgggtggatggggagatggatggatggatggatg -gatggggaagtggatggatggggaggtggatggatggataggtggatgggtggatggaca -gaaggatgaatgggtagggagatggatggatggatggatggggagggatggatggatgga -tggatggatgggtggatggatagaaggatggatgggtggggaggtgggtgggtgg----g -tggatggatggagagatggatagatggata----gatggatggatggatggatggatgga -gagaaggatggatgggtggggaggtgggtgggtgggtggatgggtggatggatggatggg -tggggaggtgggcgggtggatggatggatggatgcagaggtgggtggatggatggatgga -gagaaggatggatgggtggggaggtgggtgggtggatggatggatgagtggggaggtggg -tgggtgggtggatggatggatggatggatgcatggatggatgga---------------- ------------------------------------------------------------- ----------------------------------------tggagaggtgggtggacggat -ggatggattgggaggtgggtagatgggtggatggacagaaggatggatgggtggggaggt -gggtgggtgggtggatggatggatggggaggtggatggatggatggttagatggggaggt -gggtggatgggtggatggacagaaggatggatgggtagggaggtaggtgagtggatggat -ggatggggagatggatggatggatagagagaaggatggatgggtgggacaatggatggat -ggatggatagaaggatggacgggtggggagatggatggatggatggatggatggatggat -ggatggacagaaggatgtatgggtggggaggtgggtggatagatggatggatggatggat -ggggaaatggatggatggaaggatggatggatagggaggtgggtggatggatggatggat -ggatgtacagaaggatggatgggtggggaggtgggtgagtggatgaatggatggatggat -agatagaaggatggatgggtgggacaatagatggatggatagagagaaggatggatgggt -ggggagatggatggatggatggatggatggatggatggatggatggatagagagaaggat -ggatggttgagaca----atggatggatggatggatggagagatggatggatggacggat -ggacagaaggatggatgggtggggaggtggatggatggattgaaggatggatgggtgggg -a----catggatggatggatgga--------tggatggatggatggatggacagaaggat -gtatgggtggggaggtgggtggata--------gatggatggatggggaaatggatggat -ggaaggatggatggatagggaggtgggtggatggatggatggatggatgtacagaaggat -ggatgggtggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggat -gggtgggacaatagatggatggatagagagaaggatggatgggtggggagatggatggat -ggatggatggatggatggatagagagaaggatggatggttgagacaatggatggatggat -ggatggatggagagatggatggatggatggatggacagaaggatggatgggtggggaggt -ggatggatggatggaaggatggatggatggatagagagaaggatggatgggtgggacaat -ggatggatggatgcatggatggatggatggagggatagagagaaggatggatgggtggga -caatcaatggatggatggatggatggatggatagagagaaggatggatgggtggggagat -ggatggatggatggagaggtggatggatggatggatggatggattgatggacagaaggat -ggatgggtggggaggtggatagatggagagatggagggatggttcgatagagagaaggat -ggatggatgggacaatggatggatggatggatggagtgaaggatggatgggtggggagat -ggatggatcgatggatggatggatggatagatagatggatggagaggtggatagatggat -gggtggatggatggacagaggatggatgggtggggaggtgggtggatggatggatggatg -tgggatggactgtcccacagaaagtgtgtggtaaggggagagattggagacagcccagtc -ttgagatgc ->syndip_2_chr20:63491589-63493064 -tcagatttgtttatggtttctcttcttggtgggatggatggatggatggacggatggatg -gggaggtgggtggatggatggatggatgtatgaatggggtggtagatggatggggaggtg -gatggacagaaggatgggtggggagatggatgagtagggagatggatggatggattggtg -gatggatggatggatggatggatgaggaggtagatgagtggatggacagaaggatggatg -ggtaggaaggtgggtggatgaatggatggatggggaggtggatggatagatggatggatg -gatggatggatggatggatggatggatggggggatagatggatggatggatggatggacg -gacggatggggaggtggatggatggatggatggatggatggatggatggatggatggatg -aggagatgaatggatggatgagatggatggatggatgatggagggaaggatggctgggtg -gggagatggatggatagagaggtggatgggtggatggggagatggatggatggatggatg -gatggggaagtggatggatggggaggtggatggatggataggtggatgggtggatggaca -gaaggatgaatgggtagggagatggatggatggatggatgcggagggatggatggatgga -tggatggatgggtggatggatagaaggatggatgggtggggaggtgggtgggtgggtgcg -tggatggatggagagatggatagatggatagatggatggatggatggatggatggatgga -gagaaggatggatgggtggggaggtgggtgggtgggtggatgggtggatggatggatggg -tggggaggtgggcgggtggatggatggatggatgcagaggtgggtggatggatggatgga -gagaaggatggatgggtggggaggtgggtgggtggatggatggatgagtggggaggtggg -tgggtggatggatggatggatggatgcatggatggatggatggagaggtgggtggatggg -tggatggacagaaggatggatgggtggggaggtgggtgagtgggtggatggatgaatggg -gaggtggatggatggatggatggatgaaggatggatgggtggggaggtgggtggacggat -ggatggattgggaggtgggtagatgggtggatggacagaaggatggatgggtggggaggt -gggtgggtgggtggatggatggatggggaggtggatggatggatggttagatggggaggt -gggtggatgggtggatggacagaaggatggatgggtagggaggtaggtgagtggatggat -ggatggggagatggatggatggatagagagaaggatggatgggtgggacaatggatggat -ggatggatagaaggatggacgggtgggga----gatggatggatggatggatggatggat -ggatggacagaaggatgtatgggtggggaggtgggtggatagatggatggatggatggat -ggggaaatggatggatggaaggatggatggatagggaggtgggtggatggatggatggat -ggatgtacagaaggatggatgggtggggaggtgggtgagtggatgaatggatggatggat -agatagaaggatggatgggtgggacaatagatggatggatagagagaaggatggatgggt -gggga--------gatggatggatggatggatggatggatggatggatagagagaaggat -ggatggttgagacaatggatggatggatggatggatggagagatggatggatggatggat -ggacagaaggatggatgggtggggaggtggatggatggattgaaggatggacgggtgggg -agatggatggatggatggatgga--------tggatggatggatggatggacagaaggat -gtatgggtggggaggtgggtggatagatggatggatggatggatggggaaatggatggat -ggaaggatggatggatagggaggtgggtggatggatggatggatggatgtacagaaggat -ggatgggtggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggat -gggtgggacaaca----gatggatagagagaaggatggatgggtgggga----gatggat -ggatggatggatggatggatagagagaaggatggatggttgagacaatggatggatggat -ggatggatggagagatggatggatggatggatggacagaaggatggatgggtggggaggt -ggatggatggatggaaggatggatggatggatagagagaaggatggatgggtgggacaat -ggatggatggatgcatggatggatggatggagggatagagagaaggatggatgggtggga -caatcaatggatggatggatggatggatggatagagagaaggatggatgggtggggagat -ggatggatggatggagaggtggatggatggatggatggatggattgatggacagaaggat -ggatgggtggggaggtggatagatggagagatggagggatggttcgatagagagaaggat -ggatggatgggacaatggatggatggatggatggagtgaaggatggatgggtggggagat -ggatggatcgatggatggatggatggatagatagatggatggagaggtggatagatggat -gggtggatggatggacagaggatggatgggtggggaggtgggtggatggatggatggatg -tgggatggactgtcccacagaaagtgtgtggtaaggggagagattggagacagcccagtc -ttgagatgc ->p:HG002_1_chr20:63491589-63493064 -tcagatttgtttatggtttctcttcttggtgggatggatggatggatggacggatggatg -gggaggtgggtggatggatggatggatgtatgaatggggtggtagatggatggggaggtg -gatggacagaaggatgggtggggagatggatgagtagggagatggatggatggattggtg -gatggatggatggatggatggatgaggaggtagatgagtggatggacagaaggatggatg -ggtaggaaggtgggtggatgaatggatggatggggaggtggatggatagatggatggatg -gatggatggatggatggatggatggatggggggatagatggatggatggatggatggacg -gacggatggggaggtggatggatggatggatggatggatggatggatggatggatggatg -aggagatgaatggatggatgagatggatggatggatgatggagggaaggatggctgggtg -gggagatggatggatagagaggtggatgggtggatggggagatggatggatggatggatg -gatggggaagtggatggatggggaggtggatggatggataggtggatgggtggatggaca -gaaggatgaatgggtagggagatggatggatggatggatgcggagggatggatggatgga -tggatggatgggtggatggatagaaggatggatgggtggggaggtgggtgggtgggtgcg -tggatggatggagagatggatagatggatagatggatggatggatggatggatggatgga -gagaaggatggatgggtggggaggtgggtgggtgggtggatgggtggatggatggatggg -tggggaggtgggcgggtggatggatggatggatgcagaggtgggtggatggatggatgga -gagaaggatggatgggtggggaggtgggtgggtggatggatggatgagtggggaggtggg -tgggtggatggatggatggatggatgcatggatggatggatggagaggtgggtggatggg -tggatggacagaaggatggatgggtggggaggtgggtgagtgggtggatggatgaatggg -gaggtggatggatggatggatggatgaaggatggatgggtggggaggtgggtggacggat -ggatggattgggaggtgggtagatgggtggatggacagaaggatggatgggtggggaggt -gggtgggtgggtggatggatggatggggaggtggatggatggatggttagatggggaggt -gggtggatgggtggatggacagaaggatggatgggtagggaggtaggtgagtggatggat -ggatggggagatggatggatggatagagagaaggatggatgggtgggacaatggatggat -ggatggatagaaggatggacgggtgggga----gatggatggatggatggatggatggat -ggatggacagaaggatgtatgggtggggaggtgggtggatagatggatggatggatggat -ggggaaatggatggatggaaggatggatggatagggaggtgggtggatggatggatggat -ggatgtacagaaggatggatgggtggggaggtgggtgagtggatgaatggatggatggat -agatagaaggatggatgggtgggacaatagatggatggatagagagaaggatggatgggt -gggga--------gatggatggatggatggatggatggatggatggatagagagaaggat -ggatggttgagacaatggatggatggatggatggatggagagatggatggatggatggat -ggacagaaggatggatgggtggggaggtggatggatggattgaaggatggacgggtgggg -agatggatggatggatggatgga--------tggatggatggatggatggacagaaggat -gtatgggtggggaggtgggtggatagatggatggatggatggatggggaaatggatggat -ggaaggatggatggatagggaggtgggtggatggatggatggatggatgtacagaaggat -ggatgggtggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggat -gggtgggacaaca----gatggatagagagaaggatggatgggtgggga----gatggat -ggatggatggatggatggatagagagaaggatggatggttgagacaatggatggatggat -ggatggatggagagatggatggatggatggatggacagaaggatggatgggtggggaggt -ggatggatggatggaaggatggatggatggatagagagaaggatggatgggtgggacaat -ggatggatggatgcatggatggatggatggagggatagagagaaggatggatgggtggga -caatcaatggatggatggatggatggatggatagagagaaggatggatgggtggggagat -ggatggatggatggagaggtggatggatggatggatggatggattgatggacagaaggat -ggatgggtggggaggtggatagatggagagatggagggatggttcgatagagagaaggat -ggatggatgggacaatggatggatggatggatggagtgaaggatggatgggtggggagat -ggatggatcgatggatggatggatggatagatagatggatggagaggtggatagatggat -gggtggatggatggacagaggatggatgggtggggaggtgggtggatggatggatggatg -tgggatggactgtcccacagaaagtgtgtggtaaggggagagattggagacagcccagtc -ttgagatgc ->p:HG002_2_chr20:63491589-63493064 -tcagatttgtttatggtttctcttcttggtgggatggatggatggatggacggatggatg -gggaggtgggtggatggatggatggatgtatgaatggggtggtagatggatggggaggtg -gatggacagaaggatgggtggggagatggatgagtagggagatggatggatggattggtg -gatggatggatggatggatggatgaggaggtagatgagtggatggacagaaggatggatg -ggtaggaaggtgggtggatgaatggatggatggggaggtggatggatagatggatggatg -gatggatggatggatggatggatggatggggggatagatggatggatggatggatggatg -gacggacg----gatggggaggtggatggatggatggatggatggatggatggatggatg -aggagatgaatggatggatgagatggatggatggatgatggagggaaggatggctgggtg -gggagatggatggatagagaggtggatgggtggatggggagatggatggatggatggatg -gatggggaagtggatggatggggaggtggatggatggataggtggatgggtggatggaca -gaaggatgaatgggtagggagatggatggatggatggatggggagggatggatggatgga -tggatggatgggtggatggatagaaggatggatgggtggggaggtgggtgggtgg----g -tggatggatggagagatggatagatggata----gatggatggatggatggatggatgga -gagaaggatggatgggtggggaggtgggtgggtgggtggatgggtggatggatggatggg -tggggaggtgggcgggtggatggatggatggatgcagaggtgggtggatggatggatgga -gagaaggatggatgggtggggaggtgggtgggtggatggatggatgagtggggaggtggg -tgggtgggtggatggatggatggatggatgcatggatggatgga---------------- ------------------------------------------------------------- ----------------------------------------tggagaggtgggtggacggat -ggatggattgggaggtgggtagatgggtggatggacagaaggatggatgggtggggaggt -gggtgggtgggtggatggatggatggggaggtggatggatggatggttagatggggaggt -gggtggatgggtggatggacagaaggatggatgggtagggaggtaggtgagtggatggat -ggatggggagatggatggatggatagagagaaggatggatgggtgggacaatggatggat -ggatggatagaaggatggacgggtggggagatggatggatggatggatggatggatggat -ggatggacagaaggatgtatgggtggggaggtgggtggatagatggatggatggatggat -ggggaaatggatggatggaaggatggatggatagggaggtgggtggatggatggatggat -ggatgtacagaaggatggatgggtggggaggtgggtgagtggatgaatggatggatggat -agatagaaggatggatgggtgggacaatagatggatggatagagagaaggatggatgggt -ggggagatggatggatggatggatggatggatggatggatggatggatagagagaaggat -ggatggttgagaca----atggatggatggatggatggagagatggatggatggacggat -ggacagaaggatggatgggtggggaggtggatggatggattgaaggatggatgggtgggg -a----catggatggatggatgga--------tggatggatggatggatggacagaaggat -gtatgggtggggaggtgggtggata--------gatggatggatggggaaatggatggat -ggaaggatggatggatagggaggtgggtggatggatggatggatggatgtacagaaggat -ggatgggtggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggat -gggtgggacaatagatggatggatagagagaaggatggatgggtggggagatggatggat -ggatggatggatggatggatagagagaaggatggatggttgagacaatggatggatggat -ggatggatggagagatggatggatggatggatggacagaaggatggatgggtggggaggt -ggatggatggatggaaggatggatggatggatagagagaaggatggatgggtgggacaat -ggatggatggatgcatggatggatggatggagggatagagagaaggatggatgggtggga -caatcaatggatggatggatggatggatggatagagagaaggatggatgggtggggagat -ggatggatggatggagaggtggatggatggatggatggatggattgatggacagaaggat -ggatgggtggggaggtggatagatggagagatggagggatggttcgatagagagaaggat -ggatggatgggacaatggatggatggatggatggagtgaaggatggatgggtggggagat -ggatggatcgatggatggatggatggatagatagatggatggagaggtggatagatggat -gggtggatggatggacagaggatggatgggtggggaggtgggtggatggatggatggatg -tgggatggactgtcccacagaaagtgtgtggtaaggggagagattggagacagcccagtc -ttgagatgc ->ref_chr20:63491589-63493064 -tcagatttgtttatggtttctcttct---------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------tggtgggat -ggatggatggatggacggatggatggggaggtgggtggatgg--------atggatggat -gtatgaatggggtggtagatggatggggaggtggatggacagaaggatgggtggggagat -ggatgagtagggagatggatggatggattggtggatggatggatggatggatggatgagg -aggtagatgagtggatggacagaaggatggatgggtaggaaggtgggtggatgaatggat -gga--------------------tggggaggtggatggatagatggatggatggatggat -ggat----ggatggatggatggggggatagatggatggatggatggatggacggacggat -gggga--------ggtggatggatggatggatggatggatggatggat--------ggat -ggatggatgaggagatgaacggatggat-----------gagatggatggatggat-gat -ggagggaaggatggctgggtggggagatggatggatagagaggtggatgggtggatgggg -agatggatggatggatggatggatggggaagtggatggatggggaggtggatggatggat -gtatgggtgggtaggtgggtggatagatggatggatggatggatggataaatggatggat -ggaaggatggatggataggtaggtgggtggatggatggatggatggatgtacagaaggat -ggatgggtgggtaggtgggtgagtggatgaatggatggatggatagatagaaggatggat -gggtgggtcaatagatggatggatagagagaaggatggatgggtgggta----gatggat -ggatggatggatggatggatagagagaaggatggatggttgagacaatggatggatggat -ggatggatggagagatggatggatggatggatggacagaaggatggatgggtggggaggt -ggatggatggatggaaggatggatggatggatagagagaaggatggatgggtgggacaat -ggatggatggatgcatggatggatggatggagggatagagagaaggatggatgggtggga -caatcaatggatggatggatggatggatggatagagagaaggatggatgggtggggagat -ggatggatggatggagaggtggatggatggatggatggatggattgatggacagaaggat -ggatgggtggggaggtggatagatggagagatggagggatggttcgatagagagaa---- -ggatggatgggacaatggatggatggatggatggagtgaaggatggatgggtggggagat -ggatggatcgatggatggatggatggatagatagatggatggagaggtggatagatggat -gggtggatggatggacagaggatggatgggtggggaggtgggtggatggatggatggatg -tgggatggactgtcccacagaaagtgtgtggtaaggggagagattggagacagcccagtc -ttgagatgc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_dd4a92b7b42a66d0fbedaff6c5819fa9.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_dd4a92b7b42a66d0fbedaff6c5819fa9.msa deleted file mode 100644 index a06d7384..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_dd4a92b7b42a66d0fbedaff6c5819fa9.msa +++ /dev/null @@ -1,25 +0,0 @@ ->syndip_1_chr20:17081216-17081410 -gggtaaaggaatcaactccatgtggaattttattttattttattttattttattttattt -tattttattttattttattttatt------------------------------------ -------------------------------ttattttattttattacgacaaggtctggc -tctgtcgcctaggct ->syndip_2_chr20:17081216-17081410 -gggtaaaggaatcaactccatgtgga-----attttattttattttattttattttattt -tattttattttattttattttatt------------------------------------ -------------------------------ttattttattttattacgacaaggtctggc -tctgtcgcctaggct ->p:HG002_1_chr20:17081216-17081410 -gggtaaaggaatcaactccatgtgga-----attttattttattttattttattttattt -tattttattttattttattttatt------------------------------------ -------------------------------ttattttattttattacgacaaggtctggc -tctgtcgcctaggct ->p:HG002_2_chr20:17081216-17081410 -gggtaaaggaatcaactccatgtggaattttattttattttattttattttattttattt -tattttattttattttattttatt------------------------------------ -------------------------------ttattttattttattacgacaaggtctggc -tctgtcgcctaggct ->ref_chr20:17081216-17081410 -gggtaaaggaatcaactccatgtggaattttattttattttattttattttattttattt -tattttattttattttattttattattttattttattttattttattttattttatttta -ttttattttattttattttattttattttattattttattttattacgacaaggtctggc -tctgtcgcctaggct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_dee2cded414817616e5f55ad21aa4281.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_dee2cded414817616e5f55ad21aa4281.msa deleted file mode 100644 index 17bfe1cd..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_dee2cded414817616e5f55ad21aa4281.msa +++ /dev/null @@ -1,370 +0,0 @@ ->syndip_1_chr20:64131703-64134066 -caggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactc -cacactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagactt -ctcctggcctctctcatgtcctatgagaccccctcactgtccaccctcatgtcctgtaga -gaccccctcactgtccactctcatggcctatagagaccccctcactgtcaactctcatgt -cctat-gagaccccctcactgtccactctcatggcctgtagagaccccctcactgtccac -cctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctca -ctgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatggcctgtagaga -ccccctcactgtccaccctcatgtcctata------------------------------ ---gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctc -atggcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtc -caccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccc -tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctgtag -agaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgt -cctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccac -cctcatgtcctatgagaccccctcactgtccactctcatgtcctatgagaccccctcact -gtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagacc -ccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcgtgtccta -tagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccactctca -tgtcctatgagaccccctcactgtccactctcatggcctgtagagaccccctcactgtcc -accctcatgtcctgtaga------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------gaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccc -tcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactg -tccaccctcatgtcctatagagaccccctcactgtccactctcatgtcctatagagaccc -cctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatggcctgt -agagaccccctcactgtccactctcatggcctatagagaccccctcactgtccaccctca -tggcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtc -caccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccc -tcactgtccaccctcatggcctat-gagaccccctcactgtccactctcatggcctgtag -agaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgt -cctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccac -cctcatgtcctatagagaccccctcactgtccgccctcatgtcctat-gagaccccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagaga -ccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccgccctcatgtcctatgagaccccctcactgtccaccct -catgtcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactg -tccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatgagacccc -ctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctcgtgtcctata -gagaccccctcactgtcaactctcatgtcctatagagaccccctcactgtccaccctcgt -gtccta-tgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtcc -accctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatgagaccccctc -actgtccactctcatgtcctatgagaccccctcactgtccaccctcgtgtcctatagaga -ccccctcactgtcaactctcatgtcctatagagaccccctcactgtccaccctcgtgtcc -tatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc -tcatggcctgtagagaccccctcactgtcaactctcatgtcctat-gagaccccctcact -gtccaccctcatgtcctatagagaccccctcactgtccaccctcat-gtccaaagagacc -ccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctg -tagagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctc -atgtccaaagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtc -caccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccc -tcactgtccaccctcatgtcc-aaagagaccccctcactgtccaccctcatggcctgtag -agaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtccactctcatg -tcctatgagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccac -cctcatgtcctatgagaccccctcactgtccaccctcgtgtcctatagagaccccctcac -tgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatagagac -cccctcactgtccactctcatgtcctat-gagaccccctcactgtccaccctcatgtcct -atgagaccccctcactgtccacccatatggcctgtagagaccccctcactgtccaccctc -atgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgt -ccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagacccc -ctcactgtccaccctcatggcctgtagagaccccctcactgtccacccatatggcctgta -gagaccccctcactgtccaccctcaggaccctctgcatttgctccttgggttcccggaac -ttgagcttgggtcttggtccacagcagctttgggaagggccctcggctgctttttgcttc -agcagctggggagcagttaactttcagacccggccctcccccaagg ->syndip_2_chr20:64131703-64134066 -caggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactc -cacactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagactt -ctcctggcctctctcatgtcctatgagaccccctcactgtccaccctcatgtcctgtaga -gaccccctcactgtccactctcatggcctatagagaccccctcactgtccaccctcatgg -cctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccac -cctcatgtcctatagaga-cccctcactgtccaccctcatggcctat-gagaccccctca -ctgtccactctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagaga -ccccctcactgtccaccctcatgtcctatagagacccctcactgtccaccctcatggcct -atgagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctc -atggcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtc -caccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccc -tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctgtag -agaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcgtgt -cctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccac -c---------------------------------ctcatgtcctatgagaccccctcact -gtccaccctcatgtcctatagagaccccctcactgtccactctcatgtcctatagagacc -ccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatggcctg -tagagaccccctcactgtccactctcatggcctata------------------------ ---------gagaccccctcactgtccaccctcatggcctatagagaccccctcactgtcc -accctcatggcctgtagag----------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------accccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccc -tcatggcctat-gagaccccctcactgtccaccctcatgtcctatgagaccccctcactg -tccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccc -cctcactgtccaccctcatgtcctatagagaccccctcactgtccgccctcatgtcctat --gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctca -tggcctgtagagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtc -caccctcatgtcctatagagaccccctcactgtccaccctcatgtcctat-gagaccccc -tcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctat-g -aga-cccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgt -cctat-gagaccccctcactgtccactctcatgtcctat-gagaccccctcactgtccac -cctcatggcctgtagagaccccctcactgtccaccctcgtgtcctatagagaccccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagaga -ccccctcactgtcaactctcatgtcctat-gagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatgtccaaagagaccccctcactgtccaccct -catggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactg -tccaccctcatggcctatagagaccccctcactgtccaccctcatgtccaaagagacccc -ctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgta -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcat -ggcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtcc -accctcgtgtcctatagagaccccctcactgtccaccctcatggcctata---------- -----------------------gagaccccctcactgtccaccctcatgtcctat-gaga -ccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcgtgtcctata---------------------- -----------------------------------------------gagaccccctcact -gtccaccctcgtgtcctatagagaccccctcactgtccaccctcatggcctatagagacc -ccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtccta -tagagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctc -atgtccaaagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtc -cacccatatggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccc -tcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtag -agaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatg -gcctatgagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccac -cctcatgtcctatagagacccctcactgtccaccctcatgtcctatagagaccccctcac -tgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctat-gagac -cccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcct -atgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctc -atgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagacccc -ctcactgtccacccatatggcctgtagagaccccctcactgtccacccatatggcctgta -gagaccccctcactgtccaccctcaggaccctctgcatttgctccttgggttcccggaac -ttgagcttgggtcttggtccacagcagctttgggaagggccctcggctgctttttgcttc -agcagctggggagcagttaactttcagacccggccctcccccaagg ->p:HG002_1_chr20:64131703-64134066 -caggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactc -cacactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagactt -ctcctggcctctctcatgtcctatgagaccccctcactgtccaccctcatgtcctgtaga -gaccccctcactgtccactctcatggcctatagagaccccctcactgtccaccctcatgg -cctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccac -cctcatgtcctatagaga-cccctcactgtccaccctcatggcctat-gagaccccctca -ctgtccactctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagaga -ccccctcactgtccaccctcatgtcctatagagacccctcactgtccaccctcatggcct -atgagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctc -atggcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtc -caccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccc -tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctgtag -agaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcgtgt -cctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccac -c---------------------------------ctcatgtcctatgagaccccctcact -gtccaccctcatgtcctatagagaccccctcactgtccactctcatgtcctatagagacc -ccctcactgtccaccctcatggcctat--------------------------------- ------------------------------------------------------------- ---------gagaccccctcactgtccactctcatggcctatagagaccccctcactgtcc -accctcatggcctatagag----------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------accccctcactgtccaccctcatggcc -tgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc -tcatggcctgtagagaccccctcactgtccaccctcatggcctatgagaccccctcactg -tccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatagagaccc -cctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctat -agagaccccctcactgtccgccctcatgtcctat-gagaccccctcactgtccaccctca -tgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtc -cgccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctgtagagaccccc -tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctat-g -agaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgt -cctat-gaga-cccctcactgtccaccctcatgtcctat-gagaccccctcactgtccac -cctcatgtcctat-gagaccccctcactgtccactctcatgtcctat-gaga-cccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagaga -ccccctcactgtcaactctcatgtcctat-gagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatgtccaaagagaccccctcactgtccaccct -catggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactg -tccaccctcatggcctatagagaccccctcactgtccaccctcatgtccaaagagacccc -ctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgta -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcat -gtccaa-agagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcc -acccatatggcctgtagagaccccctcactgtccaccctcatgtcctata---------- -----------------------gagaccccctcactgtccaccctcatggcctgtagaga -ccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcc -tat-gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc -tcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcact -gtccaccctcgtgtcctatagagaccccctcactgtccaccctcatggcctatagagacc -ccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtccta -tagagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctc -atgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtc -caccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccc -tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctgtag -agaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatg -gcctatgagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccac -cctcatgtcctatagagacccctcactgtccaccctcatgtcctatagagaccccctcac -tgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctat-gagac -cccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcct -atgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctc -atgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatgtcctatagagaccccctcactgtccaccctcgtggcctgtagagacccc -ctcactgtccaccctcatggcctgtagagaccccctcactgtccacccatatggcctgta -gagaccccctcactgtccaccctcaggaccctctgcatttgctccttgggttcccggaac -ttgagcttgggtcttggtccacagcagctttgggaagggccctcggctgctttttgcttc -agcagctggggagcagttaactttcagacccggccctcccccaagg ->p:HG002_2_chr20:64131703-64134066 -caggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactc -cacactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagactt -ctcctggcctctctcatgtcctatgagaccccctcactgtccaccctcatgtcctgtaga -gaccccctcactgtccactctcatggcctatagagaccccctcactgtccaccctcatgg -cctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccac -cctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctca -ctgtccaccctcatgtcctat-gagaccccctcactgtccaccctcgtgtcctatagaga -ccccctcactgtccaccctcatgtcctata------------------------------ ---gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctc -atgtcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtc -caccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccc -tcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatag -agaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgt -cctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccac -cctcatgtcctatgagaccccctcactgtccactctcatgtcctatgagaccccctcact -gtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagacc -ccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcgtgtccta -tagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccactctca -tgtcctatgagaccccctcactgtccactctcatggcctgtagagaccccctcactgtcc -accctcatgtcctgtagagaccccctcactgtccaccctcgtgtcctatagagaccccct -cactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgag -accccctcactgtccactctcatgtcctatagagaccccctcactgtccaccctcatggc -ctatgagaccccctcactgtccactctcatggcctatagagaccccctcactgtccaccc -tcatggcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcact -gtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagacc -ccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtccta -tgagaccccctcactgtccactctcatgtcctatgagaccccctcactgtccactctcat -ggcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtcca -ccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctc -actgtccaccctcatgtcctatagagaccccctcactgtccgccctcatgtcctatgaga -ccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcc -tgtagagaccccctcactgtccgccctcatgtcctatagagaccccctcactgtccaccc -tcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactg -tccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctgtagagaccc -cctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctat ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------g -agaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgt -cctat-gaga-cccctcactgtccaccctcatgtcctat-gagaccccctcactgtccac -cctcatgtcctat-gagaccccctcactgtccactctcatgtcctat-gaga-cccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagaga -ccccctcactgtcaactctcatgtcctat-gagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatgtccaaagagaccccctcactgtccaccct -catggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactg -tccaccctcatggcctatagagaccccctcactgtccaccctcatgtccaaagagacccc -ctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgta -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcat -gtccaa-agagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcc -acccatatggcctgtagagaccccctcactgtccaccctcatgtcctata---------- -----------------------gagaccccctcactgtccaccctcatggcctgtagaga -ccccctcactgtccaccctcatggcctatagagaccccctcactgtccactctcatgtcc -tat--------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------gagaccccctcactgtccaccctcatggcctatag -agaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtccactctcatg -tcctatgagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccac -cctcatgtcctatgagaccccctcactgtccaccctcgtgtcctatagagaccccctcac -tgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatagagac -cccctcactgtccactctcatgtcctat-gagaccccctcactgtccaccctcatgtcct -atgagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctc -atgtcctat-gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatgtcctgtagagaccccctcactgtccaccctcatggcctgtagagacccc -ctcactgtccaccctcatggcctgtagagaccccctcactgtccacccatatggcctgta -gagaccccctcactgtccaccctcaggaccctctgcatttgctccttgggttcccggaac -ttgagcttgggtcttggtccacagcagctttgggaagggccctcggctgctttttgcttc -agcagctggggagcagttaactttcagacccggccctcccccaagg ->ref_chr20:64131703-64134066 -caggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactc -cacactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagactt -ctcctggcctctctcatgtcctatgagaccccctcactgtccaccctcatgtcctgtaga -gaccccctcactgtccactctcatggcctatagagaccccctcactgtccaccctcatgg -cctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccac -cctcatgt---------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------cctatagagaccccctcactgtccaccctc -atggcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtc -caccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccc -tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctgtag -agaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcgtgt -cctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccac -c---------------------------------ctcatgtcctatgagaccccctcact -gtccaccctcatgtcctatagagaccccctcactgtccactctcatgtcctatagagacc -ccctcactgtccaccctcatggcctat--------------------------------- ------------------------------------------------------------- ---------gagaccccctcactgtccactctcatggcctatagagaccccctcactgtcc -accctcatggcctatagag----------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------accccctcactgtccaccctcatggcc -tgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc -tcatggcctgtagagaccccctcactgtccaccctcatggcctatgagaccccctcactg -tccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatagagaccc -cctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctat -agagaccccctcactgtccgccctcatgtcctat-gagaccccctcactgtccaccctca -tgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtc -cgccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctgtagagaccccc -tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctat-g -agaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgt -cctat-gaga-cccctcactgtccaccctcatgtcctat-gagaccccctcactgtccac -cctcatgtcctat-gagaccccctcactgtccactctcatgtcctat-gaga-cccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagaga -ccccctcactgtcaactctcatgtcctat-gagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatgtccaaagagaccccctcactgtccaccct -catggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactg -tccaccctcatggcctatagagaccccctcactgtccaccctcatgtccaaagagacccc -ctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgta -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcat -gtccaa-agagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcc -acccatatggcctgtagagaccccctcactgtccaccctcatgtcctata---------- -----------------------gagaccccctcactgtccaccctcatggcctgtagaga -ccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctca----- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------tggcctgtagagacccc -ctcactgtccaccctcatggcctgtagagaccccctcactgtccacccatatggcctgta -gagaccccctcactgtccaccctcaggaccctctgcatttgctccttgggttcccggaac -ttgagcttgggtcttggtccacagcagctttgggaagggccctcggctgctttttgcttc -agcagctggggagcagttaactttcagacccggccctcccccaagg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_df30169fc031a64138ca04f54efb8ec9.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_df30169fc031a64138ca04f54efb8ec9.msa deleted file mode 100644 index 1b19fd10..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_df30169fc031a64138ca04f54efb8ec9.msa +++ /dev/null @@ -1,160 +0,0 @@ ->syndip_1_chr20:61783203-61785039 -gcgtcaatgattctgaaggcttcttccaaattcattacccaacattctatctgaacacac -taatatacatttctagggtcgatggtttaaactgtaaattctccaaaggcacattctata -tgatttttgcccacaacctttccttaatatgtacatgttttctagataaaaacattaaat -acagctaaagtgacatcaaggtctccctcccttcctttcctccaatacgtgagagaaatg -taatcccagttccttgggacagttctcgaggccctcagatgtcctgtgcccccgaaagaa -atgtaatcccagttccttgggatagttctcaaggccctccgatatcctgtgcccctggga -gaaatgtaagcccagttcctcaggacagttctcgaggccctcagatgtcctgtgctccca -ggagaatataagcctagttcctcgggacagttctcgaggccctcaggtgtcttgtgcccc -caagagaaatgtaatcccagttccttgggacagttctccgggccctcagatgtcctgtgc -ccccgggagaaatgtaagcctagttcctcgggacagttctcgaggccctcaggtgtcttg -tgcccccaagagaaatgtaatcccagttcctcgggacagttctcaaggccctcagatgtc -ctgtgcccccaagagaaatgtaatcccagttccttgggacagttctcaaggccctccgat -atcctgtgcccccaggagaatgtaagcccagttcctcgggacagttctcgaggccctcag -gtgtcttgtgcccccaggagaatgtaagcccagttccttgggacagttctcgaggccctc -aggtgtcttgtgcccccaagagaaatgtaatcccagttcctcgggacagttctcaaggcc -ctcagatgtcctgtgcccccaagagaaatgtaatcccagttccttgggacagttctcaag -gccctccgatatcctgtgcccccaggagaatgtaagcccagttcctcgggacagttctcg -aggccctcaggtgtcttgtgcccccaggagaatgtaagcccagttccttgggacagttct -cgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcctcgggacagt -tctcaaggccctccgatatcctgtgcccccaggagaatgtaatcccagttcctcgggaca -gttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcctcggg -acagttctccaggccctccgatatcctgtgcccccaggagaatgtaagcccagttcctcg -ggacagttctcgaggccctcagatgtcctgtgcccccaagagaaatgtaatcccagttcc -tcgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgtaag------- ---------------------------------------------------------ccca -gttcctcgggacagttctccaggccctccgatatcctgtgcccccaggagaatgtaagcc -cagttcctcggaacagttctccaggccctcagatgtcctgtgcccccggggcctcatcag -acattaagcatgcagtccctttgcagctctggatggcgcgagtttcccacgtcccatccc -cttcctggctatgggcaagtgcaggctggatcctggcctcctccttcctggcctccagct -cactgccctacccctggagcagaggggccttctacacctgagccacgctggccactcccc -aagctcactcgaggtcgaagctgtggccgacgcttgg ->syndip_2_chr20:61783203-61785039 -gcgtcaatgattctgaaggcttcttccaaattcattacccaacattctatctgaacacac -taatatacatttctagggtcgatggtttaaactgtaaattctccaaaggcacattctata -tgatttttgcccacaacctttccttaatatgtacatgttttctagataaaaacattaaat -acagctaaagtgacatcaaggtctccctcccttcctttcctccaatacgtgagagaaatg -taatcccagttccttgggacagttctcgaggccctcagatgtcctgtgcccccgaaagaa -atgtaatcccagttccttgggatagttctcaaggccctccgatatcctgtgcccctggga -gaaatgtaagcccagttcctcaggacagttctcgaggccctcagatgtcctgtgctccca -ggagaatataagcctagttcctcgggacagttctcgaggccctcaggtgtcttgtgcccc -caagagaaatgtaatcccagttccttgggacagttctccgggccctcagatgtcctgtgc -ccccgggagaaatgtaagcctagttcctcgggacagttctcgaggccctcaggtgtcttg -tgcccccaagagaaatgtaatcccagttccttgggacagttctcgaggccctcagatgtc -ctgtgcccccgggagaaatgtaagcctagttcctcgggacagttctcaaggccctccgat -atcctgtgcccccaggagaatgtaagcccagttcctc----------------------- ----------------------------------------gggacagttctcgaggccctc -aggtgtcttgtgcccccaagagaaatgtaatcccagttcctcgggacagttctcaaggcc -ctcagatgtcctgtgcccccaagagaaatgtaatcccagttccttgggacagttctcaag -gccctccgatatcctgtgcccccaggagaatgtaagcccagttcctcgggacagttctcg -aggccctcaggtgtcttgtgcccccaggagaatgtaagcccagttccttgggacagttct -cgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcctcgggacagt -tctcaaggccctccgatatcctgtgcccccaggagaatgtaagcccagttcctcgggaca -gttctcgaggccttcaggtgtcttgtgcccccaagagaaatgtaatcccagttcctcgga -acagttctccaggccctcagatgtcctgtgcccccaagaga------------------- ------------------------------------------------------------- ----------------------------------------------aatgtaat------- ---------------------------------------------------------ccca -gttcctcgggacagttctccaggccctccgatatcctgtgcccccaggagaatgtaagcc -cagttcctcggaacagttctccaggccctcagatgtcctgtgcccccggggcctcatcag -acattaagcatgcagtccctttgcagctctggatggcgcgagtttcccacgtcccatccc -cttcctggctatgggcaagtgcaggctggatcctggcctcctccttcctggcctccagct -cactgccctacccctggagcagaggggccttctacacctgagccacgctggccactcccc -aagctcactcgaggtcgaagctgtggccgacgcttgg ->p:HG002_1_chr20:61783203-61785039 -gcgtcaatgattctgaaggcttcttccaaattcattacccaacattctatctgaacacac -taatatacatttctagggtcgatggtttaaactgtaaattctccaaaggcacattctata -tgatttttgcccacaacctttccttaatatgtacatgttttctagataaaaacattaaat -acagctaaagtgacatcaaggtctccctcccttcctttcctccaatacgtgagagaaatg -taatcccagttccttgggacagttctcgaggccctcagatgtcctgtgcccccgaaagaa -atgtaatcccagttccttgggatagttctcaaggccctccgatatcctgtgcccctggga -gaaatgtaagcccagttcctcaggacagttctcgaggccctcagatgtcctgtgctccca -ggagaatataagcctagttcctcgggacagttctcgaggccctcaggtgtcttgtgcccc -caagagaaatgtaatcccagttccttgggacagttctccgggccctcagatgtcctgtgc -ccccgggagaaatgtaagcctagttcctcgggacagttctcgaggccctcaggtgtcttg -tgcccccaagagaaatgtaatcccagttccttgggacagttctcgaggccctcagatgtc -ctgtgcccccgggagaaatgtaagcctagttcctcgggacagttctcaaggccctccgat -atcctgtgcccccaggagaatgtaagcccagttcctc----------------------- ----------------------------------------gggacagttctcgaggccctc -aggtgtcttgtgcccccaagagaaatgtaatcccagttcctcgggacagttctcaaggcc -ctcagatgtcctgtgcccccaagagaaatgtaatcccagttccttgggacagttctcaag -gccctccgatatcctgtgcccccaggagaatgtaagcccagttcctcgggacagttctcg -aggccctcaggtgtcttgtgcccccaggagaatgtaagcccagttccttgggacagttct -cgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcctcgggacagt -tctcaaggccctccgatatcctgtgcccccaggagaatgtaagcccagttcctcgggaca -gttctcgaggccttcaggtgtcttgtgcccccaagagaaatgtaatcccagttcctcgga -acagttctccaggccctcagatgtcctgtgcccccaagaga------------------- ------------------------------------------------------------- ----------------------------------------------aatgtaat------- ---------------------------------------------------------ccca -gttcctcgggacagttctccaggccctccgatatcctgtgcccccaggagaatgtaagcc -cagttcctcggaacagttctccaggccctcagatgtcctgtgcccccggggcctcatcag -acattaagcatgcagtccctttgcagctctggatggcgcgagtttcccacgtcccatccc -cttcctggctatgggcaagtgcaggctggatcctggcctcctccttcctggcctccagct -cactgccctacccctggagcagaggggccttctacacctgagccacgctggccactcccc -aagctcactcgaggtcgaagctgtggccgacgcttgg ->p:HG002_2_chr20:61783203-61785039 -gcgtcaatgattctgaaggcttcttccaaattcattacccaacattctatctgaacacac -taatatacatttctagggtcgatggtttaaactgtaaattctccaaaggcacattctata -tgatttttgcccacaacctttccttaatatgtacatgttttctagataaaaacattaaat -acagctaaagtgacatcaaggtctccctcccttcctttcctccaatacgtgagagaaatg -taatcccagttccttgggacagttctcgaggccctcagatgtcctgtgcccccgaaagaa -atgtaatcccagttccttgggatagttctcaaggccctccgatatcctgtgcccctggga -gaaatgtaagcccagttcctcaggacagttctcgaggccctcagatgtcctgtgctccca -ggagaatataagcctagttcctcgggacagttctcgaggccctcaggtgtcttgtgcccc -caagagaaatgtaatcccagttccttgggacagttctccgggccctcagatgtcctgtgc -ccccgggagaaatgtaagcctagttcctcgggacagttctcgaggccctcaggtgtcttg -tgcccccaagagaaatgtaatcccagttcctcgggacagttctcaaggccctcagatgtc -ctgtgcccccaagagaaatgtaatcccagttccttgggacagttctcaaggccctccgat -atcctgtgcccccaggagaatgtaagcccagttcctcgggacagttctcgaggccctcag -gtgtcttgtgcccccaggagaatgtaagcccagttccttgggacagttctcgaggccctc -aggtgtcttgtgcccccaagagaaatgtaatcccagttcctcgggacagttctcaaggcc -ctcagatgtcctgtgcccccaagagaaatgtaatcccagttccttgggacagttctcaag -gccctccgatatcctgtgcccccaggagaatgtaagcccagttcctcgggacagttctcg -aggccctcaggtgtcttgtgcccccaggagaatgtaagcccagttccttgggacagttct -cgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcctcgggacagt -tctcaaggccctccgatatcctgtgcccccaggagaatgtaatcccagttcctcgggaca -gttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcctcggg -acagttctccaggccctccgatatcctgtgcccccaggagaatgtaagcccagttcctcg -ggacagttctcgaggccctcagatgtcctgtgcccccaagagaaatgtaatcccagttcc -tcgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgtaag------- ---------------------------------------------------------ccca -gttcctcgggacagttctccaggccctccgatatcctgtgcccccaggagaatgtaagcc -cagttcctcggaacagttctccaggccctcagatgtcctgtgcccccggggcctcatcag -acattaagcatgcagtccctttgcagctctggatggcgcgagtttcccacgtcccatccc -cttcctggctatgggcaagtgcaggctggatcctggcctcctccttcctggcctccagct -cactgccctacccctggagcagaggggccttctacacctgagccacgctggccactcccc -aagctcactcgaggtcgaagctgtggccgacgcttgg ->ref_chr20:61783203-61785039 -gcgtcaatgattctgaaggcttcttccaaattcattacccaacattctatctgaacacac -taatatacatttctagggtcgatggtttaaactgtaaattctccaaaggcacattctata -tgatttttgcccacaacctttccttaatatgtacatgttttctagataaaaacattaaat -acagctaaagtgacatcaaggtctccctcccttcctttcctccaatacgtgagagaaatg -taatcccagttccttgggacagttctcgaggccctcagatgtcctgtgcccccgaaagaa -atgtaatcccagttccttgggatagttctcaaggccctccgatatcctgtgcccctggga -gaaatgtaagcccagttcctcaggacagttctcgaggccctcagatgtcctgtgctccca -ggagaatataagcctagttcctcgggacagttctcgaggccctcaggtgtcttgtgcccc -caagagaaatgtaatcccagttccttgggacagttctccgggccctcagatgtcctgtgc -ccccgggagaaatgtaagcctagttcctcgggacagttctcgaggccctcaggtgtcttg -tgcccccaagagaaatgtaatcccagttcctcgggacagttctcaaggccctcagatgtc -ctgtgcccccaagagaaatgtaatcccagttccttgggacagttctcaaggccctccgat -atcctgtgcccccaggagaatgtaagcccagttcctcgggacagttctcgaggccctcag -gtgtcttgtgcccccaggagaatgtaagcccagttccttgggacagttctcgaggccctc -aggtgtcttgtgcccccaagagaaatgtaatcccagttcctcgggacagttctcaaggcc -ctcagatgtcctgtgcccccaagagaaatgtaatcccagttccttgggacagttctcaag -gccctccgatatcctgtgcccccaggagaatgtaagcccagttcctcgggacagttctcg -aggccctcaggtgtcttgtgcccccaggagaatgtaagcccagttccttgggacagttct -cgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcctcgggacagt -tctcaaggccctccgatatcctgtgcccccaggagaatgtaatcccagttcctcgggaca -gttctcgaggccctcagatgtcctgtgcccccaagagaaatgtaatcccagttcctcggg -acagttctcaaggccctccgatatcctgtgcccccaggagaatgtaagcccagttcctcg -ggacagttctcgaggccctcaggtgtcttgtgcccccaagagaaatgtaatcccagttcc -tcgggacagttctccaggccctccgatatcctgtgcccccaggagaatgtaagcccagtt -cctcgggacagttctcgaggccctcagatgtcctgtgcccccaagagaaatgtaatccca -gttcctcgggacagttctcaaggccctccgatatcctgtgcccccaggagaatgtaagcc -cagttcctcggaacagttctccaggccctcagatgtcctgtgcccccggggcctcatcag -acattaagcatgcagtccctttgcagctctggatggcgcgagtttcccacgtcccatccc -cttcctggctatgggcaagtgcaggctggatcctggcctcctccttcctggcctccagct -cactgccctacccctggagcagaggggccttctacacctgagccacgctggccactcccc -aagctcactcgaggtcgaagctgtggccgacgcttgg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_df55c8c1ea86802a42a7e9b21d75a6f1.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_df55c8c1ea86802a42a7e9b21d75a6f1.msa deleted file mode 100644 index fd3568ef..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_df55c8c1ea86802a42a7e9b21d75a6f1.msa +++ /dev/null @@ -1,40 +0,0 @@ ->syndip_1_chr20:23560839-23561198 -gtattctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttc -ttcagcattcctttctctttctttctttctttctttctttctttccttccttccttcctt -ccttccttccttccttccttccttccttccttc--------------------------- ------------------------------------------------------------- ---------------------------------ctttctttctttctttctttctttcttt -ctttctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgt -tgcccaggctgt ->syndip_2_chr20:23560839-23561198 -gtattctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttc -ttcagcattcctttctctttctttctttctttctttctttctttctttctttctttcttt -ccttctttccttccttccttccttccttccttccttccttccttccttccttccttcctt -ccttctttccttctttccttctttccttctttccttctttccttctttccttctttcctt -ctttctttctttctttccttctttccttctttctttctttctttctttctttctttcttt -ctttctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgt -tgcccaggctgt ->p:HG002_1_chr20:23560839-23561198 -gtattctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttc -ttcagcattcctttctctttctttctttctttctttctttctttctttctttctttcttt -ccttctttccttccttccttccttccttccttccttccttccttccttccttccttcttt -ccttctttccttctttccttctttccttctttccttctttccttctttccttctttcctt -ctttctttctttctttctttctttccttctttctttctttctttctttctttctttcttt -ctttctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgt -tgcccaggctgt ->p:HG002_2_chr20:23560839-23561198 -gtattctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttc -ttcagcattcctttctctttctttctttctttctttctttctttctttctttctttcttt -ccttctttccttccttccttccttccttccttc--------------------------- ------------------------------------------------------------- ---------------------------------ctttctttctttctttctttctttcttt -ctttctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgt -tgcccaggctgt ->ref_chr20:23560839-23561198 -gtattctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttc -ttcagcattcctttctctttctttctttctttctttctttctttctttctttctttcttt -ccttctttccttccttccttccttccttccttccttccttccttccttccttccttcctt -ccttctttccttctttccttctttccttctttccttctttccttctttccttctttcc-- -----------ttctttccttctttccttctttctttctttctttctttctttctttcttt -ctttctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgt -tgcccaggctgt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_e1c1e1257e2af6edd925e90941014ba6.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_e1c1e1257e2af6edd925e90941014ba6.msa deleted file mode 100644 index e1b19beb..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_e1c1e1257e2af6edd925e90941014ba6.msa +++ /dev/null @@ -1,95 +0,0 @@ ->syndip_1_chr20:61289452-61290483 -tgccaacagtaaggggtacggggtgtcgccagcctgcagtgctgtgggagagaaacaatc -tctgttctggtgctgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacagg -ccagtggcagtccctgcctttggattaaagagccctttgaggcttgcttggtgatgtcat -ggaaaacagcatatgacaccaagatatccccatatccaacgagacttgctgggtttatcc -ccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttat -ccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggttt -atccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggt -ttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgg -gtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgct -gggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaatgagacttg -ctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagact -tgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgaga -cttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaatga -gacttgctgggtttatccccgtatccaatgagacttgctgggtttatcccgatatccaat -gagacttgctggatttatccccgtatccaatgagacttgctgggtttatccccgtatcca -atgagacttgctgggtttatcccgatatccaatgagacttgctggatttatccccgtatc -caatgagact-------------------------------------------------- ------------- ->syndip_2_chr20:61289452-61290483 -tgccaacagtaaggggtacggggtgtcgccagcctgcagtgctgtgggagagaaacaatc -tctgttctggtgctgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacagg -ccagtggcagtccctgcctttggattaaagagccctttgaggcttgcttggtgatgtcat -ggaaaacagcatatgacaccaagatatccccatatccaacgagacttgctgggtttatcc -ccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttat -ccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggttt -atccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggt -ttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgg -gtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgct -gggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaatgagacttg -ctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagact -tgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgaga -cttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaatga -gacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaat -gagacttgctgggtttatcccgatatccaatgagacttgctggatttatccccgtatcca -atgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatcccgatatc -caatgagacttgctggatttatccccgtatccaatgagact------------------- ------------- ->p:HG002_1_chr20:61289452-61290483 -tgccaacagtaaggggtacggggtgtcgccagcctgcagtgctgtgggagagaaacaatc -tctgttctggtgctgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacagg -ccagtggcagtccctgcctttggattaaagagccctttgaggcttgcttggtgatgtcat -ggaaaacagcatatgacaccaagatatccccatatccaacgagacttgctgggtttatcc -ccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttat -ccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggttt -atccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggt -ttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgg -gtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgct -gggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaatgagacttg -ctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagact -tgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgaga -cttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaatga -gacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaat -gagacttgctgggtttatcccgatatccaatgagacttgctggatttatccccgtatcca -atgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatcccgatatc -caatgagacttgctggatttatccccgtatccaatgagact------------------- ------------- ->p:HG002_2_chr20:61289452-61290483 -tgccaacagtaaggggtacggggtgtcgccagcctgcagtgctgtgggagagaaacaatc -tctgttctggtgctgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacagg -ccagtggcagtccctgcctttggattaaagagccctttgaggcttgcttggtgatgtcat -ggaaaacagcatatgacaccaagatatccccatatccaacgagacttgctgggtttatcc -ccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttat -ccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggttt -atccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggt -ttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgg -gtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgct -gggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttg -ctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagact -tgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgaga -cttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaatga -gacttgctgggtttatccccgtatccaatgagacttgctgggtttatcccgatatccaat -gagacttgctggatttatccccgtatccaatgagacttgctgggtttatccccgtatcca -atgagacttgctgggtttatcccgatatccaatgagacttgctggatttatccccgtatc -caatgagact-------------------------------------------------- ------------- ->ref_chr20:61289452-61290483 -tgccaacagtaaggggtacggggtgtcgccagcctgcagtgctgtgggagagaaacaatc -tctgttctggtgctgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacagg -ccagtggcagtccctgcctttggattaaagagccctttgaggcttgcttggtgatgtcat -ggaaaacagcatatgacaccaagatatccccatatccaacgagacttgctgggtttatcc -ccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttat -ccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggttt -atccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggt -ttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgg -gtttatccccgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgct -gggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaatgagacttg -ctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagact -tgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgaga -cttgctgggtttatccccgtatccaatgagacttgctgggtttatccccgtatccaatga -gacttgctgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaat -gagacttgctgggtttatccccgtatccaatgagacttgctgggtttatcccgatatcca -atgagacttgctggatttatccccgtatccaatgagacttgctgggtttatccccgtatc -caatgagacttgctgggtttatcccgatatccaatgagacttgctggatttatccccgta -tccaatgagact diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_e2cfd5d9ad8fc19fe505a047e91b24e1.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_e2cfd5d9ad8fc19fe505a047e91b24e1.msa deleted file mode 100644 index 90c8b00f..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_e2cfd5d9ad8fc19fe505a047e91b24e1.msa +++ /dev/null @@ -1,70 +0,0 @@ ->syndip_1_chr20:45600369-45600946 -caactaggcattccctagtggtgccaaacaatcaatatcttttatgggccctccgttaaa -catcgctgtactcacaaagaaacataaatccaattctataaatattgggaattttactga -tggtaaaattaaaataggaggaggaggttacatcactatcatatggtaacattcccttaa -aaatcatctctttatctttcctaaatattccactgtctttgactgctatacctctctctc -ttttctttcaccaagcctctctctttgctttccttctggtaaaagcagtctctctctctc -tctctctctctctctctctctctctctatccccccctccctccctccttccctccctccc -tctctctctctctctccctttctctgtctctccctctctctctctctctctccctctctc -tctctttctccctctctctccctctctctctctctctctccctctctctctctttctccc -tctctctccctctctccccctctctctccctctctccctctctccctctctctccctctc -tctctacccctgaatctggcctttctaaacaccctcaacttgtgtacctgtatactatac -tgagctacactaaagtttctatatttagccaaatccagcccatcataccagctcttcccc -tggtatattcctaggagtggagctcggttcacgctgtttcacactttccttgggaaacac -tctgtgttcttctgcaaagaggagtaggcaatatgttttcagattcacagacaagcttct ->syndip_2_chr20:45600369-45600946 -caactaggcattccctagtggtgccaaacaatcaatatcttttatgggccctccgttaaa -catcgctgtactcacaaagaaacataaatccaattctataaatattgggaattttactga -tggtaaaattaaaataggaggaggaggttacatcactatcatatggtaacattcccttaa -aaatcatctctttatctttcctaaatattccactgtctttgactgctatacctctctctc -ttttctttcaccaagcctctctctttgctttccttctggtaaaagcagtctctctctctc -tctctctctctctct--ctctctctctatccccccctccctccctccttccctccctccc -tctctctctctctctccctttctctgtctctccctctctctctctctctctccctctctc -t----------------------------------------------------------- ------------------ccctctctccccctctctctccctctctccctctctccctctc -tctctacccctgaatctggcctttctaaacaccctcaacttgtgtacctgtatactatac -tgagctacactaaagtttctatatttagccaaatccagcccatcataccagctcttcccc -tggtatattcctaggagtggagctcggttcacgctgtttcacactttccttgggaaacac -tctgtgttcttctgcaaagaggagtaggcaatatgttttcagattcacagacaagcttct ->p:HG002_1_chr20:45600369-45600946 -caactaggcattccctagtggtgccaaacaatcaatatcttttatgggccctccgttaaa -catcgctgtactcacaaagaaacataaatccaattctataaatattgggaattttactga -tggtaaaattaaaataggaggaggaggttacatcactatcatatggtaacattcccttaa -aaatcatctctttatctttcctaaatattccactgtctttgactgctatacctctctctc -ttttctttcaccaagcctctctctttgctttccttctggtaaaagcagtctctctctctc -tctctctctctctct--ctctctctctatccccccctccctccctccttccctccctccc -tctctctctctctctccctttctctgtctctccctctctctctctctctctccctctctc -t----------------------------------------------------------- ------------------ccctctctccccctctctctccctctctccctctctccctctc -tctctacccctgaatctggcctttctaaacaccctcaacttgtgtacctgtatactatac -tgagctacactaaagtttctatatttagccaaatccagcccatcataccagctcttcccc -tggtatattcctaggagtggagctcggttcacgctgtttcacactttccttgggaaacac -tctgtgttcttctgcaaagaggagtaggcaatatgttttcagattcacagacaagcttct ->p:HG002_2_chr20:45600369-45600946 -caactaggcattccctagtggtgccaaacaatcaatatcttttatgggccctccgttaaa -catcgctgtactcacaaagaaacataaatccaattctataaatattgggaattttactga -tggtaaaattaaaataggaggaggaggttacatcactatcatatggtaacattcccttaa -aaatcatctctttatctttcctaaatattccactgtctttgactgctatacctctctctc -ttttctttcaccaagcctctctctttgctttccttctggtaaaagcagtctctctctctc -tctctctctctctctctctctctctctatccccccctccctccctccttccctccctccc -tctctctctctctctccctttctctgtctctccctctctctctctctctctccctctctc -tctctttctccctctctctccctctctctctctctctctccctctctctctctttctccc -tctctctccctctctccccctctctctccctctctccctctctccctctctctccctctc -tctctacccctgaatctggcctttctaaacaccctcaacttgtgtacctgtatactatac -tgagctacactaaagtttctatatttagccaaatccagcccatcataccagctcttcccc -tggtatattcctaggagtggagctcggttcacgctgtttcacactttccttgggaaacac -tctgtgttcttctgcaaagaggagtaggcaatatgttttcagattcacagacaagcttct ->ref_chr20:45600369-45600946 -caactaggcattccctagtggtgccaaacaatcaatatcttttatgggccctccgttaaa -catcgctgtactcacaaagaaacataaatccaattctataaatattgggaattttactga -tggtaaaattaaaataggaggaggaggttacatcactatcatatggtaacattcccttaa -aaatcatctctttatctttcctaaatattccactgtctttgactgctatacctctctctc -ttttctttcaccaagcctctctctttgctttccttctggtaaaagcagtctctctctctc -tctctctctctctct--------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------ctctatccccccctctccctctc -tctctacccctgaatctggcctttctaaacaccctcaacttgtgtacctgtatactatac -tgagctacactaaagtttctatatttagccaaatccagcccatcataccagctcttcccc -tggtatattcctaggagtggagctcggttcacgctgtttcacactttccttgggaaacac -tctgtgttcttctgcaaagaggagtaggcaatatgttttcagattcacagacaagcttct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_e4c97851db02dffe002380caf62d4e79.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_e4c97851db02dffe002380caf62d4e79.msa deleted file mode 100644 index f81aec9d..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_e4c97851db02dffe002380caf62d4e79.msa +++ /dev/null @@ -1,205 +0,0 @@ ->syndip_1_chr20:56280422-56282114 -aaaatttaaaataactatcaaaaaggtaacatccatatacagatataatatctataacat -atatagatatatggatataacatccatatatagatatatctatatatctatctatagcta -c----------------------------------------------------------- ------atctacagatatctatagccacatctacagatatctatagctacatctacagata -tctacagatatctacagctacatctacagatatctatagatatctatagctatatctaca -gatatctatcgatagatatatctatcgatagatatatccacatagatatctagatatata -tggatatatctatagatatctatctggatatatctatcgatagatatatagatatatata -gataaagctatatagatatatatagataaacctatatagatacatagatatatagagaga -aacctatatacatatatagatatatagagagaaacctatatagatatatagatatataga -gataaacctatatagatgtatagataaacctatatagatatatagataaacctatgtaga -tatatagatatatatagataaatctatatagatatataaaatag---------------- ---------ataaatctatatagatatatatacataaatctatatagatatatatacataa -atctatatatatacataaatctatatatacataaatctatatagatatatatacataaat -ctatatagatatatatacataaatctatatagatatatatacataaatctatatagatat -atatacataaatctatatagatatatatacataaatctatatagatatatacataaatct -atacagatacatatacataaatctatacagatacatatacataaatctatacagatacat -atacataaatctatacagatatatagatacatatagataaatctatacagatatatagat -acatatagataaatctatacagatatatagatacatatagatacatctatacagatatat -agatacatatagatacatctatacagatatatagatacatatagatacatctatacagat -atatagatacatatagatacatctatacagatatatagatacatatagatacatctatac -agatatatagatacatatagatacatctatacagatatatagatacatatagatacatct -atacagatatattgatacatatagatacatctatatagatatattgatacatatagatac -atctatatagatatattgatacatatagatacatctatatagatatattgatacatatag -atacatctatatagattagatatatatagatacatctatatagattagatatatatagat -acatctatatagattagatatatatagatacatctatatatagatatatagatatatata -gatacatctatatatagatatatagatatatatagatacatctatatatagatatataga -tgtatatagatacatctatatatagatatatagatgtatatagatacatctatatataga -tatatagatgtatatagatacatctatatatagatatatagatgtatatagatacatcta -tatatagatatatagatgtatatagatacatctatat--atagatatatagatgtatata -gatacatctatatatagatatatagatgtatatagatacatctatatatagatatataga -tgtatatagatacatctatatatagatatatagatgtatatagatacatctatatataga -tatatagatgtatatagatacatagatatatatagatacatttatgtatatatatatgta -tatatagatatatagatatatatagatacatctacacagagagatatatagaaacatcta -cacagggagatatatagatacatctacatagagagatatatagatacatctacatagaga -gatatatagatacatctacatagagagatatatagatacatctacatagagagatatata -gatacatctacatagagagatatatagatacatctacatagagagatatatagatacatc -tacatagagagatatatagatacatctacatagagagatatatagatacatctacataga -gagatatatagatacatctacatagagagatatatagatacatctacatagagagatata -tagatacatctacatagagatatatatagatacatctacatagagatatatatagataca -tctatatagagatatatctacctatacttcctgtgagttgtgtttctctg ->syndip_2_chr20:56280422-56282114 -aaaatttaaaataactatcaaaaaggtaacatccatatacagatataatatctataacat -atatagatatatggatataacatccatatatagatatatctatatatctatctatagcta -catctacagatatctatagctacatctacagatatctacagatatctatagctacatcta -cagatatctacagatatctatagctacatctacagatatctatagctacatctacagata -tctacagatatctacagctacatctacagatatctatagatatctatagctatatctaca -gatatctatcgatagatatatctatcgatagatatatccacatagatatctagatatata -tggatatatctatagatatctatctggatatatctatcgatagatatatagatatatata -gataaagctatatagatatatatagataaacctatatagatacatagatatatagagaga -aacctatatacatatatagatatatagagagaaacctatatagatatatagatatataga -gataaacctatatagatgtatagataaacctatatagatatatagataaacctatgtaga -tatatagatatatatagataaatctatatagatatataaaatag---------------- ---------ataaatctatatagatatatatacataaatctatatagatatatatacataa -atctatatatatacataaatctatatatacataaatctatatagatatatatacataaat -ctatatagatatatatacataaatctatatagatatatatacataaatctatatag---- -----------------------atatatacataaatctatat--atatatacataaatct -atatagatatatatacataaatctatatagatacatatagataaatctatacaga----- --------------------tatataaatatatatagataaatctatacagatatatagat -acatatagataaatctatacagatatatagatacatatagataaatctatacagatatat -agatacatatagataaatctatacagatatatagatacatatagataaatctatacagat -atatagatacatatagataaatctatacagatatatagatacatatagataaatctatac -agatatatagatacatatagataaatctatacagatatatagatacatatagataaatct -atacagatatatagatacatatagatacatctatatagatatattgatacatatagatac -atctatatagatatatagat--atatagatacatctata--------------------- ------------------------------------------------------------- ---------------tagatatatatagatacatctatatatagacatatagatatatata -gatacatctatatatagatatatagatatatatagatacatctatatatagatatataga -tatatatagatacatctacacagag------agatatatagaaacatctacacagggaga -tatatagatacatctacatagagagatatatagatacatctacatagagagatatataga -tacatctatatagagagatatatagatacatctatatagagagatatatagatacatcta -catagagagatatatagatacatctacatagagagatatatagatacatctacatagaga -tatatatagatacatctacatagagata--------tatatagatacatctatatagaga -tatatctacctata---------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------cttcctgtgagttgtgtttctctg ->p:HG002_1_chr20:56280422-56282114 -aaaatttaaaataactatcaaaaaggtaacatccatatacagatataatatctataacat -atatagatatatggatataacatccatatatagatatatctatatatctatctatagcta -catctacagatatctatagctacatctacagatatctacagatatctatagctacatcta -cagatatctacagatatctatagctacatctacagatatctatagctacatctacagata -tctacagatatctacagctacatctacagatatctatagatatctatagctatatctaca -gatatctatcgatagatatatctatcgatagatatatccacatagatatctagatatata -tggatatatctatagatatctatctggatatatctatcgatagatatatagatatatata -gataaagctatatagatatatatagataaacctatatagatacatagatatatagagaga -aacctatatacatatatagatatatagagagaaacctatatagatatatagatatataga -gataaacctatatagatgtatagataaacctatatagatatatagataaacctatgtaga -tatatagatatatatagataaatctatatagatatataaaatag---------------- ---------ataaatctatatagatatatatacataaatctatatagatatatatacataa -atctatatatatacataaatctatatatacataaatctatatagatatatatacataaat -ctatatagatatatatacataaatctatatagatatatatacataaatctatatag---- -----------------------atatatacataaatctatat--atatatacataaatct -atatagatatatatacataaatctatatagatacatatagataaatctatacaga----- --------------------tatataaatatatatagataaatctatacagatatatagat -acatatagataaatctatacagatatatagatacatatagataaatctatacagatatat -agatacatatagataaatctatacagatatatagatacatatagataaatctatacagat -atatagatacatatagataaatctatacagatatatagatacatatagataaatctatac -agatatatagatacatatagataaatctatacagatatatagatacatatagataaatct -atacagatatatagatacatatagatacatctatatagatatattgatacatatagatac -atctatatagatatatagat--atatagatacatctata--------------------- ------------------------------------------------------------- ---------------tagatatatatagatacatctatatatagacatatagatatatata -gatacatctatatatagatatatagatatatatagatacatctatatatagatatataga -tatatatagatacatctacacagag------agatatatagaaacatctacacagggaga -tatatagatacatctacatagagagatatatagatacatctacatagagagatatataga -tacatctatatagagagatatatagatacatctatatagagagatatatagatacatcta -catagagagatatatagatacatctacatagagagatatatagatacatctacatagaga -tatatatagatacatctacatagagata--------tatatagatacatctatatagaga -tatatctacctata---------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------cttcctgtgagttgtgtttctctg ->p:HG002_2_chr20:56280422-56282114 -aaaatttaaaataactatcaaaaaggtaacatccatatacagatataatatctataacat -atatagatatatggatataacatccatatatagatatatctatatatctatctatagcta -c----------------------------------------------------------- ------atctacagatatctatagccacatctacagatatctatagctacatctacagata -tctacagatatctacagctacatctacagatatctatagatatctatagctatatctaca -gatatctatcgatagatatatctatcgatagatatatccacatagatatctagatatata -tggatatatctatagatatctatctggatatatctatcgatagatatatagatatatata -gataaagctatatagatatatatagataaacctatatagatacatagatatatagagaga -aacctatatacatatatagatatatagagagaaacctatatagatatatagatatataga -gataaacctatatagatgtatagataaacctatatagatatatagataaacctatgtaga -tatatagatatatatagataaatctatatagatatataaaatag---------------- ---------ataaatctatatagatatatatacataaatctatatagatatatatacataa -atctatatatatacataaatctatatatacataaatctatatagatatatatacataaat -ctatatagatatatatacataaatctatatagatatatatacataaatctatatagatat -atatacataaatctatatagatatatatacataaatctatatagatatatacataaatct -atacagatacatatacataaatctatacagatacatatacataaatctatacagatacat -atacataaatctatacagatatatagatacatatagataaatctatacagatatatagat -acatatagataaatctatacagatatatagatacatatagatacatctatacagatatat -agatacatatagatacatctatacagatatatagatacatatagatacatctatacagat -atatagatacatatagatacatctatacagatatatagatacatatagatacatctatac -agatatatagatacatatagatacatctatacagatatatagatacatatagatacatct -atacagatatattgatacatatagatacatctatatagatatattgatacatatagatac -atctatatagatatattgatacatatagatacatctatatagatatattgatacatatag -atacatctatatagattagatatatatagatacatctatatagattagatatatatagat -acatctatatagattagatatatatagatacatctatatatagatatatagatatatata -gatacatctatatatagatatatagatatatatagatacatctatatatagatatataga -tgtatatagatacatctatatatagatatatagatgtatatagatacatctatatataga -tatatagatgtatatagatacatctatatatagatatatagatgtatatagatacatcta -tatatagatatatagatgtatatagatacatctatat--atagatatatagatgtatata -gatacatctatatatagatatatagatgtatatagatacatctatatatagatatataga -tgtatatagatacatctatatatagatatatagatgtatatagatacatctatatataga -tatatagatgtatatagatacatagatatatatagatacatttatgtatatatatatgta -tatatagatatatagatatatatagatacatctacacagagagatatatagaaacatcta -cacagggagatatatagatacatctacatagagagatatatagatacatctacatagaga -gatatatagatacatctacatagagagatatatagatacatctacatagagagatatata -gatacatctacatagagagatatatagatacatctacatagagagatatatagatacatc -tacatagagagatatatagatacatctacatagagagatatatagatacatctacataga -gagatatatagatacatctacatagagagatatatagatacatctacatagagagatata -tagatacatctacatagagatatatatagatacatctacatagagatatatatagataca -tctatatagagatatatctacctatacttcctgtgagttgtgtttctctg ->ref_chr20:56280422-56282114 -aaaatttaaaataactatcaaaaaggtaacatccatatacagatataatatctataacat -atatagatatatggatataacatccatatatagatatatctatatatctatctatagcta -c--------------------------------atctacagatatctatagctacatcta -cagatatctacagatatctatagctacatctacagatatctatagctacatctacagata -tctacagatatctacagctacatctacagatatctatagatatctatagctatatctaca -gatatctatcgatagatatatctatcgatagatatatccacatagatatctagatatata -tggatatatctatagatatctatctggatatatctatcgatagatatatagatatatata -gataaagctatatagatatatatagataaacctatatagatacatagatatatagagaga -aacctatatacatatatagatatatagagagaaacctatatagatatatagatatataga -gagaaacctatatagatgtatagataaacctatatagatatatagataaacctatgtaga -tatatagatatatatagataaatctatatagatatataaaatagataaatctatatagat -atatatacataaatctatatagatatatatacataaatctatatagatatatatacataa -atctatatatatacataaatctatatatacataaatctatatagatatatatacataaat -ctatatagatatatatacataaatctatatagatatatatacataaatctatatag---- ---------------------atatatatacataaatctatatagatatatacataaatct -atatagatatatatacataaatctatatagatatatatacataaatctatatagatatat -atacataaatc--------tatatagatacatatagataaatctatacagatatatagat -acatatagataaatctatacagatatatagatacatatagataaatctatacagatatat -agatacatatagataaatctatacagatatatagatacatatagataaatctatacagat -atatagatacatatagataaatctatacagatatatagatacatatagataaatctatac -agatatatagatacatatagatacatctatacagatatatagatacatatagatacatct -atacagatatatagatacatatagatacatctatacagatatattgatacatatagatac -atctatatagatatatagat--atatagatacatctata--------------------- ------------------------------------------------------------- ---------------tagatatatagatata----tagatacatctatatagatatatata -gatacatctatatatagacatatagatatatatagatacatctatatatagatatataga -tatatatagatacatctacacagag------agatatatagaaacatctacacagggaga -tatatagatacatctacacagagagatatatagatacatctac----------------- ----------atagagagatatatagatacatctacatagagagatatatagatacatcta -catagagagatatatagatacatctacatagagagatatatagatacatctacatagaga -tatatatagatacatctacatagagata--------tatatagatacatctatatagaga -tatatctacctata---------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------cttcctgtgagttgtgtttctctg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_e561cd35a9c0baa7a6bc82299c357dd6.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_e561cd35a9c0baa7a6bc82299c357dd6.msa deleted file mode 100644 index 365f5835..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_e561cd35a9c0baa7a6bc82299c357dd6.msa +++ /dev/null @@ -1,70 +0,0 @@ ->syndip_1_chr20:24681788-24682477 -tgtcggacgctcacagggccctcaagcagtagccatcccatgggataatcagagacccca -gagtttggaatacagggcccaggaggctgcgtccccgagactctgctgctggggtgtact -cgatgtcctggctcgactgacacagtcctgatcttgccagttggtgtctgtggacctgtg -ttttggcatggacaggcacaaggctaaggaggtcagcatgcagcaggaggcaaactgtga -agtacctctctggc---------------------------------------------- -------------ctggcctttgtgaattaccacagtgc---------------------- -------------------------------------ggggtccacccaggaaactgtgaa -gtacctctctgggcgttgtgaattaccacagttaggggtttacccaggaaactgtgaagt -atctctctggcctttgtgaatcaccacagttaggggtctatgcaggagtactggtcattc -acagactcagctcattccaggccttagcagtgtgcacctcagagtgaagcagagaggccc -caggagaagccatggccacgccctcaacctcctgctccgaggaggagacgtgtggcttca -aggggtgctcaaggcctggacttgttccctcagggcatgagtctggggcctcctcagggc -atcggtcgggggcagtgtctgcacatgg ->syndip_2_chr20:24681788-24682477 -tgtcggacgctcacagggccctcaagcagtagccatcccatgggataatcagagacccca -gagtttggaatacagggcccaggaggctgcgtccccgagactctgctgctggggtgtact -cgatgtcctggctcgactgacacagtcctgatcttgccagttggtgtctgtggacctgtg -ttttggcatggacaggcacaaggctaaggaggtcagcatgcagcaggaggcaaactgtga -agtacctctctggcctggcctttgtgaattaccacagtcaggggtctacccaggaaactg -tgaagtacctctctggcctttgtgaattaccacagtcaggggtccacccaggaaactgtg -aagtacctctctggcctttgtgaattaccacagtcaggggtccacccaggaaactgtgaa -gtacctctctgggcgttgtgaattaccacagttaggggtttacccaggaaactgtgaagt -atctctctggcctttgtgaatcaccacagttaggggtctatgcaggagtactggtcattc -acagactcagctcattccaggccttagcagtgtgcacctcagagtgaagcagagaggccc -caggagaagccatggccacgccctcaacctcctgctccgaggaggagacgtgtggcttca -aggggtgctcaaggcctggacttgttccctcagggcatgagtctggggcctcctcagggc -atcggtcgggggcagtgtctgcacatgg ->p:HG002_1_chr20:24681788-24682477 -tgtcggacgctcacagggccctcaagcagtagccatcccatgggataatcagagacccca -gagtttggaatacagggcccaggaggctgcgtccccgagactctgctgctggggtgtact -cgatgtcctggctcgactgacacagtcctgatcttgccagttggtgtctgtggacctgtg -ttttggcatggacaggcacaaggctaaggaggtcagcatgcagcaggaggcaaactgtga -agtacctctctggcctggcctttgtgaattaccacagtcaggggtccacccaggaaactg -tgaagtacctctctggcctttgtgaattaccacagtcaggggtccacccaggaaactgtg -aagtacctctctggcctttgtgaattaccacagtcaggggtccacccaggaaactgtgaa -gtacctctctgggcgttgtgaattaccacagttaggggtttacccaggaaactgtgaagt -atctctctggcctttgtgaatcaccacagttaggggtctatgcaggagtactggtcattc -acagactcagctcattccaggccttagcagtgtgcacctcagagtgaagcagagaggccc -caggagaagccatggccacgccctcaacctcctgctccgaggaggagacgtgtggcttca -aggggtgctcaaggcctggacttgttccctcagggcatgagtctggggcctcctcagggc -atcggtcgggggcagtgtctgcacatgg ->p:HG002_2_chr20:24681788-24682477 -tgtcggacgctcacagggccctcaagcagtagccatcccatgggataatcagagacccca -gagtttggagtacagggcccaggaggctgcgtccccgagactctgctgctggggtgtact -cgatgtcctggctcgactgacacagtcctgatcttgccagttggtgtctgtggacctgtg -ttttggcatggacaggcacaaggctaaggaggtcagcatgcagcaggaggcaaactgtga -agtacctctctggc---------------------------------------------- -------------ctggcctttgtgaattaccacagtgc---------------------- -------------------------------------ggggtccacccaggaaactgtgaa -gtacctctctgggcgttgtgaattaccacagttaggggtttacccaggaaactgtgaagt -atctctctggcctttgtgaatcaccacagttaggggtctatgcaggagtactggtcattc -acagactcagctcattccaggccttagcagtgtgcacctcagagtgaagcagagaggccc -caggagaagccatggccacgccctcaacctcctgctctgaggaggagacgtgtggcttca -aggggtgctcaaggcctggacttgttccctcagggcatgagtctggggcctcctcagggc -atcggtcgggggcagtgtctgcacatgg ->ref_chr20:24681788-24682477 -tgtcggacgctcacagggccctcaagcagtagccatcccatgggataatcagagacccca -gagtttggaatacagggcccaggaggctgcgtccccgagactctgctgctggggtgtact -cgatgtcctggctcgactgacacagtcctgatcttgccagttggtgtctgtggacctgtg -ttttggcatggacaggcacaaggctaaggaggtcagcatgcagcaggaggcaaactgtga -agtacctctctggc---------------------------------------------- -------------ctggcctttgtgaattaccacagtgcggggtccacccaggaaactgtg -aagtacctctgtggcctttgtgaattaccacagtcaggggtccacccaggaaactgtgaa -gtacctctctgggcgttgtgaattaccacagttaggggtttacccaggaaactgtgaagt -atctctctggcctttgtgaatcaccacagttaggggtctatgcaggagtactggtcattc -acagactcagctcattccaggccttagcagtgtgcacctcagagtgaagcagagaggccc -caggagaagccatggccacgccctcaacctcctgctccgaggaggagacgtgtggcttca -aggggtgctcaaggcctggacttgttccctcagggcatgagtctggggcctcctcagggc -atcggtcgggggcagtgtctgcacatgg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_e58988b4a4cd0e0f7c0d5df1b61a5eb9.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_e58988b4a4cd0e0f7c0d5df1b61a5eb9.msa deleted file mode 100644 index b0d189e7..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_e58988b4a4cd0e0f7c0d5df1b61a5eb9.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:13848164-13848649 -tgggggacagagggaaattgcgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacga -agatgaagaagaataagaagagagaaaagaagaagagaaggttagagaaaagaagagaag -gagaaggagaaggaggaggagaaggagaaggagaagaagaagaagaagaagaagaagaag -aagaagaagaagaagaagaagaagaagaagaagaagaagtcaaatatctggagaagaaga -agaagaagaggaagaagaagaagaggaagaagaagaagaagaggaagaggaagaaagaag -aagaacaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaggaaga -agaagaagaagaggaggaggaagaagaagaagaagaagaagaagaagaagcaggagcagg -agaagaagaagaagaagaagaagaagaggaagaggaagaggaagaggaagaagaagaaga -agaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaaga -agaagaagaagaagagaagacaaatatctggagccgggatttgagc ->syndip_2_chr20:13848164-13848649 -tgggggacagagggaaattgcgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacga -agatgaagaagaataagaagagagaaaagaagaagagaaggttagagaaaagaagagaag -gagaaggagaaggaggaggagaaggagaaggagaagaagaagaagaagaagaagaagaag -aagaagaagaagaagaagaagaagaagaagaagaagaagtcaaatatctggagaagaaga -agaagaagaggaagaagaagaagaggaagaagaagaagaagaggaagaggaagaaagaag -aagaacaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaggaaga -agaagaagaagaggaggaggaagaagaagaagaagaagaagaagaagaagcaggagcagg -agaagaagaagaagaagaagaagaagaggaagaggaagaggaagag-------------- --gaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaaga -agaagaagaagaagagaagacaaatatctggagccgggatttgagc ->p:HG002_1_chr20:13848164-13848649 -tgggggacagagggaaattgcgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacga -agatgaagaagaataagaagagagaaaagaagaagagaaggttagagaaaagaagagaag -gagaaggagaaggaggaggagaaggagaaggagaagaagaagaagaagaagaagaagaag -aagaagaagaagaagaagaagaagaagaagaagaagaagtcaaatatctggagaagaaga -agaagaagaggaagaagaagaagaggaagaagaagaagaagaggaagaggaagaaagaag -aagaacaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaggaaga -agaagaagaagaggaggaggaagaagaagaagaagaagaagaagaagaagcaggagcagg -agaagaagaagaagaagaagaagaagaggaagaggaagaggaagag-------------- --gaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaaga -agaagaagaagaagagaagacaaatatctggagccgggatttgagc ->p:HG002_2_chr20:13848164-13848649 -tgggggacagagggaaattgcgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacga -agatgaagaagaataagaagagagaaaagaagaagagaaggttagagaaaagaagagaag -gagaaggagaaggaggaggagaaggagaaggagaagaagaagaagaagaagaagaagaag -aagaagaagaagaagaagaagaagaagaagaagaagaagtcaaatatctggagaagaaga -agaagaagaggaagaagaagaagaggaagaagaagaagaagaggaagaggaagaaagaag -aagaacaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaggaaga -agaagaagaagaggaggaggaagaagaagaagaagaagaagaagaagaagcaggagcagg -agaagaagaagaagaagaagaagaagaggaagaggaagaggaagaggaagaagaagaaga -agaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaaga -agaagaagaagaagagaagacaaatatctggagccgggatttgagc ->ref_chr20:13848164-13848649 -tgggggacagagggaaattgcgtctcaaaaaaaaaaaagaagaagaaaagtagaagacga -agatgaagaagaataagaagagagaaaagaagaagagaaggttagagaaaagaagagaa- -------------------------gagaaggagaaggagaaggaggaggagaaggagaag -gagaagaagaagaagaagaagaagaagaagaagaagaagtcaaatatctgg---agaaga -agaagaagaggaagaagaagaaaaggaagaagaagaagaagaggaagaggaagaaagaag -aagaacaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaaga -agaagaagaggaggaggaagaaggagaaggagaaggagaaggagaagga----------- ------------------------------------------------------------- --gaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaaga -agaagaagaagaagaaaatacaaatatctggagccgggatttgagc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_e5c29704e745bf1432e1c17b5cccc7f5.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_e5c29704e745bf1432e1c17b5cccc7f5.msa deleted file mode 100644 index c06ddbe7..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_e5c29704e745bf1432e1c17b5cccc7f5.msa +++ /dev/null @@ -1,50 +0,0 @@ ->syndip_1_chr20:63027997-63028166 -tgttccctgtgaagagtgaagaaccaacgcgggcggggagtggaccggtggggagagggc -cggtggggagagggccggtggggagaggaccggtggggagggggccggtggagagggggc -cggtggggagggggccggtggggagaggaccggtggggagggg---------------cc -ggtggggagggggccggtggggagaggaccggtgggga-ggggccggtggggagggggcc -ggtggggagaggaccggtgggga-ggggccggtggggagggggccggcggggagggggcc -ggcggggagggtgccggtggggagtggtctggtggggagggggccggtggggagggggcc -cgcggggaggggccggtggggagggggcctgcggggagggggccggcggggaggggccgg -tggggaggggccggtggggtggggccggtggggagggggccggtgggggggggcctgcag -ggagggggccggtggggaggaggctggtgaagtagcgtcaggtgc ->syndip_2_chr20:63027997-63028166 -tgttccctgtgaagagtgaagaaccaacgcgggcggggagtggaccggtggggagagggc -cggtggggagaggaccggtggggag-gggccggtggagagggggccggtggggagggggc -cggcggggagtggtttggtggggagggggccggtggggagggggcctgcggggaggggcc -ggtggggagggggccggtggggagggggccggcggggagggggccggcggggagggggcc -ggcggggagtggtctggtggggagggggccggtggggagggggccggcggggagggggcc -ggcggggaggg-gccggtggggagtggtctggtggggagggggccggtggggaggaggct -ggtgaagtagcgtcag-------------------------------------------- ------------------------------------------------------------- ------------------------------------------gtgc ->p:HG002_1_chr20:63027997-63028166 -tgttccctgtgaagagtgaagaaccaacgcgggcggggagtggaccggtggggagagggc -cggtggggagaggaccggtggggag-gggccggtggagagggggccggtggggagggggc -cggcggggagtggtttggtggggagggggccggtggggagggggcctgcggggaggggcc -ggtggggagggggccggtggggagggggccggcggggagggggccggcggggagggggcc -ggcggggagtggtctggtggggagggggccggtggggagggggccggcggggagggggcc -ggcggggaggg-gccggtggggagtggtctggtggggagggggccggtggggaggaggct -ggtgaagtagcgtcag-------------------------------------------- ------------------------------------------------------------- ------------------------------------------gtgc ->p:HG002_2_chr20:63027997-63028166 -tgttccctgtgaagagtgaagaaccaacgcgggcggggagtggaccggtggggagagggc -cggtggggagagggccggtggggagaggaccggtggggagggggccggtggagagggggc -cggtggggagggggccggtggggagaggaccggtggggagggg---------------cc -ggtggggagggggccggtggggagaggaccggtgggga-ggggccggtggggagggggcc -ggtggggagaggaccggtgggga-ggggccggtggggagggggccggcggggagggggcc -ggcggggagggtgccggtggggagtggtctggtggggagggggccggtggggagggggcc -cgcggggaggggccggtggggagggggcctgcggggagggggccggcggggaggggccgg -tggggaggggccggtggggtggggccggtggggagggggccggtgggggggggcctgcag -ggagggggccggtggggaggaggctggtgaagtagcgtcaggtgc ->ref_chr20:63027997-63028166 -tgttccctgtgaagagtgaagaaccaacgcgggcggggagtggaccggtggggagagggc -cggtggggagaggaccggtggggag-gggccggtggagagggggccggtggggagggggc -cggcggggagtggtttggtggggaggaggctggtgaagtagcgtcaggtgc--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_e6f9cd298d13f4ee45a91c7ce72023a5.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_e6f9cd298d13f4ee45a91c7ce72023a5.msa deleted file mode 100644 index 31014860..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_e6f9cd298d13f4ee45a91c7ce72023a5.msa +++ /dev/null @@ -1,165 +0,0 @@ ->syndip_1_chr20:20320129-20320729 -aatggaggggggcctatgaattagcatagtttttaaaaacatatcaccctatttggatcc -tgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaatttga -aacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaagatggt -atttcagatatatagatatatatatattatatatatgtaatatatataatatatgtaata -tatattatatatatgtaatatatataatatatgtaatatattatatatatgtaatatata -taatatatgtaatatatattatatatgtaatatatataatatatgtaatatatattatat -atgtaatata----atatatgtaatatatattatatatgtaatatataatatatgtaata -tatattatatatgtaatataatatatgtaatatatattatatatgtaatatatattacat -atattatatatgcaatatatattatatatattatatatgcaatatatattatatatatta -tatatgcaatatatattatatatgcaatatatattatatatattatatatgcaatatata -ttatatatattacatatgtaatatatattacatatgtaatatataatatattatatatta -catatgtaatatataatatattatatattacatatgtaatatataatatatattacatat -gtaatatataatatatattacatatgtaatatattatatattacatatgtaatatattat -atattacatatgtaatatattatatattacatatgtaatatattatatattacatatgta -atatattatatattacatatgtaatatatataatatattacatatgtaatatataatata -ttatatatgtaatatatattacatatataatatatataatatatatgtaatatattatat -atattatatatgtaatatatattacatatataatatatattatatatattacatatatta -tatatgtaatatatattacatatgtaatatatgtaatatatattacatatgtaatatata -ttatatatgtaatatatattacatatattatatatgtaatatatattatatatattatat -atgtaatgtataatatatatattatatatgtaatatatattatatataatatatgtaata -tatattatatatgtaatgtatattatatatattatatatgtaatgtatattatatataat -atatgtaatgtatattatatatgtaatatatattatgtatattatatatgtaatatatat -tatatatattatatatgtaatatatattatatatattatatatgtaatatatattatata -tattatatatgtaatatatattatatatattatatatgtaatatatattatatatattat -atatgtaatatatattatatatattatatatgtaatatatattatatatattatatatgt -aatatatattatatatattatatatgtaatatatattatatatattatatatgtaatata -tattatatatattatatatgtaatatatattatatatattatatatgtaatatatattat -atatattatatatgtaatatatattatatatattatatatgtaatatatattatatatat -tatatatgtaatatatatatatttaaaaacagaaccattatcttttagagatacatactg -aagtgtctggagacatgcttcaagataacccaggagggagaatggtagaaggaactagag -atgacccaagactgcccttgagctaataactgttttaattgggtaatggatgatgggagc -tcattataggtatatttctaac ->syndip_2_chr20:20320129-20320729 -aatggaggggggcctatgaattagcatagtttttaaaaacatatcaccctatttggatcc -tgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaatttga -aacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaagatggt -atttcagatatatagatatatatatattatatatatgtaatatatataatatatgtaata -tata---------------------------ttatatatatgtaatatatataatatatg -taatatatgtaatatatattatatatgta----atataatatatgtaatatatattatat -atgtaatatata--------------------atatatgtaatatataatatatgtaata -tatattatatatgtaatata-------taatatatattatatatgtaatatatatatatt -taaaaacagaaccattatcttttagagatac----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------atactg -aagtgtctggagacatgcttcaagataacccaggagggagaatggtagaaggaactagag -atgacccaagactgcccttgagctaataactgttttaattgggtaatggatgatgggagc -tcattataggtatatttctaac ->p:HG002_1_chr20:20320129-20320729 -aatggaggggggcctatgaattagcatagtttttaaaaacatatcaccctatttggatcc -tgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaatttga -aacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaagatggt -atttcagatatatagatatatatatattatatatatgtaatatatataatatatgtaata -tata---------------------------ttatatatatgtaatatatataatatatg -taatatatgtaatatatattatatatgta----atataatatatgtaatatatattatat -atgtaatatata--------------------atatatgtaatatataatatatgtaata -tatattatatatgtaatata-------taatatatattatatatgtaatatatatatatt -taaaaacagaaccattatcttttagagatac----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------atactg -aagtgtctggagacatgcttcaagataacccaggagggagaatggtagaaggaactagag -atgacccaagactgcccttgagctaataactgttttaattgggtaatggatgatgggagc -tcattataggtatatttctaac ->p:HG002_2_chr20:20320129-20320729 -aatggaggggggcctatgaattagcatagtttttaaaaacatatcaccctatttggatcc -tgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaatttga -aacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaagatggt -atttcagatatatagatatatatatat--tatatatgtaatatatataatatatgtaata -tgta--atatatataatatatgtaatatatattatatatatgtaatatatataatatatg -taatatatgtaatatatattatatatgta----atataatatatgtaatatatattatat -atgtaatatataatatatgtaatatatatattatatatgtaatatataatatatgtaata -tatattatatatgtaatataatatatgtaatatatattatatatgtaatatatattacat -atattatatatgcaatatatattatatatattatatatgcaatatatattatatatatta -tatatgcaatatatattatatatgcaatatatattatatatattatatatgcaatatata -ttatatatattacatatgtaatatatattacatatgtaatatataatatattatatatta -catatgtaatatataatatattatatattacatatgtaatatataatatatattacatat -gtaatatataatatatattacatatgtaatatattatatattacatatgtaatatattat -atattacatatgtaatatattatatattacatatgtaatatattatatattacatatgta -atatattatatattacatatgtaatatatataatatattacatatgtaatatataatata -ttatatatgtaatatatattacatatataatatatataatatatatgtaatatattatat -atattatatatgtaatatatattacatatataatatatattatatatattacatatatta -tatatgtaatatatattacatatgtaatatatgtaatatatattacatatgtaatatata -ttatatatgtaatatatattacatatattatatatgtaatatatattatatatattatat -atgtaatgtataatatatatattatatatgtaatatatattatatataatatatgtaata -tatattatatatgtaatgtatattatatatattatatatgtaatgtatattatatataat -atatgtaatgtatattatatatgtaatatatattatgtatattatatatgtaatatatat -tatatatattatatatgtaatatatattatatatattatatatgtaatatatattatata -tattatatatgtaatatatattatatatattatatatgtaatatatattatatatattat -atatgtaatatatattatatatattatatatgtaatatatattatatatattatatatgt -aatatatattatatatattatatatgtaatatatattatatatattatatatgtaatata -tattatatatattatatatgtaatatatattatatatattatatatgtaatatatattat -atatattatatatgtaatatatatgtaatatatattatatatgtaatatataatatatat -tatatatgtaatatatatatatttaaaaacagaaccattatcttttagagatacatactg -aagtgtctggagacatgcttcaagataacccaggagggagaatggtagaaggaactagag -atgacccaagactgcccttgagctaataactgttttaattgggtaatggatgatgggagc -tcattataggtatatttctaac ->ref_chr20:20320129-20320729 -aatggaggggggcctatgaattagcatagtttttaaaaacatatcaccctatttggatcc -tgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaatttga -aacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaagatggt -atttcagatatatagatatatatatattatatatatgtaatatatataatatatgtaata -tata---------------------------ttatatatatgtaatatatataatatatg -taatatatgtaatatatattatatatgta----atataatatatgtaatatatattatat -atgtaatatata--------------------atatatgtaatatataatatatgtaata -tatattatatatgtaatata-------taatatatattatatatgtaatatatatatatt -taaaaacagaaccattatcttttagagatac----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------atactg -aagtgtctggagacatgcttcaagataacccaggagggagaatggtagaaggaactagag -atgacccaagactgcccttgagctaataactgttttaattgggtaatggatgatgggagc -tcattataggtatatttctaac diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_e82174c474aa4624f7a1c120a21eed8b.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_e82174c474aa4624f7a1c120a21eed8b.msa deleted file mode 100644 index ab67c51b..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_e82174c474aa4624f7a1c120a21eed8b.msa +++ /dev/null @@ -1,75 +0,0 @@ ->syndip_1_chr20:63221480-63221876 -gtgagcgtgccttgctcatcgcagtagcttc----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------------gg -actgcagggactgcagggattgcagggactgcagggattgcagggactgcagggattgca -gggattgcagggattgcagggattgcagggactgcagggactgcattgctcttgcagcac -cacccgcctccgtggacaccttcagcagtgagacaatgcaggctctgctacaagaggtgc -ttactgggctctgctctggtgaggagaggcctcgcctggc ->syndip_2_chr20:63221480-63221876 -gtgagcgtgccttgctcatcgcagtagcttcggactgcagggattgcagggactgcaggg -attgcagggattgcagggagtgcagggactgcagggactgcagggattgcagggactgca -gggactgcagggactgcagggactgcagggactgcagggactgcagggattgcagggact -gcagggactgcagggattgcagggattgcagggactgcagggactgcagggattgcaggg -actgcagggactgcagggactgcagggactgcagggactgcagggactgcagggattgca -gggattgcagggattgcagggattgcagggactgcagggactgcagggactgcagggact -gcagggactgcagggactgcagggattgcagggattgcagggattgcagggattgcaggg -attgcagggactgcagggactgcagggactgcagggactgcagggattgcagggattgca -gggattgcagggattgcagggactgcagggactgcagggattgcagggattgcagggatt -gcagggattgcagggattgcagggattgcagggactgcagggactgcagggactgcaggg -attgcagggattgcagggattgcagggattgcagggactgcagggactgcagggattgca -gggattgcagggattgcagggattgcagggactgcagggcctgcattgctcttgcagcac -cacccgcctccgtggacaccttcagcagtgagacaatgcaggctctgctacaagaggtgc -ttactgggctctgctctggtgaggagaggcctcgcctggc ->p:HG002_1_chr20:63221480-63221876 -gtgagcgtgccttgctcatcgcagtagcttcggactgcagggattgcagggactgcaggg -attgcagggattgcagggagtgcagggactgcagggactgcagggattgcagggactgca -gggactgcagggactgcagggactgcagggactgcagggactgcagggattgcagggact -gcagggactgcagggattgcagggattgcagggactgcagggactgcagggattgcaggg -actgcagggactgcagggactgcagggactgcagggactgcagggactgcagggattgca -gggattgcagggattgcagggattgcagggactgcagggactgcagggactgcagggact -gcagggactgcagggactgcagggattgcagggattgcagggattgcagggattgcaggg -attgcagggactgcagggactgcagggactgcagggactgcagggattgcagggattgca -gggattgcagggattgcagggactgcagggactgcagggattgcagggattgcagggatt -gcagggattgcagggattgcagggattgcagggactgcagggactgcagggactgcaggg -attgcagggattgcagggattgcagggattgcagggactgcagggactgcagggattgca -gggattgcagggattgcagggattgcagggactgcagggcctgcattgctcttgcagcac -cacccgcctccgtggccaccttcagcagtgagacaatgcaggctctgctacaagaggtgc -ttactgggctctgctctggtgaggagaggcctcgcctggc ->p:HG002_2_chr20:63221480-63221876 -gtgagcgtgccttgctcatcgcagtagcttc----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------------gg -actgcagggactgcagggattgcagggactgcagggattgcagggactgcagggattgca -gggattgcagggattgcagggattgcagggactgcagggactgcattgctcttgcagcac -cacccgcctccgtggccaccttcagcagtgagacaatgcaggctctgctacaagaggtgc -ttactgggctctgctctggtgaggagaggcctcgcctggc ->ref_chr20:63221480-63221876 -gtgagcgtgccttgctcatcgcagtagcttc----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------ggactgcagggattgcagggactgca -gggattgcagggattgcagggattgcagggactgcagggattgcagggactgcagggact -gcagggactgcagggactgcagggactgcagggattgcagggattgcagggattgcaggg -actgcagggattgcagggactgcagggactgcagggattgcagggactgcagggactgca -gggactgcagggattgcagggattgcagggactgcagggactgcattgctcttgcagcac -cacccgcctccgtggacaccttcagcagtgagacaatgcaggctctgctacaagaggtgc -ttactgggctctgctctggtgaggagaggcctcgcctggc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_e89731d3c39c6c9c40860a9bcd465472.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_e89731d3c39c6c9c40860a9bcd465472.msa deleted file mode 100644 index ac83f8a5..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_e89731d3c39c6c9c40860a9bcd465472.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:60702795-60703297 -tttttatttctcttggttaaatacctaggagtggaactgccaggtcatatggtaactgca -tgttgactcttttgaggagcttccagactgtttttcaaagtgatggcacaattttccttt -cccctcaataatgtatgagggttgcaatgtcgctacatattaccaacatttgtcattgtc -tttctttcttttctttctctctctctctttcttttccttctttctttctttctttctttc -tttctttctttctttctttctttctttctttcttttctttccttcttctttctttctttc -tttctttctttctttctttctttctttctttctttctttctttctttctttctttctttc -tttcttctttctttctttttctttcttttttttttgggatggagtctcgctctgtcaccc -aggctggagtgcagtggcatgatctcggctcgctgcaatctccacctcccaggttcaagc -gattgaactcactgcctcagcctcccaagtagctgggaccacagccgcatgccaccacac -ccagctaattttttgtatttttagtagagacggggtttcaccatgttagccaggat ->syndip_2_chr20:60702795-60703297 -tttttatttctcttggttaaatacctaggagtggaactgccaggtcatatggtaactgca -tgttgactcttttgaggagcttccagactgtttttcaaagtgatggcacaattttccttt -cccctcaataatgtatgagggttgcaatgtcgctacatattaccaacatttgtcattgtc -tttctttcttttctttctctctctctctttcttttccttctttctttctttctttctttc -tttcttc----------------------------------------ctttctttctttc -tttctttctttctttctttctttctttcttt-------------------------tctt -tccttctttctttctttctttctttctttttttttgggatggagtctcgctctgtcaccc -aggctggagtgcagtggcatgatctcggctcgctgcaatctccacctcccaggttcaagc -gattgaactcactgcctcagcctcccaagtagctgggaccacagccgcatgccaccacac -ccagctaattttttgtatttttagtagagacggggtttcaccatgttagccaggat ->p:HG002_1_chr20:60702795-60703297 -tttttatttctcttggttaaatacctaggagtggaactgccaggtcatatggtaactgca -tgttgactcttttgaggagcttccagactgtttttcaaagtgatggcacaattttccttt -cccctcaataatgtatgagggttgcaatgtcgctacatattaccaacatttgtcattgtc -tttctttcttttctttctctctctctctttctttcttttccttctttctttctttctttc -tttcctt----------------------------------------ctttctttctttc -tttctttctttctttctttctttctttcttt-------------------------tctt -tccttctttctttctttctttctttctttttttttgggatggagtctcgctctgtcaccc -aggctggagtgcagtggcatgatctcggctcgctgcaatctccacctcccaggttcaagc -gattgaactcactgcctcagcctcccaagtagctgggaccacagccgcatgccaccacac -ccagctaattttttgtatttttagtagagacggggtttcaccatgttagccaggat ->p:HG002_2_chr20:60702795-60703297 -tttttatttctcttggttaaatacctaggagtggaactgccaggtcatatggtaactgca -tgttgactcttttgaggagcttccagactgtttttcaaagtgatggcacaattttccttt -cccctcaataatgtatgagggttgcaatgtcgctacatattaccaacatttgtcattgtc -tttctttcttttctttctctctctctctttcttttccttctttctttctttctttctttc -tttctttctttctttctttctttctttctttcttttctttccttcttctttctttctttc -tttctttctttctttctttctttctttctttctttctttctttctttctttctttctttc -tttcttcttctttctttctttctttctttttttttgggatggagtctcgctctgtcaccc -aggctggagtgcagtggcatgatctcggctcgctgcaatctccacctcccaggttcaagc -gattgaactcactgcctcagcctcccaagtagctgggaccacagccgcatgccaccacac -ccagctaattttttgtatttttagtagagacggggtttcaccatgttagccaggat ->ref_chr20:60702795-60703297 -tttttatttctcttggttaaatacctaggagtggaactgccaggtcatatggtaactgca -tgttgactcttttgaggagcttccagactgtttttcaaagtgatggcacaattttccttt -cccctcaataatgtatgagggttgcaatgtcgctacatattaccaacatttgtcattgtc -tttctttcttttctttctctctctctctttcttttcctt--------------------- ------------------------------------------------ctttctttctttc -tttctttctttctttctttctttctttcttt-------------------------tctt -tccttctttctttctttctttctttctttttttttgggatggagtctcgctctgtcaccc -aggctggagtgcagtggcatgatctcggctcgctgcaatctccacctcccaggttcaagc -gattgaactcactgcctcagcctcccaagtagctgggaccacagccgcatgccaccacac -ccagctaattttttgtatttttagtagagacggggtttcaccatgttagccaggat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_e8eb923241a4227ce80f8e8413e57b9f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_e8eb923241a4227ce80f8e8413e57b9f.msa deleted file mode 100644 index 7a233757..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_e8eb923241a4227ce80f8e8413e57b9f.msa +++ /dev/null @@ -1,70 +0,0 @@ ->syndip_1_chr20:57948791-57949556 -ccatccaagacttggcccactgctgtgccctgcacagatggacagatggttggaaggatg -gatggatggatggatggatggatggatggatggggttggatggatggatggatggatgga -tggatagtggatagatggatgaatagtggatggataaatggattaatggatggatgaatg -gatgatggatggatgaatgagatggatggatt----------------gatggatggatg -gatggatggatggatggaagaatggatgatggatggatga-------------------- -gatggatggatggatggatggaagaatggatgatggatggatga--------gatggatg -gatggatggggggttggatggatggatggatggatggatggatagtggatagatggatga -atagtggatggataaatggattaatggatggatgaatgg--------------------- ----------------------------------atgatggatggatgaatg--------- ----agatggatggattgatggatggatggatggatggaagaatggatgatggatggatga -atgagatgggtggattgatggatggatggatggatggatggatggatggatggatggcag -atggatggatccatctatgtcaggcctgcatgacacctggtgtggaggagccacccagtc -aacatttgctgacaggatggacagacagagaggaggtgagtgacag ->syndip_2_chr20:57948791-57949556 -ccatccaagacttggcccactgctgtgccctgcacagatggacagatggttggaaggatg -gatggatggatggatggatggatggatggatggggttggatggatggatggatggatgga -tggatagtggatagatggatgaatagtggatggataaatggattaatggatggatgaatg -gatgatggatggatgaatgagatggatggattgatggatggatggatggatggatggatg -gatggatggatggatggaagaatggatgatggatggatgagatggatggatggatggatg -gatggatggatggatggatggaagaatggatgatggatggatgagatggatggatggatg -gatggatggggggttggatggatggatggatggatggatggatagtggatagatggatga -atagtgaatggataaatggattaatggatggatggatagtggatagatggatgaatagtg -gatggataaatggattaatggatggatgaatggatgatggatggatgaatgagatggatg -gattgatggatggatggatggatggatggatggatggaagaatggatgatggatggatga -atgagatgggtggattgatggatggatggatggatggatggatggatggatggatggcag -atggatggatccatctatgtcaggcctgcatgacacctggtgtggaggagccacccagtc -aacatttgctgacaggatggacagacagagaggaggtgagtgacag ->p:HG002_1_chr20:57948791-57949556 -ccatccaagacttggcccactgctgtgccctgcacagatggacagatggttggaaggatg -gatggatggatggatggatggatggatggatggggttggatggatggatggatggatgga -tggatagtggatagatggatgaatagtggatggataaatggattaatggatggatgaatg -gatgatggatggatgaatgagatggatggattgatggatggatggatggatggatggatg -gatggatggatggatggaagaatggatgatggatggatgagatggatggatggatggatg -gatggatggatggatggatggaagaatggatgatggatggatgagatggatggatggatg -gatggatggggggttggatggatggatggatggatggatggatagtggatagatggatga -atagtgaatggataaatggattaatggatggatggatagtggatagatggatgaatagtg -gatggataaatggattaatggatggatgaatggatgatggatggatgaatgagatggatg -gattgatggatggatggatggatggatggatggatggaagaatggatgatggatggatga -atgagatgggtggattgatggatggatggatggatggatggatggatggatggatggcag -atggatggatccatctatgtcaggcctgcatgacacctggtgtggaggagccacccagtc -aacatttgctgacaggatggacagacagagaggaggtgagtgacag ->p:HG002_2_chr20:57948791-57949556 -ccatccaagacttggcccactgctgtgccctgcacagatggacagatggttggaaggatg -gatggatggatggatggatggatggatggatggggttggatggatggatggatggatgga -tggatagtggatagatggatgaatagtggatggataaatggattaatggatggatgaatg -gatgatggatggatgaatgagatggatggattgatggatggatggatggatggatggatg -gatggatggatggatggaaga------------------------------------atg -gatggatggatggatggatggaagaatggatgatggatggatgagatggatggatggatg -gatggatggggggttggatggatggatggatggatggatggatagtggatagatggatga -atagtgaatggataaatggattaatggatggatggatag--------------------- ------------------------------------------tggatagatg--------- ----tgatggatggatggatggatggatggatggatggaagaatggatgatggatggatga -atgagatgggtggattgatggatggatggatggatggatggatggatggatggatggcag -atggatggatccatctatgtcaggcctgcatgacacctggtgtggaggagccacccagtc -aacatttgctgacaggatggacagacagagaggaggtgagtgacag ->ref_chr20:57948791-57949556 -ccatccaagacttggcccactgctgtgccctgcacagatggacagatggttggaaggatg -gatggatggatggatggatggatggatggatggggttggatggatggatggatggatgga -tggatagtggatagatggatgaatagtggatggataaatggattaatggatggatgaatg -gatgatggatggatgaatgagatggatggattgatggatggatggatggatggatggatg -gatggatggatggatggaagaatggatgatggatggatgagatggatggatggatggatg -gatggatggatggatggatggaagaatggatgatggatggatgagatggatggatggatg -gatggatggggggttggatggatggatggatggatggatggatagtggatagatggatga -atagtgaatggataaatggattaatggatggatggatagtggatagatggatgaatagtg -gatggataaatggattaatggatggatgaatggatgatggatggatgaatgagatggatg -gattgatggatggatggatggatggatggatggatggaagaatggatgatggatggatga -atgagatgggtggattgatggatggatggatggatggatggatggatggatggatggcag -atggatggatccatctatgtcaggcctgcatgacacctggtgtggaggagccacccagtc -aacatttgctgacaggatggacagacagagaggaggtgagtgacag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ebf476a7f02b11a3b6ed6aeba24742c2.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ebf476a7f02b11a3b6ed6aeba24742c2.msa deleted file mode 100644 index 1859738e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ebf476a7f02b11a3b6ed6aeba24742c2.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:50775544-50776023 -gctttctcattctgtctctccaaagatttcc--------------------atatatata -tatatatatatataaatataaatatattctatatattcatatatatatattctatatatt -catatatataaatatattctatatattcatatatataaatatattctatatattcatata -taaatatattccatatatataaatatattccatatatttatatataaatatatatcatat -atttatatataaatatatatcatatatttatatataaatatatatcatatatttatatat -aaatatatatcatatatttatatataaatatatatcatatatttatatataaatatatat -catatatttatatataatatatatcatatattatatataaatatatatcatatatttata -tataaatatatatcatatattaatatatatcatatatttatatattaatatatatcatat -atttatatattaatatatatcatatatttatatataaatatatatcatatatttatatat -aaatatatatctacattttttgagacagagtctggctctgt ->syndip_2_chr20:50775544-50776023 -gctttctcattctgtctctccaaagatttccatatatatatatatatatatatatatata -tatatatatatataaatataaatatattctatatattcatatatatatattctatatatt -catatatataaatatattctatatattcatatatataaatatattctatatattcatata -taaatatattccatatatataaatatattc-------------------------catat -atttatatataaatatatatcatatatttatatataaatatatatcatatatttatatat -aaatatatatcatatatttatatataaatatatatcatatatttatatataaatatatat -catatatttatatataatatatatcatatattatatataaatatatatcatatatttata -tataaatatatatcatatattaatatatatcatatatttatatattaatatatatcatat -atttatatattaatatatatcatatatttatatataaatatatatcatatatttatatat -aaatatatatctacattttttgagacagagtctggctctgt ->p:HG002_1_chr20:50775544-50776023 -gctttctcattctgtctctccaaagatttccatatatatatatatatatatatatatata -tatatatatatataaatataaatatattctatatattcatatatatatattctatatatt -catatatataaatatattctatatattcatatatataaatatattctatatattcatata -taaatatattccatatatataaatatattc-------------------------catat -atttatatataaatatatatcatatatttatatataaatatatatcatatatttatatat -aaatatatatcatatatttatatataaatatatatcatatatttatatataaatatatat -catatatttatatataatatatatcatatattatatataaatatatatcatatatttata -tataaatatatatcatatattaatatatatcatatatttatatattaatatatatcatat -atttatatattaatatatatcatatatttatatataaatatatatcatatatttatatat -aaatatatatctacattttttgagacagagtctggctctgt ->p:HG002_2_chr20:50775544-50776023 -gctttctcattctgtctctccaaagatttcc--------------------atatatata -tatatatatatataaatataaatatattctatatattcatatatatatattctatatatt -catatatataaatatattctatatattcatatatataaatatattctatatattcatata -taaatatattccatatatataaatatattccatatatttatatataaatatatatcatat -atttatatataaatatatatcatatatttatatataaatatatatcatatatttatatat -aaatatatatcatatatttatatataaatatatatcatatatttatatataaatatatat -catatatttatatataatatatatcatatattatatataaatatatatcatatatttata -tataaatatatatcatatattaatatatatcatatatttatatattaatatatatcatat -atttatatattaatatatatcatatatttatatataaatatatatcatatatttatatat -aaatatatatctacattttttgagacagagtctggctctgt ->ref_chr20:50775544-50776023 -gctttctcattctgtctctccaaagatttccatatatatatatatatatatatatatata -tatatatatatataaatataaatatattctatatattcatatat---------------- ------------atatattctatatattcatatatataaatatattctatatattcatata -taaatatattccatatatataaatatattc-------------------------catat -atttatatataaatatatatcatatatttatatataaatatatatcatatatttatatat -aaatatatatcatatatttatatat-aatatatatcatatat------------------ -------------------------------ttatatataaatatatatcatatatttata -tataaatatatatcatatattaatatatatcatatatttatatattaatatatatcatat -atttatatattaatatatatcatatatttatatataaatatatatcatatatttatatat -aaatatatatctacattttttgagacagagtctggctctgt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_f328fb5ed3385e1b3cad0fe424579df0.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_f328fb5ed3385e1b3cad0fe424579df0.msa deleted file mode 100644 index 8c540051..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_f328fb5ed3385e1b3cad0fe424579df0.msa +++ /dev/null @@ -1,100 +0,0 @@ ->syndip_1_chr20:63049033-63049412 -ttggaggtcagcaaggtcatgtgggggcagactcctcctcctcctcctcttcctcctcc- ---------------------------tcctcctcttcctcttcctcctcctcctcctctt -cctcttcctcctcctcctcctcttcctcctcctcctcttcctcctccccctcctcttcct -cctcctcctcttccttctcctcctccttctcctcctcctcttcctcctcttcctcttcct -cctcctcttcctcctcctcttcctcctcctctttctcctcctcttcctcttcctcctctt -cctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcct -ccttctcttcctcttcctcctcctcttcctcttcctcctcctcttcctctttctcctcct -cctcctcttcctcttcctcctcc------------------------------------- ---tcttcctctttctcctcctcctcctcttcctcctcttcctcctcctcttcctcctcct -cctcctcttcctcctcctcctcgtcttcctccttctcctcttcctcctcttcctcttcct -cctcctcttcctcttcctcttcctcttcctcttcctcctcctcctcctctttctcctcct -cctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcct -cttcctcctcctcctcttcctcctcttcttcctcctcttcctcctcctcctcttcctcct -cttcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcctcctctt -cctcct-cctcctcttcctcctcctcctcttcctcctcctcttcctcctcctcctcctct -tcctcccctcctcctcctcttcctcctcctcctcttcctcccctcctcctcctcctcttc -ctcctcctcctcctcttcctcccctcctcctcctcttcctcctcgtcctcttcctccttc -tgccaggacccttcttccaggacccctgagaagcgcatagaatagcgtccaggactgtct -gccccaggcacgctgaccac ->syndip_2_chr20:63049033-63049412 -ttggaggtcagcaaggtcatgtgggggcagactcctcctcctcctcctcttcctcctcct -cctcttcctcctcctcctcttcctcttcctcctcctcctcctcttcctcttcctcctcct -cctcctcttcctcctcctcctcttcctcctcctcctcttcctcctccccctcctcttcct -cctcctcctcttcctcctcctcctccttctcctcctcctcttcctcctcttcctcttcct -cctcctcttcctcctcctctttctcctcctcttcctcttcctcctcttcctcctcctctt -cctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcctcttcct -ccttctcttcctcttcctcctcctcttcctcttcctcctcctcttcctctttctcctcct -cctcctcttcctcctcttcctcctcctcttcctcctcctcctcctcttcctcctcctcct -cgtcttcctccttctcctcttcctcctcttcctcttcctcctcctcttcctcttcctctt -cctcttcctcctcctcctcctcttcctcctcctcctcctcttcctcctcctcctcttcct -cctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcttcctcctcct -cctcttcctcctcttcttcctcctcttcctcctcctcctcttcctcctcttcctcctcct -cttcctcctcctcctcttcctcctcctcttcctcctcttcttcctcctcttcctcctcct -cctcttcctcctcttcctcctcctcttcctcctcctcctcctcttcctcc-cctcctctt -cctcct-cctcctcttcctcctcctcctcttcctcctcctcttcctcctcctcctcctct -tcctcccctcctcctcctcttcctcctcctcctcttcctcccctcctcctcctcctcttc -ctcctcctcctcctcttcctcccctcctcctcctcttcctcctcgtcctcttcctccttc -tgccaggacccttcttccaggacccctgagaagcgcatagaatagcgtccaggactgtct -gccccaggcacgctgaccac ->p:HG002_1_chr20:63049033-63049412 -ttggaggtcagcaaggtcatgtgggggcagactcctcctcctcctcctcttcctcctcct -cctcttcctcctcctcctcttcctcttcctcctcctcctcctcttcctcttcctcctcct -cctcctcttcctcctcctcctcttcctcctcctcctcttcctcctccccctcctcttcct -cctcctcctcttcctcctcctcctccttctcctcctcctcttcctcctcttcctcttcct -cctcctcttcctcctcctctttctcctcctcttcctcttcctcctcttcctcctcctctt -cctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcctcttcct -ccttctcttcctcttcctcctcctcttcctcttcctcctcctcttcctctttctcctcct -cctcctcttcctcctcttcctcctcctcttcctcctcctcctcctcttcctcctcctcct -cgtcttcctccttctcctcttcctcctcttcctcttcctcctcctcttcctcttcctctt -cctcttcctcctcctcctcctcttcctcctcctcctcctcttcctcctcctcctcttcct -cctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcttcctcctcct -cctcttcctcctcttcttcctcctcttcctcctcctcctcttcctcctcttcctcctcct -cttcctcctcctcctcttcctcctcctcttcctcctcttcttcctcctcttcctcctcct -cctcttcctcctcttcctcctcctcttcctcctcctcctcctcttcctcc-cctcctctt -cctcct-cctcctcttcctcctcctcctcttcctcctcctcttcctcctcctcctcctct -tcctcccctcctcctcctcttcctcctcctcctcttcctcccctcctcctcctcctcttc -ctcctcctcctcctcttcctcccctcctcctcctcttcctcctcgtcctcttcctccttc -tgccaggacccttcttccaggacccctgagaagcgcatagaatagcgtccaggactgtct -gccccaggcacgctgaccac ->p:HG002_2_chr20:63049033-63049412 -ttggaggtcagcaaggtcatgtgggggcagactcctcctcctcctcctcttcctcctcc- ---------------------------tcctcctcttcctcttcctcctcctcctcctctt -cctcttcctcctcctcctcctcttcctcctcctcctcttcctcctccccctcctcttcct -cctcctcctcttccttctcctcctccttctcctcctcctcttcctcctcttcctcttcct -cctcctcttcctcctcctcttcctcctcctctttctcctcctcttcctcttcctcctctt -cctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcct -ccttctcttcctcttcctcctcctcttcctcttcctcctcctcttcctctttctcctcct -cctcctcttcctcttcctcctcc------------------------------------- ---tcttcctctttctcctcctcctcctcttcctcctcttcctcctcctcttcctcctcct -cctcctcttcctcctcctcctcgtcttcctccttctcctcttcctcctcttcctcttcct -cctcctcttcctcttcctcttcctcttcctcttcctcctcctcctcctctttctcctcct -cctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcct -cttcctcctcctcctcttcctcctcttcttcctcctcttcctcctcctcctcttcctcct -cttcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcctcctctt -cctcct-cctcctcttcctcctcctcctcttcctcctcctcttcctcctcctcctcctct -tcctcccctcctcctcctcttcctcctcctcctcttcctcccctcctcctcctcctcttc -ctcctcctcctcctcttcctcccctcctcctcctcttcctcctcgtcctcttcctccttc -tgccaggacccttcttccaggacccctgagaagcgcatagaatagcgtccaggactgtct -gccccaggcacgctgaccac ->ref_chr20:63049033-63049412 -ttggaggtcagcaaggtcatgtgggggcaga----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------ctcctcctcctcctcctcttcctcctcct -cctcttcctcctcctcctcttcctcttcctcctcctcctcctcttcctcctcctcctcct -cttcctccctcctcttcctcctcctcctcttcctcctcctcttcctcctcctcctcctct -tcctcccctcctcctcctcttcctcctcctcctcttcctctcctcctcctcctcctcttc -ctcctcctcctcctcttcctcccctcctcctcctcttcctcctcgtcctcttcctccttc -tgccaggacccttcttccaggacccctgagaagcgcatagaatagcgtccaggactgtct -gccccaggcacgctgaccac diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_f6c1a597d80bac4f7dabc75d287d7e0e.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_f6c1a597d80bac4f7dabc75d287d7e0e.msa deleted file mode 100644 index da823986..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_f6c1a597d80bac4f7dabc75d287d7e0e.msa +++ /dev/null @@ -1,140 +0,0 @@ ->syndip_1_chr20:20320285-20320579 -aatttttttagcagtaaagatggtatttcagatatatag--atatatatattatatatat -gtaatatatataatatatgta--atatattatatatatgtaatatatataatatatgtaa -tatattatatatatgtaatatatataatatatgtaatatatattatatatgtaatatata -taatatatgtaatatatattatatatgtaatatatataatatatgtaatatatattatat -atgtaatatataatatatgtaatatatattatatatgtaatataatatatgtaatatata -ttatatatgtaatatatattacatatattatatatgcaatatatattatatatattatat -atgcaatatatattatatatattatatatgcaatatatattatatatgcaatatatatta -tatatattatatatgcaatatatattatatatattacatatgtaatatatattacatatg -taatatataatatattatatattacatatgtaatatataatatattatatattacatatg -taatatataatatatattacatatgtaatatataatatatattacatatgtaatatatta -tatattacatatgtaatatattatatattacatatgtaatatattatatattacatatgt -aatatattatatattacatatgtaatatattatatattacatatgtaatatatataatat -attacatatgtaatatataatatattatatatgtaatatatattacatatataatatata -taatatatatgtaatatattatatatattatatatgtaatatatattacatatataatat -atattatatatattacatatattatatatgtaatatatattacatatgtaatatatgtaa -tatatattacatatgtaatatatattatatatgtaatatatattacatatattatatatg -taatatatattatatatattatatatgtaatgtataatatatatattatatatgtaatat -atattatatataatatatgtaatatatattatatatgtaatgtatattatatatattata -tatgtaatgtatattatatataatatatgtaatgtatattatatatgtaatatatattat -gtatattatatatgtaatatatattatatatattatatatgtaatatatattatatatat -tatatatgtaatatatattatatatattatatatgtaatatatattatatatattatata -tgtaatatatattatatatattatatatgtaatatatattatatatattatatatgtaat -atatattatatatattatatatgtaatatatattatatatattatatatgtaatatatat -tatatatattatatatgtaatatatattatatatattatatatgtaatatatattatata -tattatatatgtaatatatattatatatattatatatgtaatatatattatatatattat -atatgtaatatatattatatatattatatatgtaatatatatatatttaaaaacagaacc -attatcttttagagat ->syndip_2_chr20:20320285-20320579 -aatttttttagcagtaaagatggtatttcagatatatagatatatatatattatatatat -gtaatatatataatatatgtaatatatattatatatatgtaatatatataatatatgta- ---------atatatgtaatatatattatatatgtaatata----atatatgtaatatata -ttatatatgtaatatataatatatgta----atatataatatatgtaatatatattatat -atgtaatatataatatatattatatatgtaatatatatatatttaaaaacagaaccatta -tctttta----------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------gagat ->p:HG002_1_chr20:20320285-20320579 -aatttttttagcagtaaagatggtatttcagatatatagatatatatatattatatatat -gtaatatatataatatatgtaatatatattatatatatgtaatatatataatatatgta- ---------atatatgtaatatatattatatatgtaatata----atatatgtaatatata -ttatatatgtaatatataatatatgta----atatataatatatgtaatatatattatat -atgtaatatataatatatattatatatgtaatatatatatatttaaaaacagaaccatta -tctttta----------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------gagat ->p:HG002_2_chr20:20320285-20320579 -aatttttttagcagtaaagatggtatttcagatatatag--atatatatattatatatat -gtaatatatataatatatgta--atatattatatatatgtaatatatataatatatgtaa -tatattatatatatgtaatatatataatatatgtaatatatattatatatgtaatatata -taatatatgtaatatatattatatatgtaatatatataatatatgtaatatatattatat -atgtaatatataatatatgtaatatatattatatatgtaatataatatatgtaatatata -ttatatatgtaatatatattacatatattatatatgcaatatatattatatatattatat -atgcaatatatattatatatattatatatgcaatatatattatatatgcaatatatatta -tatatattatatatgcaatatatattatatatattacatatgtaatatatattacatatg -taatatataatatattatatattacatatgtaatatataatatattatatattacatatg -taatatataatatatattacatatgtaatatataatatatattacatatgtaatatatta -tatattacatatgtaatatattatatattacatatgtaatatattatatattacatatgt -aatatattatatattacatatgtaatatattatatattacatatgtaatatatataatat -attacatatgtaatatataatatattatatatgtaatatatattacatatataatatata -taatatatatgtaatatattatatatattatatatgtaatatatattacatatataatat -atattatatatattacatatattatatatgtaatatatattacatatgtaatatatgtaa -tatatattacatatgtaatatatattatatatgtaatatatattacatatattatatatg -taatatatattatatatattatatatgtaatgtataatatatatattatatatgtaatat -atattatatataatatatgtaatatatattatatatgtaatgtatattatatatattata -tatgtaatgtatattatatataatatatgtaatgtatattatatatgtaatatatattat -gtatattatatatgtaatatatattatatatattatatatgtaatatatattatatatat -tatatatgtaatatatattatatatattatatatgtaatatatattatatatattatata -tgtaatatatattatatatattatatatgtaatatatattatatatattatatatgtaat -atatattatatatattatatatgtaatatatattatatatattatatatgtaatatatat -tatatatattatatatgtaatatatattatatatattatatatgtaatatatattatata -tattatatatgtaatatatattatatatattatatatgtaatatatattatatatattat -atatgtaatatatattatatatattatatatgtaatatatatatatttaaaaacagaacc -attatcttttagagat ->ref_chr20:20320285-20320579 -aatttttttagcagtaaagatggtatttcagatatatagatatatatatattatatatat -gtaatatatataatatatgtaatatatattatatatatgtaatatatataatatatgta- ---------atatatgtaatatatattatatatgtaatata----atatatgtaatatata -ttatatatgtaatatataatatatgta----atatataatatatgtaatatatattatat -atgtaatatataatatatattatatatgtaatatatatatatttaaaaacagaaccatta -tctttta----------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------gagat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_f7c5ca36d463cc7cabf9cb401fc27789.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_f7c5ca36d463cc7cabf9cb401fc27789.msa deleted file mode 100644 index 47b15f8c..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_f7c5ca36d463cc7cabf9cb401fc27789.msa +++ /dev/null @@ -1,135 +0,0 @@ ->syndip_1_chr20:53203889-53204462 -taccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgtaa -gtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctcct -tcatttttataatatgatactattatatcataattttataatatactattatatcatatt -atatgatactatttatatcatcatatgatgatatactat--tatatcatcatatgatgat -ata--ctattatatcatcatatgatgatatg--atactatatcatcatatgatgatatga -tactatatcatcatatgatgat-----------------------------atactatat -catcatatgatgatatgatatactatatcatcatatgatgatatgatactatatcatcat ------atgatgatatgatactatatcatcat-----atgatgatatgatactatatcatc -at-----atgatgatatgatactatatcatcat-----atgatgatatgatactatatca -tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga -tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcacat -gatgatatgatactatatcatcacatgatgatatgatactatatcatcacatgatgatat -gatactatatcatcacatgatgatatgatactatatcatcacatgatgatatgatactat -atcatcacatgatgatatgatactatatcatcacatgatgatatgatactatatcatcac -atgatgatatgatactatatcatcatata---------------------acatgatgat -atgatactatatcatcatata---------------------acatgatgatatgatact -atatcatcat-----------------------------------------------ata -acatgatgatatgatactatatcatcatataacatgatgatatgatactatatcatcata -taacatgatgatatgatactatatcatcatataacatgatgatatgatactattatatca -taatatgatataatat-------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------tttggac -atactag ->syndip_2_chr20:53203889-53204462 -taccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgtaa -gtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctcct -tcatttttataatatgatactattatatcataattttataatatactattatatcatatt -atatgatactatttatatcatcatatgatgatatgatat--tatatcatcatatgatgat -atg--atactatatcatcatatgatgatatgatatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcatatgatgatatg--atactatatcatcatatgatgatatgatactatatcatcat ------atgatgatatgatactatatcatcat-----atgatgatatgatactatatcatc -at-----atgatgatatgatactatatcatcat-----atgatgatatgatactatatca -tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga -tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatat -gatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatat -gatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactat -atcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcat -atgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgat -atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcatatgatgatatgatactatatcataacatgatgatatgatactatatcata -acatgatgatatgatactatatcatcatataacatgatgatatgatactatatcatcata -taacatgatgatatgatactatatcatcatataacatgatgatatgatactatatcatca -tataacatgatgatatgatactatatcatcatataacatgatgatatgatactatatcat -catataacatgatgatatgatactatatcatcatataacatgatgatatgatactatatc -atcatataacatgatgatatgatactatatcatcatataacatgatgatatgatactata -tcatcatataacatgatgatatgatactattatatcataatatgatataatattttggac -atactag ->p:HG002_1_chr20:53203889-53204462 -taccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgtaa -gtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctcct -tcatttttataatatgatactattatatcataattttataatatactattatatcatatt -atatgatactatttatatcatcatatgatgatatgatatactatatcatcatatgatgat -atgatatactatatcatcatatgatgatatg--atactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcatatgatgatatg--atactatatcatcatatgatgatatgatactatatcatcat ------atgatgatatgatactatatcatcat-----atgatgatatgatactatatcatc -at-----atgatgatatgatactatatcatcat-----atgatgatatgatactatatca -tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga -tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatat -gatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatat -gatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactat -atcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcat -atgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgat -atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcatatgatgatatgatactatatcataacatgatgatatgatactatatcata -acatgatgatatgatactatatcatcatataacatgatgatatgatactatatcatcata -taacatgatgatatgatactatatcatcatataacatgatgatatgatactatatcatca -tataacatgatgatatgatactatatcatcatataacatgatgatatgatactatatcat -catataacatgatgatatgatactatatcatcatataacatgatgatatgatactatatc -atcatataacatgatgatatgatactatatcatcatataacatgatgatatgatactata -tcatcatataacatgatgatatgatactattatatcataatatgatataatattttggac -atactag ->p:HG002_2_chr20:53203889-53204462 -taccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgtaa -gtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctcct -tcatttttataatatgatactattatatcataattttataatatactattatatcatatt -atatgatactatttatatcatcatatgatgatatgatatactatatcatcatatgatgat -atg----attatatcatcatatgatgatatg--atactatatcatcatatgatgatatga -tactatatcatcatatgatgat-----------------------------atactatat -catcatatgatgatatg--atactatatcatcatatgatgatatgatactatatcatcat ------atgatgatatgatactatatcatcat-----atgatgatatgatactatatcatc -at-----atgatgatatgatactatatcatcat-----atgatgatatgatactatatca -tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga -tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcacat -gatgatatgatactatatcatcacatgatgatatgatactatatcatcacatgatgatat -gatactatatcatcacatgatgatatgatactatatcatcatatgatgatatgatactat -atcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcat -atgatgatatgatactatatcatcatata---------------------acatgatgat -atgatactatatcatcatata---------------------acatgatgatatgatact -atatcatcat-----------------------------------------------ata -acatgatgatatgatactatatcatcatataacatgatgatatgatactatatcatcata -taacatgatgatatgatactatatcatcatataacatgatgatatgatactattatatca -taatatgatataatat-------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------tttggac -atactag ->ref_chr20:53203889-53204462 -taccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgtaa -gtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctcct -tcatttttataatatgatactattatatcataattttataatatactattatatcatatt -atatgatactatttatatcatcatatgatgatatgatatactatatcatcatatgatgat -atgatatactatatcatcatatgatgatatg--atactatatcatcatatgatgatatga -tactatatcatcatatgatgatatg--------------------------atactatat -catcatatgatgatatg--atactatatcatcatatgatgatatgatactatatcatcat -ataacatgatgatatgatactatatcatcatataacatgatgatatgatactatatcatc -atataacatgatgatatgatactatatcatcatataacatgatgatatgatactatatca -tcatataacatgatgatatgatactattatatcataatatgatataatat---------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------tttggac -atactag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_f948393d54df6d4839d008016d5b4721.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_f948393d54df6d4839d008016d5b4721.msa deleted file mode 100644 index bbee428a..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_f948393d54df6d4839d008016d5b4721.msa +++ /dev/null @@ -1,125 +0,0 @@ ->syndip_1_chr20:62349612-62349932 -tgcatttcaggaaggaggaagcagcaacccaggggatggggatggggatggggatgggga -tggtgggggtgatgggggtgatgatggtgatggtgggggtgatgatggtgatggtgatgg -tgatggtgggggtggtgatggtgggggtgggggtggtgatggtgggggtgggggtgatga -tggtgatggtgggggtgatgacggtggggctgggggtgatgatggtgggggtgatgacgg -tgatgatgggggtggaggggtgatgacggtgatgatgggggtgggggggtgatgacggtg -atgtgggggtgatgacggtgggggtgggggtgatgacggtgat----------------- -----ggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatga -cggtgggggtgggggtgatgacggtgggggtgggggtgatgatggtgatggtgggggtga -tgatggtgggggtgggggtgatgatggtgagggtgatgatggtgggggtaatgacggtgg -ggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtgggggtgatgacgat -gatggtgggggtgatgacggtgatggcggtgggggtgatgacggtgggggtgggggtgat -gacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggt -gatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggg -ggtgatgacggtgatggtagaggtgatgatggtgggggtgatggtgggggtgggggtggg ----------ggtgggggtgatgatggtgatggtgggggtgatgatggtgagggtgatgat -ggtgggggtgatggtggggg---tgggggtg--------------ggggtgggggtgatg -acggtgatggtgggggtgatgatggtgggagtggg------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------ctggtagtgggggtgatggtttgggtgggagtaaggtgatggtgga -ggtaaagaggcagaaaattgctggctgatgaca ->syndip_2_chr20:62349612-62349932 -tgcatttcaggaaggaggaagcagcaacccaggggatggggatggggatggggatgggga -tggtgggggtgatgggggtgatgatggtgatggtgggggtgatgatggtgatggtga--- -------------tggtgatggtgatggtgggggtggtgatggtgggggtgggggtgatga -tggtgatggtgggggtgatgacggtggggctgggggtgatgatggtgggggtgatgacgg -tgatgatgggggtggaggggtgatgacggtgatgatgggggtgggggggtgatgacggtg -atgtgggggtgatgacggtgggggtgggggtgatgacggtgatggtgggggtgatgacgg -tgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatga -cggtgggggtgggggtgatgacggtgggggtgggggtgatgatggtgatggtgggggtga -tgatggtgggggtgggggtgatgatggtgagggtgatgatggtgggggtaatgacggtgg -ggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtgggggtgatgacgat -gatggtgggggtgatgacggtgatggcggtgggggtgatgacggtgggggtgggggtgat -gacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggt -gatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggg -ggtgatgacggtgatggtagaggtgatgatggtgggggtgggggtgggggtgggggtgag -ggtgatgatggtgggggtgatgatggtgatggtgggggtgatgatggtgagggtgatgat -ggtgggggtgatggtggggg---tgggggtgggggtaatgacggtggggtgggggtaatg -acggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtgggggtg -atgacgatgatggtgggggtgatgacggtgatggcggtgggggtgatgacggtgggggtg -ggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggg -gtgggggtgatgacggtgggggtgggggtgatgacggtgatggtagaggtgatgatggtg -ggggtgatggtgggggtgggggtgggggtgggggtgatgatggtgatggtgggggtgatg -atggtgagggtgatgatggtgggggtgatggtgggggtgggggtgggggtgggggtgatg -atggtgggagtgggctggtagtgggggtgatggtttgggtgggagtaaggtgatggtgga -ggtaaagaggcagaaaattgctggctgatgaca ->p:HG002_1_chr20:62349612-62349932 -tgcatttcaggaaggaggaagcagcaacccaggggatggggatggggatggggatgggga -tggtgggggtgatgggggtgatgatggtgatggtgggggtgatgatggtgatggtga--- -------------tggtgatggtgatggtgggggtggtgatggtgggggtgggggtgatga -tggtgatggtgggggtgatgacggtggggctgggggtgatgatggtgggggtgatgacgg -tgatgatgggggtggaggggtgatgacggtgatgatgggggtgggggggtgatgacggtg -atgtgggggtgatgacggtgggggtgggggtgatgacggtgatggtgggggtgatgacgg -tgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatga -cggtgggggtgggggtgatgacggtgggggtgggggtgatgatggtgatggtgggggtga -tgatggtgggggtgggggtgatgatggtgagggtgatgatggtgggggtaatgacggtgg -ggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtgggggtgatgacgat -gatggtgggggtgatgacggtgatggcggtgggggtgatgacggtgggggtgggggtgat -gacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggt -gatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggg -ggtgatgacggtgatggtagaggtgatgatggtgggggtgggggtgggggtgggggtgag -ggtgatgatggtgggggtgatgatggtgatggtgggggtgatgatggtgagggtgatgat -ggtgggggtgatggtggggg---tgggggtgggggtaatgacggtggggtgggggtaatg -acggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtgggggtg -atgacgatgatggtgggggtgatgacggtgatggcggtgggggtgatgacggtgggggtg -ggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggg -gtgggggtgatgacggtgggggtgggggtgatgacggtgatggtagaggtgatgatggtg -ggggtgatggtgggggtgggggtgggggtgggggtgatgatggtgatggtgggggtgatg -atggtgagggtgatgatggtgggggtgatggtgggggtgggggtgggggtgggggtgatg -atggtgggagtgggctggtagtgggggtgatggtttgggtgggagtaaggtgatggtgga -ggtaaagaggcagaaaattgctggctgatgaca ->p:HG002_2_chr20:62349612-62349932 -tgcatttcaggaaggaggaagcagcaacccaggggatggggatggggatggggatgggga -tggtgggggtgatgggggtgatgatggtgatggtgggggtgatgatggtgatggtgatgg -tgatggtgggggtggtgatggtgggggtgggggtggtgatggtgggggtgggggtgatga -tggtgatggtgggggtgatgacggtggggctgggggtgatgatggtgggggtgatgacgg -tgatgatgggggtggaggggtgatgacggtgatgatgggggtgggggggtgatgacggtg -atgtgggggtgatgacggtgggggtgggggtgatgacggtgat----------------- -----ggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatga -cggtgggggtgggggtgatgacggtgggggtgggggtgatgatggtgatggtgggggtga -tgatggtgggggtgggggtgatgatggtgagggtgatgatggtgggggtaatgacggtgg -ggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtgggggtgatgacgat -gatggtgggggtgatgacggtgatggcggtgggggtgatgacggtgggggtgggggtgat -gacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggt -gatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggg -ggtgatgacggtgatggtagaggtgatgatggtgggggtgatggtgggggtgggggtggg ----------ggtgggggtgatgatggtgatggtgggggtgatgatggtgagggtgatgat -ggtgggggtgatggtggggg---tgggggtg--------------ggggtgggggtgatg -acggtgatggtgggggtgatgatggtgggagtggg------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------ctggtagtgggggtgatggtttgggtgggagtaaggtgatggtgga -ggtaaagaggcagaaaattgctggctgatgaca ->ref_chr20:62349612-62349932 -tgcatttcag-------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------gaaggaggaagcagcaacccaggggatggggatggggatggggatggtggg -ggtgatgggggtgatgatggtgatggtgatggtgatggtgatggtgatggtgatggtggg ----------ggtggtgatg-----------ggtgggggtgatgacggtgggagtgggggt -gatgacggtgatggtgggggtgatgacggtg--------------atggtgggggtgatg -acggtgatggtgggggtgatgatggtgggagtggg------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------ctggtagtgggggtgatggtttgggtgggagtaaggtgatggtgga -ggtaaagaggcagaaaattgctggctgatgaca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_fa91a80c012b3dea4b79f7b64e5bca29.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_fa91a80c012b3dea4b79f7b64e5bca29.msa deleted file mode 100644 index 243162b0..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_fa91a80c012b3dea4b79f7b64e5bca29.msa +++ /dev/null @@ -1,60 +0,0 @@ ->syndip_1_chr20:63372065-63372691 -acggaacaccggggctgccacaggtcgcagagaccctgtgtcaacacccttgttttgagg -tgcagagaccaaagttgagacctggccatgcagcaggtctgcagggacctcagagcccag -ggccactgtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagccc -cattaaacgcccagggccactgtcctgtccccagccccattaaacgcccagggccactgt -cctgtccccagccccattaaacgcccagggccactgtcctgtccccagccccattaaacg -cccagggccactggcctgtccccagccccattaaacgcccagggccactgtcctgtcccc -agccccattaaacgcccagggccactggcctgtccccagccccattaaatgcccagggcc -actgtcctgtccccagtctcattaaacgc------------------------------- ------------------------------------------------------------- ----------------------------------------------------------agc -aaacgtcttctggacgtgccgccagtc ->syndip_2_chr20:63372065-63372691 -acggaacaccggggctgccacaggtcgcagagaccctgtgtcaacacccttgttttgagg -tgcagagaccaaagttgagacctggccatgcagcaggtctgcagggacctcagagcccag -ggccactgtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagccc -cattaaacgcccagggccactgtcctgtccccagccccattaaacgcccagggccactgt -cctgtccccagccccattaaacgcccagggccactgt----------------------- ---------------cctgtccccagccccattaaacgcccagggccactgtcctgtcccc -agccccattaaacgcccagggccactggcctgtccccagccccattaaatgcccagggcc -actgtcctgtccccagtctcattaaacgc------------------------------- ------------------------------------------------------------- ----------------------------------------------------------agc -aaacgtcttctggacgtgccgccagtc ->p:HG002_1_chr20:63372065-63372691 -acggaacaccggggctgccacaggtcgcagagaccctgtgtcaacacccttgttttgagg -tgcagagaccaaagttgagacctggccatgcagcaggtctgcagggacctcagagcccag -ggccactgtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagccc -cattaaacgcccagggccactgtcctgtccccagccccattaaacgcccagggccactgt -cctgtccccagccccattaaacgcccagggccactgt----------------------- ---------------cctgtccccagccccattaaacgcccagggccactgtcctgtcccc -agccccattaaacgcccagggccactggcctgtccccagccccattaaatgcccagggcc -actgtcctgtccccagtctcattaaacgc------------------------------- ------------------------------------------------------------- ----------------------------------------------------------agc -aaacgtcttctggacgtgccgccagtc ->p:HG002_2_chr20:63372065-63372691 -acggaacaccggggctgccacaggtcgcagagaccctgtgtcaacacccttgttttgagg -tgcagagaccaaagttgagacctggccatgcagcaggtctgcagggacctcagagcccag -ggccactgtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagccc -cattaaacgcccagggccactgtcctgtccccagccccattaaacgcccagggccactgt -cctgtccccagccccattaaacgcccagggccactgtcctgtccccagccccattaaacg -cccagggccactggcctgtccccagccccattaaacgcccagggccactgtcctgtcccc -agccccattaaacgcccagggccactggcctgtccccagccccattaaatgcccagggcc -actgtcctgtccccagtctcattaaacgc------------------------------- ------------------------------------------------------------- ----------------------------------------------------------agc -aaacgtcttctggacgtgccgccagtc ->ref_chr20:63372065-63372691 -acggaacaccggggctgccacaggtcgcagagaccctgtgtcaacacccttgttttgagg -tgcagagaccaaagttgagacctggccatgcagcaggtctgcagggacctcagagcccag -ggccactgtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagccc -cattaaacgcccagggccactgtcctgtccccagccccattaaacgcccagggccactgt -cctgtccccagccccattaaacgcccagggccactgtcctgtccccagccccattaaacg -cccagggccactgtcctgtccccagccccattaaatgcccagggccactgtcctgtcccc -agccccattaaacgcccagggccactgtcctgtccccagccccattaaacgcccagggcc -actgtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagccccatt -aaacgcccagggccactgtcctgtccccagccccattaaacgcccagggccactggcctg -tccccagccccattaaatgcccagggccactgtcctgtccccagtctcattaaacgcagc -aaacgtcttctggacgtgccgccagtc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_fab829612d8c5cf9d944a8e0df516b52.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_fab829612d8c5cf9d944a8e0df516b52.msa deleted file mode 100644 index e999e45c..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_fab829612d8c5cf9d944a8e0df516b52.msa +++ /dev/null @@ -1,35 +0,0 @@ ->syndip_1_chr20:16395149-16395421 -cagtttagtcaaggcagaaaggagatgaggaaggggagaggaggggagaggagggaagag -gaggggaggggaggggagaggaggagaggggaggagaggggaggccaagggaggggaggg -gaggggaggagaggggaggccaagggaggggaggggaggggaggagaggggaggccaagg -gaggggaggggaggggaggagaggggaggccaagggaggggaggggaggagaggggaggc -caagggaggggaggggaggggaggagaggggaggccaagggaggggaggggaggggagga -gaggggaggccaagggagaagatatgaaagaaatagggaaggagtggg ->syndip_2_chr20:16395149-16395421 -cagtttagtccaggcagaaaggagatgaggaaggggagaggaggggagaggaggggaggg -gaggggaggggagaggaggggaggccaagggagaagatatgaaagaaatagggaaggagt -ggg--------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------- ->p:HG002_1_chr20:16395149-16395421 -cagtttagtccaggcagaaaggagatgaggaaggggagaggaggggagaggaggggaggg -gaggggaggggagaggaggggaggccaagggagaagatatgaaagaaatagggaaggagt -ggg--------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------- ->p:HG002_2_chr20:16395149-16395421 -cagtttagtcaaggcagaaaggagatgaggaaggggagaggaggggagaggagggaagag -gaggggaggggaggggagaggaggagaggggaggagaggggaggccaagggaggggaggg -gaggggaggagaggggaggccaagggaggggaggggaggggaggagaggggaggccaagg -gaggggaggggaggggaggagaggggaggccaagggaggggaggggaggagaggggaggc -caagggaggggaggggaggggaggagaggggaggccaagggaggggaggggaggggagga -gaggggaggccaagggagaagatatgaaagaaatagggaaggagtggg ->ref_chr20:16395149-16395421 -cagtttagtcaaggcagaaaggagatgaggaaggggagaggaggggagaggagggaagag -gaggggaggggaggggagaggaggagaggggaggagaggggaggccaagggaggggaggg -gaggggaggagaggggaggccaa-----gggaggggaggggaggagaggggaggccaagg -gaggggaggggaggggaggagaggggaggccaagggaggggaggggaggagaggggaggc -caagggagaagatatgaaagaaatagggaaggagt------------------------- ----------------------------------------------ggg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_fb0cbaa1eb297ef09be0ae1b7c267a30.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_fb0cbaa1eb297ef09be0ae1b7c267a30.msa deleted file mode 100644 index 27cca120..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_fb0cbaa1eb297ef09be0ae1b7c267a30.msa +++ /dev/null @@ -1,95 +0,0 @@ ->syndip_1_chr20:63371865-63372891 -gagaagtgtggcagggttgggcgcagccacctatgagcccctgaacctccccaggccgtc -ggatctcacttcagagtggcctgggcatggcctcaggttaggtcaggtgaagactctatt -cctggctcaggaaaaccaccaggacaggtgagcccagcagcatctcgtggagggaggctc -tgagtcccgtgaggacaaggacggaacaccggggctgccacaggtcgcagagaccctgtg -tcaacacccttgttttgaggtgcagagaccaaagttgagacctggccatgcagcaggtct -gcagggacctcagagcccagggccactgtcctgtccccagccccattaaacgcccagggc -cactgtcctgtccccagccccattaaac-------------------------------- ------------------------------------------------------------- ---------------------------------------------------------gccc -agggccactgtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagc -cccattaaacgcccagggccactgtcctgtccccagccccattaaacgcccagggccact -ggcctgtccccagccccattaaacgcccagggccactgtcctgtccccagccccattaaa -cgcccagggccactggcctgtccccagccccattaaatgcccagggccactgtcctgtcc -ccagtctcattaaacgcagcaaacgtcttctggacgtgccgccagtcccacagaaaacca -aagcaaggcagactcaccgctcctgcatcccggagctcaggtccaggagggtctcgggaa -aggatgggggcaactggagtaccatcctaaagccgtctcagccccagggggccgcagggg -tctaccctgtcttctctcttgcaggtgtgtggttggttctagaagatgctgagccccccc -ccgcgca ->syndip_2_chr20:63371865-63372891 -gagaagtgtggcagggttgggcgcagccacctatgagcccctgaacctccccaggccgtc -ggatctcacttcagagtggcctgggcatggcctcaggttaggtcaggtgaagactctatt -cctggctcaggaaaaccaccaggacaggtgagcccagcagcatctcgtggagggaggctc -tgagtcccgtgaggacaaggacggaacaccggggctgccacaggtcgcagagaccctgtg -tcaacacccttgttttgaggtgcagagaccaaagttgagacctggccatgcagcaggtct -gcagggacctcagagcccagggccactgtcctgtccccagccccattaaacgcccagggc -cactgtcctgtccccagccccattaaac-------------------------------- ------------------------------------------------------------- ---------------------------------------------------------gccc -agggccactgtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagc -cccattaaacgcccagggccactgt----------------------------------- ---cctgtccccagccccattaaacgcccagggccactgtcctgtccccagccccattaaa -cgcccagggccactggcctgtccccagccccattaaatgcccagggccactgtcctgtcc -ccagtctcattaaacgcagcaaacgtcttctggacgtgccgccagtcccacagaaaacca -aagcaaggcagactcaccgctcctgcatcccggagctcaggtccaggagggtctcgggaa -aggatgggggcaactggagtaccatcctaaagccgtctcagccccagggggccgcagggg -tctaccctgtcttctctcttgcaggtgtgtggttggttctagaagatgctgagccccccc -ccgcgca ->p:HG002_1_chr20:63371865-63372891 -gagaagtgtggcagggttgggcgcagccacctatgagcccctgaacctccccaggccgtc -ggatctcacttcagagtggcctgggcatggcctcaggttaggtcaggtgaagactctatt -cctggctcaggaaaaccaccaggacaggtgagcccagcagcatctcgtggagggaggctc -tgagtcccgtgaggacaaggacggaacaccggggctgccacaggtcgcagagaccctgtg -tcaacacccttgttttgaggtgcagagaccaaagttgagacctggccatgcagcaggtct -gcagggacctcagagcccagggccactgtcctgtccccagccccattaaacgcccagggc -cactgtcctgtccccagccccattaaac-------------------------------- ------------------------------------------------------------- ---------------------------------------------------------gccc -agggccactgtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagc -cccattaaacgcccagggccactgt----------------------------------- ---cctgtccccagccccattaaacgcccagggccactgtcctgtccccagccccattaaa -cgcccagggccactggcctgtccccagccccattaaatgcccagggccactgtcctgtcc -ccagtctcattaaacgcagcaaacgtcttctggacgtgccgccagtcccacagaaaacca -aagcaaggcagactcaccgctcctgcatcccggagctcaggtccaggagggtctcgggaa -aggatgggggcaactggagtaccatcctaaagccgtctcagccccagggggccgcagggg -tctaccctgtcttctctcttgcaggtgtgtggttggttctagaagatgctgagccccccc -ccgcgca ->p:HG002_2_chr20:63371865-63372891 -gagaagtgtggcagggttgggcgcagccacctatgagcccctgaacctccccaggccgtc -ggatctcacttcagagtggcctgggcatggcctcaggttaggtcaggtgaagactctatt -cctggctcaggaaaaccaccaggacaggtgagcccagcagcatctcgtggagggaggctc -tgagtcccgtgaggacaaggacggaacaccggggctgccacaggtcgcagagaccctgtg -tcaacacccttgttttgaggtgcagagaccaaagttgagacctggccatgcagcaggtct -gcagggacctcagagcccagggccactgtcctgtccccagccccattaaacgcccagggc -cactgtcctgtccccagccccattaaac-------------------------------- ------------------------------------------------------------- ---------------------------------------------------------gccc -agggccactgtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagc -cccattaaacgcccagggccactgtcctgtccccagccccattaaacgcccagggccact -ggcctgtccccagccccattaaacgcccagggccactgtcctgtccccagccccattaaa -cgcccagggccactggcctgtccccagccccattaaatgcccagggccactgtcctgtcc -ccagtctcattaaacgcagcaaacgtcttctggacgtgccgccagtcccacagaaaacca -aagcaaggcagactcaccgctcctgcatcccggagctcaggtccaggagggtctcgggaa -aggatgggggcaactggagtaccatcctaaagccgtctcagccccagggggccgcagggg -tctaccctgtcttctctcttgcaggtgtgtggttggttctagaagatgctgagccccccc -ccgcgca ->ref_chr20:63371865-63372891 -gagaagtgtggcagggttgggcgcagccacctatgagcccctgaacctccccaggccgtc -ggatctcacttcagagtggcctgggcatggcctcaggttaggtcaggtgaagactctatt -cctggctcaggaaaaccaccaggacaggtgagcccagcagcatctcgtggagggaggctc -tgagtcccgtgaggacaaggacggaacaccggggctgccacaggtcgcagagaccctgtg -tcaacacccttgttttgaggtgcagagaccaaagttgagacctggccatgcagcaggtct -gcagggacctcagagcccagggccactgtcctgtccccagccccattaaacgcccagggc -cactgtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagccccat -taaacgcccagggccactgtcctgtccccagccccattaaacgcccagggccactgtcct -gtccccagccccattaaacgcccagggccactgtcctgtccccagccccattaaatgccc -agggccactgtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagc -cccattaaacgcccagggccactgtcctgtccccagccccattaaacgcccagggccact -gtcctgtccccagccccattaaacgcccagggccactgtcctgtccccagccccattaaa -cgcccagggccactggcctgtccccagccccattaaatgcccagggccactgtcctgtcc -ccagtctcattaaacgcagcaaacgtcttctggacgtgccgccagtcccacagaaaacca -aagcaaggcagactcaccgctcctgcatcccggagctcaggtccaggagggtctcgggaa -aggatgggggcaactggagtaccatcctaaagccgtctcagccccagggggccgcagggg -tctaccctgtcttctctcttgcaggtgtgtggttggttctagaagatgctgagccccccc -ccgcgca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_fb1e3d08ab0d6833b9dcb209316bd32a.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_fb1e3d08ab0d6833b9dcb209316bd32a.msa deleted file mode 100644 index 991c2414..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_fb1e3d08ab0d6833b9dcb209316bd32a.msa +++ /dev/null @@ -1,185 +0,0 @@ ->syndip_1_chr20:60314130-60315220 -tagggagatttcaggcacttttctgtcatccactacctgcccttctgccattgcagggtc -tagttatctttatctcctctgaggtctgagttctacattcacttgtttcctcatttattc -attaacaatattcatttcttagccaaggatggtggtgcacacctgtacttccagctactc -aggaggctgaggtggaaggattgaaaatccatccatctgtcctcctacccatcctgctat -ccatccatccatccatcctcccataatctatcttcccatccatttgtccttccttccttc -cttccttccttccttccttccttccttccttccttccttccacccatccatcctcccatt -catcctcccatgcatcctcccatccatccacccaaccatcctcccatccatcctcacatc -catcttcgcatccatccatccatccatctatccatccatccatccatcctcccatccatc -ctcccatccattatcccattcatccatcctcccatccatcctcctatccatccatccatc -catccaccctcccatccatccatcctcccatccatccactcttccatccatccatccacc -caccctt----------------ccatccatccatcctcccatccatccatcctcccatt -catctatccatccatccctcgatcctcccatccatccatcctcccatccatccatccatc -ctcccatccatccatccaccctcccatccatccatcctcccatccatctaccctcccatc -catccatcctcccacccaccctcccatccatccatcctcccatcctcccatccatccatc -catcctcccatccgtccatccatccttccatccac----------------cctcccatc -catccatcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatc -catccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcc -catccatccatcatccatccatccatccatccatcctcccataatctatcttcccatcca -tttgtccttccttccttccttccttccttccttccttcgttccacccatccatcctc--- -ccattcatcctcccatgcatcctcccatccatccaccca--------------------- --accatcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatct -atccat--------------------ccatcctcccatccatcctcccatcctcccatcc -attctcccattcatccatcctcccatccatcctcctatccatccatccatccatccaccc -tcccatccatccatcctcccatccatccacccttccatccatccatccacccacccttcc -atccatccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcc -tcccatccatccatccatcctcccatccgtccatccatccttccatccaccctcccatcc -atccatcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatcc -atccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctccc -atcctcccatccatccatccatccatccatccatcctcccatcctcccatcctcccatcc -atcgtcccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctccc -atccatcttcccatccattcatccatccatcttcccatccattcatccatccatcctgcc -atccatccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgcc -gtgagttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctcca -aaaatgaaaaaaagaatatattgatttcaggccagttacatagattctgtgttgaacaaa -actagatgtgtttcattcctgtctttaaggagcataaatctaataggaacaacagataat -ttttaaaaaatatatcaatgtgt ->syndip_2_chr20:60314130-60315220 -tagggagatttcaggcacttttctgtcatccactacctgcccttctgccattgcagggtc -tagttatctttatctcctctgaggtctgagttctacattcacttgtttcctcatttattc -attaacaatattcatttcttagccaaggatggtggtgcacacctgtacttccagctactc -aggaggctgaggtggaaggattgaaaatccatccatctgtcgtcctacccatcctgctat -ccatccatccatccatcctcccataatctatcttcccatccatttg-------------- -------tccttccttccttccttccttccttccttccttccacccatccatcctcccatg -catcctcccatgcatcctcccatccatccacccaaccatcctcccatccatcctcacatc -catcttcgcatccatccatccatccatctatccatccatccatccatcctcccatccatc -ctcccatccattatcccattcatccatcctcccatccatcctcctatccatccatccatc -catccaccctctcatccatccatcctcccatccatccacccttccatccatccatccacc -cacccttccatccatccatcctcccatccatccatcctcccatccatccatcctcccatt -catctatccatccatccctcgatcctcccatccatccatcctcccatccatccatccatc -ctcccatccatccatccaccctcccatccatccatcctcccatccatctaccctcccatc -catccatcctcccatccaccctcccatccatccatccatccatccaccctctcatccatc -catcctcccatccgtccatccatccttccatccaccctcccatccatccatcctcccatc -catccatcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatc -catccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcc -catccatccatcatccatccatccatccatccatcctcccataatctatcttcccatcca -tttgtccttccttccttccttccttccttcc--------ttccacccatccatcctc--- -ccattcatcctcccatgcatcctcccatccatccaccca--------------------- --accatcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatct -atccatccatcctcccatccatcctcccatcctcccatccatcctcccatcctcccatcc -attctcccattcatccatcctcccatccatcctcctatccatccatccatccatccaccc -tcccatccatccatcctcccatccatccacccttccatccatccatccacccacccttcc -atccatccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcc -tcccatccatccatccatcctcccatccgtccatccatccttccatccaccctcccatcc -atccatcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatcc -atccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctccc -atcctc----ccatccatccatccatccatccatcctcccatcctcccatcctcccatcc -atcgtcccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctccc -atccatcttcccatccattcatccatccatcttcccatccattcatccatccatcctgcc -atccatccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgcc -gtgagttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctcca -aaaatgaaaaaaagaatatattgatttcaggccagttacatagattctgtgttgaacaaa -actagatgtgtttcattcctgtctttaaggagcataaatctaataggaacaacagataat -ttttaaaaaatatatcaatgtgt ->p:HG002_1_chr20:60314130-60315220 -tagggagatttcaggcacttttctgtcatccactacctgcccttctgccactgcagggtc -tagttatctttatctcctctgaggtctgagttctacattcacttgtttcctcatttattc -attaacaatattcatttcttagccaaggatggtggtgcacacctgtacttccagctactc -aggaggctgaggtggaaggattgaaaatccatccatctgtcgtcctacccatcctgctat -ccatccatccatccatcctcccataatctatcttcccatccatttg-------------- -------tccttccttccttccttccttccttccttccttccacccatccatcctcccatg -catcctcccatgcatcctcccatccatccacccaaccatcctcccatccatcctcacatc -catcttcgcatccatccatccatccatctatccatccatccatccatcctcccatccatc -ctcccatccattatcccattcatccatcctcccatccatcctcctatccatccatccatc -catccaccctctcatccatccatcctcccatccatccacccttccatccatccatccacc -cacccttccatccatccatcctcccatccatccatcctcccatccatccatcctcccatt -catctatccatccatccctcgatcctcccatccatccatcctcccatccatccatccatc -ctcccatccatccatccaccctcccatccatccatcctcccatccatctaccctcccatc -catccatcctcccatccaccctcccatccatccatccatccatccaccctctcatccatc -catcctcccatccgtccatccatccttccatccaccctcccatccatccatcctcccatc -catccatcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatc -catccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcc -catccatccatcatccatccatccatccatccatcctcccataatctatcttcccatcca -tttgtccttccttccttccttccttccttcc--------ttccacccatccatcctc--- -ccattcatcctcccatgcatcctcccatccatccaccca--------------------- --accatcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatct -atccatccatcctcccatccatcctcccatcctcccatccatcctcccatcctcccatcc -attctcccattcatccatcctcccatccatcctcctatccatccatccatccatccaccc -tcccatccatccatcctcccatccatccacccttccatccatccatccacccacccttcc -atccatccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcc -tcccatccatccatccatcctcccatccgtccatccatccttccatccaccctcccatcc -atccatcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatcc -atccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctccc -atcctc----ccatccatccatccatccatccatcctcccatcctcccatcctcccatcc -atcgtcccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctccc -atccatcttcccatccattcatccatccatcttcccatccattcatccatccatcctgcc -atccatccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgcc -gtgagttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctcca -aaaatgaaaaaaagaatatattgatttcaggccagttacatagattctgtgttgaacaaa -actagatgtgtttcattcctgtctttaaggagcataaatctaataggaacaacagataat -ttttaaaaaatatatcaatgtgt ->p:HG002_2_chr20:60314130-60315220 -tagggagatttcaggcacttttctgtcatccactacctgcccttctgccattgcagggtc -tagttatctttatctcctctgaggtctgagttctacattcacttgtttcctcatttattc -attaacaatattcatttcttagccaaggatggtggtgcacacctgtacttccagctactc -aggaggctgaggtggaaggattgaaaatccatccatctgtcctcctacccatcctgctat -ccatccatccatccatcctcccataatctatcttcccatccatttgtccttccttccttc -cttccttccttccttccttccttccttccttccttccttccacccatccatcctcccatt -catcctcccatgcatcctcccatccatccacccaaccatcctcccatccatcctcacatc -catcttcgcatccatccatccatccatctatccatccatccatccatcctcccatccatc -ctcccatccattatcccattcatccatcctcccatccatcctcctatccatccatccatc -catccaccctcccatccatccatcctcccatccatccactcttccatccatccatccacc -caccctt----------------ccatccatccatcctcccatccatccatcctcccatt -catctatccatccatccctcgatcctcccatccatccatcctcccatccatccatccatc -ctcccatccatccatccaccctcccatccatccatcctcccatccatctaccctcccatc -catccatcctcccacccaccctcccatccatccatcctcccatcctcccatccatccatc -catcctcccatccgtccatccatccttccatccac----------------cctcccatc -catccatcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatc -catccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcc -catccatccatcatccatccatccatccatccatcctcccataatctatcttcccatcca -tttgtccttccttccttccttccttccttccttccttcgttccacccatccatcctc--- -ccattcatcctcccatgcatcctcccatccatccaccca--------------------- --accatcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatct -atccat--------------------ccatcctcccatccatcctcccatcctcccatcc -attctcccattcatccatcctcccatccatcctcctatccatccatccatccatccaccc -tcccatccatccatcctcccatccatccacccttccatccatccatccacccacccttcc -atccatccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcc -tcccatccatccatccatcctcccatccgtccatccatccttccatccaccctcccatcc -atccatcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatcc -atccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctccc -atcctcccatccatccatccatccatccatccatcctcccatcctcccatcctcccatcc -atcgtcccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctccc -atccatcttcccatccattcatccatccatcttcccatccattcatccatccatcctgcc -atccatccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgcc -gtgagttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctcca -aaaatgaaaaaaagaatatattgatttcaggccagttacatagattctgtgttgaacaaa -actagatgtgtttcattcctgtctttaaggagcataaatctaataggaacaacagataat -ttttaaaaaatatatcaatgtgt ->ref_chr20:60314130-60315220 -tagggagatttcaggca------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------ctttt -ctgtcatccactacctgcccttctgccattgcagggtctagttatctttatctcctctga -ggtctgagttctacattcacttgtttcctcatttattcattaacaatattcatttcttag -ccaaggatggtggtgcacacctgtacttccagctactcaggaggctgaggtggaaggatt -gaaaatccatccatctgtcctcctacccatcctgctatccatccatccatccatcctccc -at-aat--------------------ctatcttcccatccatttgtccttccttccttcc -ttccttcc-----ttccttcttccttccttccttccttccttccttccacccatccatcc -tcccattcatcctcccatgcatcctcccatccatccacccaaccatcctcccatccatcc -tcacatcgatcttcgcatccatccatcgatcgatctatccatccatccattctcccattc -atccatcctcccatccatcctcctatccatccatcca----tccatccaccctcccatcc -atccatcctcccatccatccacccttccatccatccat----ccacccacccttccatcc -atccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctccc -atcctcccatccatccatccatccatccatccatcctcccatcctcccatcctcccatcc -atcgtcccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctccc -atccatcttcccatccattcatccatccatcttcccatccattcatccatccatcctgcc -atccatccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgcc -gtgagttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctcca -aaaatgaaaaaaagaatatattgatttcaggccagttacatagattctgtgttgaacaaa -actagatgtgtttcattcctgtctttaaggagcataaatctaataggaacaacagataat -ttttaaaaaatatatcaatgtgt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_fb2c7d222388665a15e2429f8ef24422.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_fb2c7d222388665a15e2429f8ef24422.msa deleted file mode 100644 index b4160297..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_fb2c7d222388665a15e2429f8ef24422.msa +++ /dev/null @@ -1,360 +0,0 @@ ->syndip_1_chr20:64131604-64134155 -tactgtgctgctctgtgtttagctgggcatgtgctctgggctgggcatgagacaaaatga -ggatagctgctgggctgtggatagttgttcacaggggtgcaggctgttgtaggtgggcca -ggaggggctgggcagcccatgagggtgaggctgagactccacactgagcccaggtttagg -ggacctggtgggggtcacagcctcccctgtcccagacttctcctggcctctctcatgtcc -tatgagaccccctcactgtccactctcatggcctgtagagaccccctcactgtcaactct -catgtcctatagagaccccctcactgtcaactctcatgtcctatgagaccccctcactgt -ccactctcatggcctgtagagaccccctcactgtccaccctcatgtcctata-------- -------------------------gagaccccctcactgtccaccctcatggcctgtaga -gaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatgg -cctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccacc -ctcatgtcctatagagaccccctcactgtccactctcatgtcctatagagaccccctcac -tgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagagacc -ccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtccta -tagagaccccctcactgtccactctcatgtcctatagagaccccctcactgtccaccctc -atgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtc -caccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccct -cactgtccactctcatgtcctatgagaccccctcactgtccaccctcgtgtcctatagag -accccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggc -ctgtagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccacc -ctcatgtcctatgagaccccctcactgtccactctcatgtcctatgagaccccctcactg -tccactctcatggcctgtagagaccccctcactgtccaccctcatgtcctgtagagaccc -cctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctat -agagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcat -gtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcc -accctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccct -cactgtccactctcatgtcctatagagacccctcactgtccaccctcatggcctatagag -accccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcgtgtc -ctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccactc -tcatgtcctatgagaccccctcactgtccactctcatggcctgtagagaccccctcactg -tccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctgtagagacccc -ctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatg -tcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcca -ccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctc -actgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagaga -ccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc -tcatgtcctatgagaccccctcactgtccaccctcgtgtcctatagagaccccctcactg -tcaactctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatgagacccc -ctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcat -gtcctat----------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------gaga -ccccctcactgtccaccctcgtgtcctatagagaccccctcactgtcaactctcatgtcc -tatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactctccaccc -tcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcact -gtccaccctcatgtcctat-----------------------------------gagacc -ccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtccta -tgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctca -----------------------------------tggcctatagagaccccctcactgtc -caccctcatgtcctatagagaccccctcactctccaccctcatggcctatagagaccccc -tcactgtccaccctcgtgtcctatagagaccccctcactctccaccctcatggcctatag -agaccccctcactgtccaccctcatggcctatagagaccccctcactgtccactctcatg -tcctatgagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccac -cctcatgtcctat-----------------------------------gagaccccctca -ctgtccactctcatgtccta-----------------------------------tgaga -ccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcc -tatgagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccct -catgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccactctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatgagaccccc -tcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctatga -gaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgt -cctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccac -tctc-------------------------------------------------------- -------------atggcctgtagagaccccctcactgtccacccatatggcctgtagaga -ccccctcactgtccaccctcaggaccctctgcatttgctccttgggttcccggaacttga -gcttgggtcttggtccacagcagctttgggaagggccctcggctgctttttgcttcagca -gctggggagcagttaactttcagacccggccctcccccaaggcagctcagggaggggctg -gacactcggttatttatgtatttacttatttttaaatcaaagcacagcaaacatgaccat -gtgggggtggc ->syndip_2_chr20:64131604-64134155 -tactgtgctgctctgtgtttagctgggcatgtgctctgggctgggcatgagacaaaatga -ggatagctgctgggctgtggatagttgttcacaggggtgcaggctgttgtaggtgggcca -ggaggggctgggcagcccatgagggtgaggctgagactccacactgagcccaggtttagg -ggacctggtgggggtcacagcctcccctgtcccagacttctcctggcctctctcatgtcc -tatgagaccccctcactgtccactctcatggcctgtagagaccccctcactgtccaccct -catgtcctatagagaccccctcactgtccaccctcatggcctatgagaccccctcactgt -ccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagacccc -tcactgtccaccctcatggcctatgagaccccctcactgtccactctcatgtcctataga -gaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgt -cctatagaga-cccctcactgtccaccctcatggcctatgagaccccctcactgtccacc -ctcatggcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcac -tgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagagacc -ccctcactgtccaccctcatgtcctat-gagaccccctcactgtccactctcatgtccta -tagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctc -gtgtcctatgagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtc -caccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccct -cactgtccaccctcatgtccta-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------tagagaccccctcactgtccaccctcatgtcctatagagaccc -cctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatggcctgt -a---------------------------------gagaccccctcactgtccaccctcat -gtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtcc -accctcatggcctatagagaccccctcactgtccaccctcatgtcctatagagaccccct -cactgtccaccctcatgtcctat----------------------------------gag -accccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtc -ctatagagaccccctcactgtccaccctcatgtcctat---------------------- ------------------------------------------------------------- -----------------------------------------------------gagacccc -ctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcgtgtcctata -gagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatg -tcctatagagaccccctcactgtccaccctcatggcctatagagaccccctcactgtcca -ccctcatggcctgtagagaccccctcactgtccaccctcatggcctatagagaccccctc -actgtccaccctcgtgtcctatgagaccccctcactgtccaccctcatggcctatagaga -ccccctcactgtccaccctcatggcctat-gagaccccctcactgtccaccctcgtgtcc -tat-gagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccc -tcatggcctatgagaccccctcactgtccaccctcatggcctgta--------------- -----------------------------------------------------gagacccc -ctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcat -gtcctatgagaccccctcactgtccactctcatgtcctatagagacccctcactgtccac -cctcatggcctatagagaccccctcactgtccaccctcatggcctatagagaccccctca -ctgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagaga -ccccctcactgtccaccctcatgtcctgtagagaccccctcactgtccaccctcatggcc -tgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc -tcatgtcctatagagaccccctcactgtccaccctcatggcctatagagaccccctcact -gtccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagacc -ccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtccta -tgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctca -tgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtc -caccctcgtgtcctatagagaccccctcactgtccaccctcatggcctatagagaccccc -tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatag -agaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatg -tcctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccac -cctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctgtagaga -ccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatggcc -tatgagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccct -catgtcctatagagacccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccc -tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatga -gaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgt -cctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccac -cctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctca -ctgtccacccatatggcctgtagagaccccctcactgtccaccctcatggcctgtagaga -ccccctcactgtccaccctcaggaccctctgcatttgctccttgggttcccggaacttga -gcttgggtcttggtccacagcagctttgggaagggccctcggctgctttttgcttcagca -gctggggagcagttaactttcagacccggccctcccccaaggcagctcagggaggggctg -gacactcggttatttatgtatttacttatttttaaatcaaagcacagcaaacatgaccat -gtgggggtggc ->p:HG002_1_chr20:64131604-64134155 -tactgtgctgctctgtgtttagctgggcatgtgctctgggctgggcatgagacaaaatga -ggatagctgctgggctgtggatagttgttcacaggggtgcaggctgttgtaggtgggcca -ggaggggctgggcagcccatgagggtgaggctgagactccacactgagcccaggtttagg -ggacctggtgggggtcacagcctcccctgtcccagacttctcctggcctctctcatgtcc -tatgagaccccctcactgtccactctcatggcctgtagagaccccctcactgtccaccct -catgtcctatagagaccccctcactgtccaccctcatggcctatgagaccccctcactgt -ccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagacccc -tcactgtccaccctcatggcctatgagaccccctcactgtccactctcatgtcctataga -gaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgt -cctatagaga-cccctcactgtccaccctcatggcctatgagaccccctcactgtccacc -ctcatggcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcac -tgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagagacc -ccctcactgtccaccctcatgtcctat-gagaccccctcactgtccactctcatgtccta -tagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctc -gtgtcctatgagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtc -caccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccct -cactgtccaccctcatgtccta-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------tagagaccccctcactgtccaccctcatgtcctatagagaccc -cctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatggcctgt -a---------------------------------gagaccccctcactgtccaccctcat -gtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtcc -accctcatggcctatagagaccccctcactgtccaccctcatgtcctatagagaccccct -cactgtccaccctcatgtcctat----------------------------------gag -accccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtc -ctatagagaccccctcactgtccaccctcatgtcctat---------------------- ------------------------------------------------------------- -----------------------------------------------------gagacccc -ctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcgtgtcctata -gagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatg -tcctatagagaccccctcactgtccaccctcatggcctatagagaccccctcactgtcca -ccctcatggcctgtagagaccccctcactgtccaccctcatggcctatagagaccccctc -actgtccaccctcgtgtcctatgagaccccctcactgtccaccctcatggcctatagaga -ccccctcactgtccaccctcatggcctat-gagaccccctcactgtccaccctcgtgtcc -tat-gagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccc -tcatggcctatgagaccccctcactgtccaccctcatggcctgta--------------- -----------------------------------------------------gagacccc -ctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcat -gtcctatgagaccccctcactgtccactctcatgtcctatagagacccctcactgtccac -cctcatggcctatagagaccccctcactgtccaccctcatggcctatagagaccccctca -ctgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagaga -ccccctcactgtccaccctcatgtcctgtagagaccccctcactgtccaccctcatggcc -tgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc -tcatgtcctatagagaccccctcactgtccaccctcatggcctatagagaccccctcact -gtccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagacc -ccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtccta -tgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctca -tgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtc -caccctcgtgtcctatagagaccccctcactgtccaccctcatggcctatagagaccccc -tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatag -agaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatg -tcctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccac -cctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctgtagaga -ccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatggcc -tatgagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccct -catgtcctatagagacccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccc -tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatga -gaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgt -cctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccac -cctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctca -ctgtccacccatatggcctgtagagaccccctcactgtccaccctcatggcctgtagaga -ccccctcactgtccaccctcaggaccctctgcatttgctccttgggttcccggaacttga -gcttgggtcttggtccacagcagctttgggaagggccctcggctgctttttgcttcagca -gctggggagcagttaactttcagacccggccctcccccaaggcagctcagggaggggctg -gacactcggttatttatgtatttacttatttttaaatcaaagcacagcaaacatgaccat -gtgggggtggc ->p:HG002_2_chr20:64131604-64134155 -tactgtgctgctctgtgtttagctgggcatgtgctctgggctgggcatgagacaaaatga -ggatagctgctgggctgtggatagttgttcacaggggtgcaggctgttgtaggtgggcca -ggaggggctgggcagcccatgagggtgaggctgagactccacactgagcccaggtttagg -ggacctggtgggggtcacagcctcccctgtcccagacttctcctggcctctctcatgtcc -tatgagaccccctcactgtccactctcatggcctgtagagaccccctcactgtcaactct -catgtcctatagagaccccctcactgtcaactctcatgtcctatgagaccccctcactgt -ccactctcatggcctgtagagaccccctcactgtccaccctcatgtcctata-------- -------------------------gagaccccctcactgtccaccctcatggcctgtaga -gaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatgg -cctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccacc -ctcatgtcctatagagaccccctcactgtccactctcatgtcctatagagaccccctcac -tgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagagacc -ccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtccta -tagagaccccctcactgtccactctcatgtcctatagagaccccctcactgtccaccctc -atgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtc -caccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccct -cactgtccactctcatgtcctatgagaccccctcactgtccaccctcgtgtcctatagag -accccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggc -ctgtagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccacc -ctcatgtcctatgagaccccctcactgtccactctcatgtcctatgagaccccctcactg -tccactctcatggcctgtagagaccccctcactgtccaccctcatgtcctgtagagaccc -cctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctat -agagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcat -gtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcc -accctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccct -cactgtccactctcatgtcctatagagacccctcactgtccaccctcatggcctatagag -accccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcgtgtc -ctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccactc -tcatgtcctatgagaccccctcactgtccactctcatggcctgtagagaccccctcactg -tccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctgtagagacccc -ctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatg -tcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcca -ccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctc -actgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagaga -ccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc -tcatgtcctatgagaccccctcactgtccaccctcgtgtcctatagagaccccctcactg -tcaactctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatgagacccc -ctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcat -gtcctat----------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------gaga -ccccctcactgtccaccctcgtgtcctatagagaccccctcactgtcaactctcatgtcc -tatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactctccaccc -tcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcact -gtccaccctcatgtcctat-----------------------------------gagacc -ccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtccta -tgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctca -----------------------------------tggcctatagagaccccctcactgtc -caccctcatgtcctatagagaccccctcactctccaccctcatggcctatagagaccccc -tcactgtccaccctcgtgtcctatagagaccccctcactctccaccctcatggcctatag -agaccccctcactgtccaccctcatggcctatagagaccccctcactgtccactctcatg -tcctatgagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccac -cctcatgtcctat-----------------------------------gagaccccctca -ctgtccactctcatgtccta-----------------------------------tgaga -ccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcc -tatgagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccct -catgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccactctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatgagaccccc -tcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctatga -gaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgt -cctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccac -tctc-------------------------------------------------------- -------------atggcctgtagagaccccctcactgtccacccatatggcctgtagaga -ccccctcactgtccaccctcaggaccctctgcatttgctccttgggttcccggaacttga -gcttgggtcttggtccacagcagctttgggaagggccctcggctgctttttgcttcagca -gctggggagcagttaactttcagacccggccctcccccaaggcagctcagggaggggctg -gacactcggttatttatgtatttacttatttttaaatcaaagcacagcaaacatgaccat -gtgggggtggc ->ref_chr20:64131604-64134155 -tactgtgctgctctgtgtttagctgggcatgtgctctgggctgggcatgagacaaaatga -ggatagctgctgggctgtggatagttgttcacaggggtgcaggctgttgtaggtgggcca -ggaggggctgggcagcccatgagggtgaggctgagactccacactgagcccaggtttagg -ggacctggtgggggtcacagcctcccctgtcccagacttctcctggcctctctcatgtcc -tatgagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtccactct -catggcctata------------------------------------------------- ------------------------------------------------------------- -------------------------gagaccccctcactgtccaccctcatggcctgtaga -gaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgt -cctatagaga-------------------------------------------------- ------------------ccccctcactgtccaccctcatggcctgtagagaccccctcac -tgtccaccctcatgtcctatgagaccccctcactgtccaccctcgtgtcctatagagacc -ccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtccta -tagagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtccaccctc -atgtcctatgagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtc -caccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccct -cactgtccaccctcatgtccta-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------tagagaccccctcactgtccactctcatgtcctatagagaccc -cctcactgtccaccctcatggcctat-gagaccccctcactgtccactctcatggcctat -a---------------------------------gagaccccctcactgtccaccctcat -ggcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcc -accctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccct -cactgtccaccctcatggcctat----------------------------------gag -accccctcactgtccaccctcatgtcctat------------------------------ ------gagaccccctcactgtccaccctcatgtcctat---------------------- ------------------------------------------------------------- ----------------------------------------------------agagacccc -ctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccgccctcatgtcctatgagaccccctcactgtccaccctcatg -tcctatagagaccccctcactgtccaccctcatggcctg--------------------- ------------------------------------------------tagagaccccctc -actgtccgccctcatgtcctatgagaccccctcactgtccaccctcatgtcctgtagaga -ccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcc -tat-gagaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccc -tcatgtcctatgaga--------------------------------------------- ------------------------------------------------------------- --------------------------------cccctcactgtccaccctcatgtcctat- -----------------------------------gagaccccctcactgtccaccctcat -gtcctat----------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------gaga -ccccctcactgtccactctcatgtcctatgaga--------------------------- --------------------------------------------cccctcactgtccaccc -tcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcact -gtcaactctcatgtcctat-----------------------------------gagacc -ccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtccaa -agagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctca ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------tggcctgtag -agaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatg -tccaaagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccac -cctcatggcctgt----------------------------------------------- --------------------------------------------------------agaga -ccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcc -aaagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccca -tatggcctgta------------------------------------------------- -------------------gagaccccctcactgtccaccctcatgtcctata-------- -----------------------------------------------------------ga -gaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgg -cctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccac -cctc-------------------------------------------------------- -------------atggcctgtagagaccccctcactgtccacccatatggcctgtagaga -ccccctcactgtccaccctcaggaccctctgcatttgctccttgggttcccggaacttga -gcttgggtcttggtccacagcagctttgggaagggccctcggctgctttttgcttcagca -gctggggagcagttaactttcagacccggccctcccccaaggcagctcagggaggggctg -gacactcggttatttatgtatttacttatttttaaatcaaagcacagcaaacatgaccat -gtgggggtggc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_fba649023d92213d13abd6e375f45b15.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_fba649023d92213d13abd6e375f45b15.msa deleted file mode 100644 index 4c11a937..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_fba649023d92213d13abd6e375f45b15.msa +++ /dev/null @@ -1,495 +0,0 @@ ->syndip_1_chr20:20354370-20358523 -gtatgcacctgtaatcccagctactcaggaggctgaggcaggagaattgcttgcacccag -gaggcagaggttgtggtgagccaagatcataccactgcactccagtctgggtgacagaga -gagaccttgtctcaaaaaaaaaaaaaaaaaaatcaggtacagaaaggtaaatactgcacg -atctcacttacatgtggaatctaaagaagttgaattcataagggtaatgaggggaggaag -gggtggtcatactgtgtgaagggagatggtcacactgagggaaggtggtcacactgtgag -aagggaggtagtcacattgtgagagaaaaagtgatcacactgtgtgaggggaggtggtca -cactgtgagagaaaaagtaatcatactgtgaaagggaggtggtcacgctgagaggggagg -tggtcacactgtgtcaggggaggtggtcacactgtgagagaaaaagtaatcacactgtga -ggggatgtggtcacactgagaggggaggtggtcagactgtgtcagaggaggtggtcacac -tgaggggaggtggtcacactgtgagaggggaggtggtcagactctgtcagaggaggtggt -cacactgtgagaggggaggtggtcacactgaggggaagtggtcacactgtgagaggggag -gtggtcacactgaggggagatggtcacactgcaagaggggaggtgatcacactgagggg- -----------------------aggtggtcacactgtgagagggaaggtggtcacactgt -gagagggaaggtggtcacactgtgtgaggggaggtggtcacactgtgaggggaggtggtc -acattgtgagagggaagggggtcactgtgagaggggagaaggtcacactaaggggaggta -gtcacactgtgaggggaggtgatcacactaaggggaggtggtcacactgtgagaggaggt 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-ggggaggtggtcacactgaggggaagtggtcacactgaggggaatggtcatactgtgagg -ggaggtggtcacactgtgaaagaagatgatcacagtatgagaggtcatccttcaagaggc -aagtgcccaaaaatctgtttataatctagagcaatatttgcctgaaataaactttaaaag -tggttttacgctatttaacccagtgtcagaacagcagcatacaatatgagctcaaaatct -tgtataattttagtaaggtaattgtttttggttggtttgatacaattctccagaaaaatt -aaggaagaa ->p:HG002_2_chr20:20354370-20358523 -gtatgcacctgtaatcccagctactcaggaggctgaggcaggagaattgcttgcacccag -gaggcagaggttgtggtgagccaagatcataccactgcactccagtctgggtgacagaga -gagaccttgtctcaaaaaaaaaaaaaaaaaaatcaggtacagaaaggtaaatactgcacg -atctcacttacatgtggaatctaaagaagttgaattcataagggtaatgaggggaggaag -gggtggtcatactgtgtgaagggagatggtcacactgagggaaggtggtcacactgtgag -aagggaggtagtcacattgtgagagaaaaagtgatcacactgtgtgaggggaggtggtca -cactgtgagagaaaaagtaatcatactgtgaaagggaggtggtcacgctgagaggggagg -tggtcacactgtgtcaggggaggtggtcacactgtgagagaaaaagtaatcacactgtga -ggggatgtggtcacactgagaggggaggtggtcagactgtgtcagaggaggtggtcacac -tgaggggaggtggtcacactgtgagaggggaggtggtcagactctgtcagaggaggtggt 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-acactgaggggaggtggtcacagtgtgaggggagatggtcacactgaggggaggtggtca -cagtgtgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtc -acactggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca -ctgaggggaagtggtcacactgaggggaggtggtcaca--ctgaggggaggtggtcatag -tgtgaggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca -ctgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg -tgaggggaggtggtcacactggggaggtggtcacactgtgaggggaggtggtcacactgt -gaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgag -gggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcatactgtga -gtgaggaggtagtcacac--tgaggggagggggtcatactgcgagtggaggtagtcacac -tgtgaagggtggtagtcacactgagaggaggtggtcacactgaggggaagtggtcacact -gaggggaggtggtcatactg---------------------------------------- -tgaggggaagtggtcacactgaggggaggtggtcatagtgtga--ggggaggtggtcaca -ctgaggggaggtggtcacagtgtgaggggaggtggtcacac--tgaggggaggtggtcac -actgaggggaggtggtcacagtgtgagaggaggtggtcacactgaggggaggtggtcaca -gtgtgaggggagatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcac -actgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcaca -ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag -tgtgaggggagatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcaca -ctgaggggaggtggtcaca-------------------gtgtgaggggaggtggtcacac -tgaggggaggtggtcacactgagaggaggtggtcacactgaggggaggtggtcatactgt -gagtgaggaggtagtcacactgaggggaagtggtcacactgaggggaggtg--------- ----------------------------------gtcacactgaggggagggggtcatact -gcgagtggaggtagtcacactgtgaagggtggtagtcacactgagaggaggtggtcacac -tgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcacact -gaggggaggtggtcatagtgtgaggggag------------------------------- ------------------------------------------------------------- -----------gtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtg -tga--ggggaggtggtcacactgaggggaggtggtcacagtgtacggggaggtggtcata -c--tgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcac -actgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcaca -ctgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcac -actgaggggaggtggtcaca-c-tgaggagaggtggtcat-------------------a -gtgtgaggggaggtggtcacac-------------------------------------- ------------------------------------------------------------- ----tgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcac -actgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcaca -ctgaggggaggtggtcatagtgtgaggggaggtggtcacagtg----------------- ----------------------tgaggggaggtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg -tgaggggaggtggtcacactgtgaggggaggtggtcacattgaggagaggtggtcatagt -gtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg -tgaggggaggtggtcacactgaggagaggtggtcatagtgtgcggggaggtggtcacact -gaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacagtg -tgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacact -gaggggaggtggtcacactgagggaaggtggtcacactgaggggaggtggtcatagtgtg -aggggaggtggtcatagtgtgaggggaggtggtcacagtgtgaggggaggtggtcacact -gaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactg -tgaggggaggtgggcacactgtgaggggtggtagtcacactgagaggaggtggtcacact -gaggggaggtggtcacactgaggggaggtggtcacactgaggggaatggtcatactgtga -ggggaggtggtcacactgaggggaagtggtcacactgaggggaatggtcatactgtgagg -ggaggtggtcacactgtgaaagaagatgatcacagtatgagaggtcatccttcaagaggc -aagtgcccaaaaatctgtttataatctagagcaatatttgcctgaaataaactttaaaag -tggttttacgctatttaacccagtgtcagaacagcagcatacaatatgagctcaaaatct -tgtataattttagtaaggtaattgtttttggttggtttgatacaattctccagaaaaatt -aaggaagaa ->ref_chr20:20354370-20358523 -gtatgcacctgtaatcccagctactcaggaggctgaggcaggagaattgcttgcacccag -gaggcagaggttgtggtgagccaagatcataccactgcactccagtctgggtgacagaga -gagaccttgtctc-aaaaaaaaaaaaaaaaaatcaggtacagaaaggtaaatactgcacg -atctcacttacatgtggaatctaaagaagttgaattcataagggtaatgaggggaggaag -gggtggtcatactgtgtgaagggagatagtcacactgagggaaggtggtcacactgtgag -aagggaggtagtcacattgtgagagaaaaagtgatcacactgtgtgaggggaggtggtca -cactgtgagagaaaaagtaatcatactgtgaaagggaggtggtcacgctgagaggggagg -tggtcacactgtgtcaggggaggtggtcacactgtgagagaaaaagtaatcacactgtga -ggggatgtggtcacactgagaggggaggtggtcagactgtgtcagaggaggtggtcacac -tgagg----------------------------------------------ggaggtggt -cacactgtgagaggggaggtggtcacactgaggggaagtggtcacactgtgagaggggag -gtggtcacactgaggggagatggtcacactgcaagaggggaggtgatcacactgagggg- -----------------------aggtggtcacactgtgagagggaaggtggtcacactgt -gagagggaaggtggtcacactgtgtgaggggaggtggtcacactgtgaggggaggtggtc -acattgtgagagggaagggggtcactgtgagaggggagaaggtcacactaaggggaggta -gtcacactgtgaggggaggtgatcacactaaggggaggtggtcacactgtgagaggaggt -ggtcacactgtgaggggtggtcacactgtgaggggaggtcacactgaggggaggtagtga -cactatgagcagagatggtcacactgtgaggggaggtggtcacactgaggggaggtagtg -acactgtgagcagagatggtcacactgtgaggggaggtggtcacactgaggggagg---- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------tggtcacactgtgagg -ggaggtggtcacactgaggggaggtggtcacactgtgaggggaggtggtcacactgtgag -gggaggtggtcacactgaggggaggtagtgacactgtgagcagagatggtcacactgtga -ggggagggggtcacactgtgagggggaaggtggtcacactgtgagaggggagaaggtcac -actaaggggaggtagtcacactgtgaggggaggtgatcacactaaggggaggtggtcaca -ctgtgagaggaggtggtcacactgtgaggggaggtcacactgaggggaggtagtgacact -atgagcagagatggtcacactgtgaggggaggtggtcacactgaggggaggtagtgacac -tgtgagcagagatggtcacactgtgaggggaggtggtcacactgaggggaggtagtcaca -ctgtgaggggaggtggtcacactgtgaggggaggtggtcacactgaggggaggtagtgac -actgtgagcagagatggtcacactgtaaggggaggtgatcacactgtgaggggac---gt -cacactgtgaggggaggtggtcacactgtgagaggggaggtgaccacacaggggaggtgg -tcacactgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggaggtg -gtcacac--tgaggggaggtagtcacactgagaggaggtggtcacactgaggggaagtgg -tcacactgagggggggtggtcacactgaggggaggtggtcatactgtgagtgaggagcta -gtcacactgaggggaggggtcatactgcgagtggaggtagtcacactgtgaagggtggta -gtcacactgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtc -atactgtgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggt -cacactgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtc -acactgaggggaggtggtcacagtgtgaggggagatggtcacactgaggggaggtggtca -cagtgtgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtc -acactggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca -ctgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacac -t----ggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca -ctgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg -tgaggggaggtggtcacact---------------------ggggaggtggtcacactgt -gaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgag -gggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacac----- --tggggaggtggtcacactgtgaggggaggtggtcacactgtgaggggaggtggtcacac ---tgagaggaggtggtcacactgaggggaagtggtcacactgagaggaggtggtcacact -gaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggaagtggtcacac -tgaggggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcaca -ctgaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcac -actgagaggaggtggtcaca--ctgaggggaagtggtcacactgaggggaggtggtcata -ctgtgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcac -actgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcaca ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------gtgtgcggggaggtggtcatac -tgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatactgt -gagt-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------gaggaggtagtcacactgaggggagggggtcatactgcgagtggaggtagtcaca -ctgtgaagggtggtagtcaca--ctgagaggaggtggtcacactgaggggaagtggtcac -actgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtcata -gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcac -actgaggggaggtggtcacagtgtgcggggaggtggtcat-------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------actgaggggaggtggtcacagtgtgaggggaggtggtcacagtg -tgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacact -gaggggaggtggtcacactgagggaaggtggtcacactgaggggaggtggtcatagtgtg -aggggaggtggtcatagtgtgaggggaggtggtcacagtgtgaggggaggtggtcacact -gaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactg -tgaggggaggtgggcacactgtgaggggtggtagtcacactgagaggaggtggtcacact -gaggggaggtggtcacactgaggggaagtggtcacactgaggggaatggtcatactgtga -ggggaggtggtcacactgaggggaagtggtcacactgaggggaatggtcatactgtgagg -ggaggtggtcacactgtgaaagaagatgatcacagtatgagaggtcatccttcaagaggc -aagtgcccaaaaatctgtttataatctagagcaatatttgcctgaaataaactttaaaag -tggttttacgctatttaacccagtgtcagaacagcagcatacaatatgagctcaaaatct -tgtataattttagtaaggtaattgtttttggttggtttgatacaattctccagaaaaatt -aaggaagaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_fbe2022855d4e2527c86f41fc179b80f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_fbe2022855d4e2527c86f41fc179b80f.msa deleted file mode 100644 index 5023fb05..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_fbe2022855d4e2527c86f41fc179b80f.msa +++ /dev/null @@ -1,150 +0,0 @@ ->syndip_1_chr20:60314330-60315020 -ttgaaaatccatccatctgtcctcctacccatcctgctatccatccatccatccatcctc -ccataatctatcttcccatccatttgtccttccttccttccttccttccttc---cttcc -ttccttccttccttccttccttccacccatccatcctcccattcatcctcccatgcatcc -tcccatccatccacccaaccatcctcccatccatcctcacatccatcttcgcatccatcc -atccatccatctatccatccatccatccatcctcccatccatcctcccatccattatccc -attcatccatcctcccatccatcctcctatccatccatccatccatccaccctcccatcc -atccatcctcccatccatccactcttccatccatccatccacccaccctt---------- -------ccatccatccatcctcccatccatccatcctcccattcatctatccatccatcc -ctcgatcctcccatccatccatcctcccatccatccatccatcctcccatccatccatcc -accctcccatccatccatcctcccatccatctaccctcccatccatccatcctcccaccc -accctcccatccatccatcctcccatcctcccatccatccatccatcctcccatccgtcc -atccatccttccatccac----------------cctcccatccatccatcctcccatcc -atctaccctcccatccatccatcctcccacccaccctcccatccatccaccctcccatcc -atccatcctcccatccatctatccatccatcctcccatcctcccatccatccatcatcca -tccatccatccatccatcctcccataatctatcttcccatccatttgtccttccttcctt -ccttccttccttccttccttcgttccacccatccatcctcccattcatcctcccatgcat -cctcccatccatccacccaaccatcctcccatccatcctcacatccatcttcgcatccat -ccatccatccatccatctatccat--------------------ccatcctcccatccat -cctcccatcctcccatccattctcccattcatccatcctcccatccatcctcctatccat -ccatccatccatccaccctcccatccatccatcctcccatccatccacccttccatccat -ccatccacccacccttccatccatccaccctcccatccatccatcctcccattcatctat -ccatccatccctcgatcctcccatccatccatccatcctcccatccgtccatccatcctt -ccatccaccctcccatccatccatcctcccatccatctaccctcccatccatccatcctc -ccacccaccctcccatccatccaccctcccatccatccatcctcccatccatctatccat -ccatcctcccatcctcccatcctcccatccatccatccatccatccatccatcctcccat -cctcccatcctcccatccatcgtcccatgtgtacatctgtcctgccatctatccatacat -ccatttctccgtcctcccatccatcttcccatccattcatccatccatcttcccatccat -tcatccatccatcctgccatccatccttccattgatccatccatccatcctgcaggagac -caggagttcaaggctgccgtg ->syndip_2_chr20:60314330-60315020 -ttgaaaatccatccatctgtcgtcctacccatcctgctatccatccatccatccatcctc -ccataatctatcttcccatccatttg--------------------tccttc---cttcc -ttccttccttccttccttccttccacccatccatcctcccatgcatcctcccatgcatcc -tcccatccatccacccaaccatcctcccatccatcctcacatccatcttcgcatccatcc -atccatccatctatccatccatccatccatcctcccatccatcctcccatccattatccc -attcatccatcctcccatccatcctcctatccatccatccatccatccaccctctcatcc -atccatcctcccatccatccacccttccatccatccatccacccacccttccatccatcc -atcctcccatccatccatcctcccatccatccatcctcccattcatctatccatccatcc -ctcgatcctcccatccatccatcctcccatccatccatccatcctcccatccatccatcc -accctcccatccatccatcctcccatccatctaccctcccatccatccatcctcccatcc -accctcccatccatccatccatccatccaccctctcatccatccatcctcccatccgtcc -atccatccttccatccaccctcccatccatccatcctcccatccatccatcctcccatcc -atctaccctcccatccatccatcctcccacccaccctcccatccatccaccctcccatcc -atccatcctcccatccatctatccatccatcctcccatcctcccatccatccatcatcca -tccatccatccatccatcctcccataatctatcttcccatccatttgtccttccttcctt -ccttccttccttcc--------ttccacccatccatcctcccattcatcctcccatgcat -cctcccatccatccacccaaccatcctcccatccatcctcacatccatcttcgcatccat -ccatccatccatccatctatccatccatcctcccatccatcctcccatcctcccatccat -cctcccatcctcccatccattctcccattcatccatcctcccatccatcctcctatccat -ccatccatccatccaccctcccatccatccatcctcccatccatccacccttccatccat -ccatccacccacccttccatccatccaccctcccatccatccatcctcccattcatctat -ccatccatccctcgatcctcccatccatccatccatcctcccatccgtccatccatcctt -ccatccaccctcccatccatccatcctcccatccatctaccctcccatccatccatcctc -ccacccaccctcccatccatccaccctcccatccatccatcctcccatccatctatccat -ccatcctcccatcctcccatcctc----ccatccatccatccatccatccatcctcccat -cctcccatcctcccatccatcgtcccatgtgtacatctgtcctgccatctatccatacat -ccatttctccgtcctcccatccatcttcccatccattcatccatccatcttcccatccat -tcatccatccatcctgccatccatccttccattgatccatccatccatcctgcaggagac -caggagttcaaggctgccgtg ->p:HG002_1_chr20:60314330-60315020 -ttgaaaatccatccatctgtcgtcctacccatcctgctatccatccatccatccatcctc -ccataatctatcttcccatccatttg--------------------tccttc---cttcc -ttccttccttccttccttccttccacccatccatcctcccatgcatcctcccatgcatcc -tcccatccatccacccaaccatcctcccatccatcctcacatccatcttcgcatccatcc -atccatccatctatccatccatccatccatcctcccatccatcctcccatccattatccc -attcatccatcctcccatccatcctcctatccatccatccatccatccaccctctcatcc -atccatcctcccatccatccacccttccatccatccatccacccacccttccatccatcc -atcctcccatccatccatcctcccatccatccatcctcccattcatctatccatccatcc -ctcgatcctcccatccatccatcctcccatccatccatccatcctcccatccatccatcc -accctcccatccatccatcctcccatccatctaccctcccatccatccatcctcccatcc -accctcccatccatccatccatccatccaccctctcatccatccatcctcccatccgtcc -atccatccttccatccaccctcccatccatccatcctcccatccatccatcctcccatcc -atctaccctcccatccatccatcctcccacccaccctcccatccatccaccctcccatcc -atccatcctcccatccatctatccatccatcctcccatcctcccatccatccatcatcca -tccatccatccatccatcctcccataatctatcttcccatccatttgtccttccttcctt -ccttccttccttcc--------ttccacccatccatcctcccattcatcctcccatgcat -cctcccatccatccacccaaccatcctcccatccatcctcacatccatcttcgcatccat -ccatccatccatccatctatccatccatcctcccatccatcctcccatcctcccatccat -cctcccatcctcccatccattctcccattcatccatcctcccatccatcctcctatccat -ccatccatccatccaccctcccatccatccatcctcccatccatccacccttccatccat -ccatccacccacccttccatccatccaccctcccatccatccatcctcccattcatctat -ccatccatccctcgatcctcccatccatccatccatcctcccatccgtccatccatcctt -ccatccaccctcccatccatccatcctcccatccatctaccctcccatccatccatcctc -ccacccaccctcccatccatccaccctcccatccatccatcctcccatccatctatccat -ccatcctcccatcctcccatcctc----ccatccatccatccatccatccatcctcccat -cctcccatcctcccatccatcgtcccatgtgtacatctgtcctgccatctatccatacat -ccatttctccgtcctcccatccatcttcccatccattcatccatccatcttcccatccat -tcatccatccatcctgccatccatccttccattgatccatccatccatcctgcaggagac -caggagttcaaggctgccgtg ->p:HG002_2_chr20:60314330-60315020 -ttgaaaatccatccatctgtcctcctacccatcctgctatccatccatccatccatcctc -ccataatctatcttcccatccatttgtccttccttccttccttccttccttc---cttcc -ttccttccttccttccttccttccacccatccatcctcccattcatcctcccatgcatcc -tcccatccatccacccaaccatcctcccatccatcctcacatccatcttcgcatccatcc -atccatccatctatccatccatccatccatcctcccatccatcctcccatccattatccc -attcatccatcctcccatccatcctcctatccatccatccatccatccaccctcccatcc -atccatcctcccatccatccactcttccatccatccatccacccaccctt---------- -------ccatccatccatcctcccatccatccatcctcccattcatctatccatccatcc -ctcgatcctcccatccatccatcctcccatccatccatccatcctcccatccatccatcc -accctcccatccatccatcctcccatccatctaccctcccatccatccatcctcccaccc -accctcccatccatccatcctcccatcctcccatccatccatccatcctcccatccgtcc -atccatccttccatccac----------------cctcccatccatccatcctcccatcc -atctaccctcccatccatccatcctcccacccaccctcccatccatccaccctcccatcc -atccatcctcccatccatctatccatccatcctcccatcctcccatccatccatcatcca -tccatccatccatccatcctcccataatctatcttcccatccatttgtccttccttcctt -ccttccttccttccttccttcgttccacccatccatcctcccattcatcctcccatgcat -cctcccatccatccacccaaccatcctcccatccatcctcacatccatcttcgcatccat -ccatccatccatccatctatccat--------------------ccatcctcccatccat -cctcccatcctcccatccattctcccattcatccatcctcccatccatcctcctatccat -ccatccatccatccaccctcccatccatccatcctcccatccatccacccttccatccat -ccatccacccacccttccatccatccaccctcccatccatccatcctcccattcatctat -ccatccatccctcgatcctcccatccatccatccatcctcccatccgtccatccatcctt -ccatccaccctcccatccatccatcctcccatccatctaccctcccatccatccatcctc -ccacccaccctcccatccatccaccctcccatccatccatcctcccatccatctatccat -ccatcctcccatcctcccatcctcccatccatccatccatccatccatccatcctcccat -cctcccatcctcccatccatcgtcccatgtgtacatctgtcctgccatctatccatacat -ccatttctccgtcctcccatccatcttcccatccattcatccatccatcttcccatccat -tcatccatccatcctgccatccatccttccattgatccatccatccatcctgcaggagac -caggagttcaaggctgccgtg ->ref_chr20:60314330-60315020 -ttgaaaatccatccatctgtcctcctacccatcctgctatccatccatccatccatcctc -ccataatctatcttcccatccatttgtccttccttccttccttccttccttccttcttcc -ttccttccttccttccttccttccacccatccatcctcccattcatcctcccatgcatcc -tcccatccatccacccaaccatcctcccatccatcctcacatcgatcttcgcatccatcc -atcgatcgatctatccatccatccattc----------------------------tccc -attcatccatcctcccatccatcctcctatccatccatccatccatccaccctcccatcc -atccatcctcccatccatccacccttccatccatccatccacccaccctt---------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------ccatccatccaccctcccatccatccatcctcccatccatctatccat -ccatcctcccatcctcccatcctcccatccatccatccatccatccatccatcctcccat -cctcccatcctcccatccatcgtcccatgtgtacatctgtcctgccatctatccatacat -ccatttctccgtcctcccatccatcttcccatccattcatccatccatcttcccatccat -tcatccatccatcctgccatccatccttccattgatccatccatccatcctgcaggagac -caggagttcaaggctgccgtg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_fc40819c3b411d6b2869794670b475f9.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_fc40819c3b411d6b2869794670b475f9.msa deleted file mode 100644 index 9d83252e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_fc40819c3b411d6b2869794670b475f9.msa +++ /dev/null @@ -1,40 +0,0 @@ ->syndip_1_chr20:60702905-60703187 -attttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaacatt -tgtcattgtctttctttcttttctttctctctctctctttcttttccttctttctttctt -tctttctttctttctttctttctttctttctttctttctttcttttctttccttcttctt -tctttctttctttctttctttctttctttctttctttctttctttctttctttctttctt -tctttctttctttcttctttctttctttttctttcttttttttttgggatggagtctcgc -tctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacctccc -aggttcaagcgattga ->syndip_2_chr20:60702905-60703187 -attttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaacatt -tgtcattgtctttctttcttttctttctctctctctctttcttttccttctttctttctt -tctttctttctttcttc----------------------------------------ctt -tctttctttctttctttctttctttctttctttctttcttt------------------- -------tctttccttctttctttctttctttctttctttttttttgggatggagtctcgc -tctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacctccc -aggttcaagcgattga ->p:HG002_1_chr20:60702905-60703187 -attttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaacatt -tgtcattgtctttctttcttttctttctctctctctctttctttcttttccttctttctt -tctttctttctttcctt----------------------------------------ctt -tctttctttctttctttctttctttctttctttctttcttt------------------- -------tctttccttctttctttctttctttctttctttttttttgggatggagtctcgc -tctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacctccc -aggttcaagcgattga ->p:HG002_2_chr20:60702905-60703187 -attttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaacatt -tgtcattgtctttctttcttttctttctctctctctctttcttttccttctttctttctt -tctttctttctttctttctttctttctttctttctttctttcttttctttccttcttctt -tctttctttctttctttctttctttctttctttctttctttctttctttctttctttctt -tctttctttctttcttcttctttctttctttctttctttttttttgggatggagtctcgc -tctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacctccc -aggttcaagcgattga ->ref_chr20:60702905-60703187 -attttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaacatt -tgtcattgtctttctttcttttctttctctctctctctttcttttcctt----------- ----------------------------------------------------------ctt -tctttctttctttctttctttctttctttctttctttcttt------------------- -------tctttccttctttctttctttctttctttctttttttttgggatggagtctcgc -tctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacctccc -aggttcaagcgattga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_fee04a9e0fd9ad6a70af99f071a34ce2.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_fee04a9e0fd9ad6a70af99f071a34ce2.msa deleted file mode 100644 index 3ae88d82..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_fee04a9e0fd9ad6a70af99f071a34ce2.msa +++ /dev/null @@ -1,165 +0,0 @@ ->syndip_1_chr20:64134683-64136586 -ttatactttaagttctagggtacatgtgcacaacatgcaggtttgttacatatgtataca -tgtgccgtgttggtgtgctgcacccattaactcatcatttagcattaggtgtatctccta -atgctatccctcccctctccccgcaccccacaaaagtccccggtgtgtgatgttcccctt -gaaaaggaggcgtttctgcttctcctctttccggtccttgacagtgattccgtgcatcac -aaacacacacgctccctcagttacacgaatcacaaacacacgctccctcagttttgtgca -tcacaaacgcacacgctccctcagttttgtgcgtcacacacacgctccctcagttttgtg -cgtc-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------acacaca -cgctccctcagttttgtgcgccacaaacacgcgcactccctcagttatgtgcgtcacaaa -cacagacgctccctcagttttgcgcatcacaaacacacacgctccctcagttatggacat -cacaaacacacacgctccctcagttttgtgcttcacaaacacacacgctccctcagttat -ggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacacacgctccctc -agttatggacatcacaaacacacacgctccctcagttttgtgcgtcacaaacacagacgc -tccctcagttttgcgcatcacacacacgctccctcagttttgtgtgtcacaaacacacac -gctccttcagttttgtgcttcacaaacacacacgctccctcagttttgtgcatcacacac -acattccctcagttttgtgcgccacaaacacgcgcgctccctcagttttgtgcatcacaa -acgcacatgctccctcagttttgggcatcacaaacacattccctcagttttgtgcatcac -aaacgcacacgctccctcagttttgtgcgtcacaaacacacacgctacctcagttttgtg -tgttacaaacacacacgctccctcagtttcgtgcatcccaaacatgctccctcagttatg -tgcgtcacaaacacgctccctcagttttgtgtgtcacaaacacacacgctccctcagttt -tgtgcatcacaaacacacacattccctcagttttgtgcgtcacaaacacgcgtgctctct -cagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctcc -ctcagctttgtgcttcacaaacacacacgctccctcagttttgtgtgttacaaacacaca -cgctccctcagtttcgtgcatcccaaagacgattcctcagttttgtgcatcacaaacaca -tatgctccctcagttttgtgcgtcacaaacgcgcgctccctcagttatgtgcgtcacaaa -cacagacgctccctcagttttgcgcatcacacacacgctccctcagttttgtgtg----- -----------------------------tcacaaacacacacgctccctcagttgtcagg -ggactttgcactgtgcctttgcatgaaacaccatggcttgaagaggtcccgcatcgttag -ggcccccttgcccatggtgtggcgt----------------------------------- --------------------cccctgaccgatttagccgttattgagagacagccaggttg -ctttcaacgttttctttttcacagacagtggtgccaaaggcgtc ->syndip_2_chr20:64134683-64136586 -ttatactttaagttctagggtacatgtgcacaacatgcaggtttgttacatatgtataca -tgtgccgtgttggtgtgctgcacccattaactcatcatttagcattaggtgtatctccta -atgctatccctcccctctccccgcaccccacaaaagtccccggtgtgtgatgttcccctt -gaaaaggaggcgtttctgcttctcctctttccggtccttgacagtgattccgtgcatcac -aaacacacacgctccctcagttacacgaatcacaaacacacgctccctcagttttgtgca -tcacaaacgcacacgctccctcagttttgtgcgtcacacacacgctccctcagttttgtg -cgccacaaacacgcgcactccctcagttatgtgcgtcacaa------------------- ------------------------------------------------------------- ------------------------------------------------------acacaga -cgctccctcagttttgcgcatcacaaacacacacgctccctcagttatggacatcacaaa -cacacacgctccctcagttttgtgcttcacaaacacacacgctccctcagttatggacat -cacaaacacacacgctccctcagttttgtgcttcacaaacacacacgctccctcagttat -ggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacacacgctccctc -agttatggacatcacaaacacacacgctccctcagttttgtgcgtcacaaacacagacgc -tccctcagttttgcgcatcacacacacgctccctcagttttgtgtgtcacaaacacacac -gctccttcagttttgtgcttcacaaacacacacgctccctcagttttgtgcatcacacac -acattccctcagttttgtgcgccacaaacacgcgcgctccctcagttttgtgcatcacaa -acgcacatgctccctcagttttgggcatcacaaacacattccctcagttttgtgcatcac -aaacgcacacgctccctcagttttgtgcgtcacaaacacacacgctacctcagttttgtg -tgttacaaacacacacgctccctcagtttcgtgcatcccaaacatgctccctcagttatg -tgcgtcacaaacacgctccctcagttttgtgtgtcacaaacacacacgctccctcagttt -tgtgcatcacaaacacacacattccctcagttttgtgcgtcacaaacacgcgtgctctct -cagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctcc -ctcagctttgtgcttcacaaacacacacgctccctcagttttgtgtgttacaaacacaca -cgctccctcagtttcgtgcatcccaaagacgattcctcagttttgtgcatcacaaacaca -tatgctccctcagttttgtgcgtcacaaacgcgcgctccctcagttatgtgcgtcacaaa -cacagacgctccctcagttttgcgcatcacacacacgctccctcagttttgtgtgtcaca -aacacacacgctccctcagttttgcgcatcacaaacacacacgctccctcagttgtcagg -ggactttgcactgtgcctttgcatgaaacaccatggcttgaagaggtcccgcatcgttag -ggcccccttgcccatggtgtggcgt----------------------------------- --------------------cccctgaccgatttagccgttattgagagacagccaggttg -ctttcaacgttttctttttcacagacagtggtgccaaaggcgtc ->p:HG002_1_chr20:64134683-64136586 -ttatactttaagttctagggtacatgtgcacaacatgcaggtttgttacatatgtataca -tgtgccgtgttggtgtgctgcacccattaactcatcatttagcattaggtgtatctccta -atgctatccctcccctctccccgcaccccacaaaagtccccggtgtgtgatgttcccctt -gaaaaggaagcgtttctgcttctcctctttccggtccttgacagtgattccgtgcatcac -aaacacacacgctccctcagttacacgaatcacaaacacacgctccctcagttttgtgca -tcacaaacgcacacgctccctcagttttgtgcgtcacacacacgctccctcagttttgtg -cgccacaaacacgcgcactccctcagttatgtgcgtcacaa------------------- ------------------------------------------------------------- ------------------------------------------------------acacaga -cgctccctcagttttgcgcatcacaaacacacacgctccctcagttatggacatcacaaa -cacacacgctccctcagttttgtgcttcacaaacacacacgctccctcagttatggacat -cacaaacacacacgctccctcagttttgtgcttcacaaacacacacgctccctcagttat -ggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacacacgctccctc -agttatggacatcacaaacacacacgctccctcagttttgtgcgtcacaaacacagacgc -tccctcagttttgcgcatcacacacacgctccctcagttttgtgtgtcacaaacacacac -gctccttcagttttgtgcttcacaaacacacacgctccctcagttttgtgcatcacacac -acattccctcagttttgtgcgccacaaacacgcgcgctccctcagttttgtgcatcacaa -acgcacatgctccctcagttttgggcatcacaaacacattccctcagttttgtgcatcac -aaacgcacacgctccctcagttttgtgcgtcacaaacacacacgctacctcagttttgtg -tgttacaaacacacacgctccctcagtttcgtgcatcccaaacatgctccctcagttatg -tgcgtcacaaacacgctccctcagttttgtgtgtcacaaacacacacgctccctcagttt -tgtgcatcacaaacacacacattccctcagttttgtgcgtcacaaacacgcgtgctctct -cagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctcc -ctcagctttgtgcttcacaaacacacacgctccctcagttttgtgtgttacaaacacaca -cgctccctcagtttcgtgcatcccaaagacgattcctcagttttgtgcatcacaaacaca -tatgctccctcagttttgtgcgtcacaaacgcgcgctccctcagttatgtgcgtcacaaa -cacagacgctccctcagttttgcgcatcacacacacgctccctcagttttgtgtgtcaca -aacacacacgctccctcagttttgcgcatcacaaacacacacgctccctcagttgtcagg -ggactttgcactgtgcctttgcatgaaacaccatggcttgaagaggtcccgcatcgttag -ggcccccttgcccatggtgtggcgt----------------------------------- --------------------cccctgaccgatttagccgttattgagagacagccaggttg -ctttcaacgttttctttttcacagacagtggtgccaaaggcgtc ->p:HG002_2_chr20:64134683-64136586 -ttatactttaagttctagggtacatgtgcacaacatgcaggtttgttacatatgtataca -tgtgccgtgttggtgtgctgcacccattaactcatcatttagcattaggtgtatctccta -atgctatccctcccctctccccgcaccccacaaaagtccccggtgtgtgatgttcccctt -gaaaaggaagcgtttctgcttctcctctttccggtccttgacagtgattccgtgcatcac -aaacacacacgctccctcagttacacgaatcacaaacacacgctccctcagttttgtgca -tcacaaacgcacacgctccctcagttttgtgcgtcacacacacgctccctcagttttgtg -cgtc-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------acacaca -cgctccctcagttttgtgcgccacaaacacgcgcactccctcagttatgtgcgtcacaaa -cacagacgctccctcagttttgcgcatcacaaacacacacgctccctcagttatggacat -cacaaacacacacgctccctcagttttgtgcttcacaaacacacacgctccctcagttat -ggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacacacgctccctc -agttatggacatcacaaacacacacgctccctcagttttgtgcgtcacaaacacagacgc -tccctcagttttgcgcatcacacacacgctccctcagttttgtgtgtcacaaacacacac -gctccttcagttttgtgcttcacaaacacacacgctccctcagttttgtgcatcacacac -acattccctcagttttgtgcgccacaaacacgcgcgctccctcagttttgtgcatcacaa -acgcacatgctccctcagttttgggcatcacaaacacattccctcagttttgtgcatcac -aaacgcacacgctccctcagttttgtgcgtcacaaacacacacgctacctcagttttgtg -tgttacaaacacacacgctccctcagtttcgtgcatcccaaacatgctccctcagttatg -tgcgtcacaaacacgctccctcagttttgtgtgtcacaaacacacacgctccctcagttt -tgtgcatcacaaacacacacattccctcagttttgtgcgtcacaaacacgcgtgctctct -cagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctcc -ctcagctttgtgcttcacaaacacacacgctccctcagttttgtgtgttacaaacacaca -cgctccctcagtttcgtgcatcccaaagacgattcctcagttttgtgcatcacaaacaca -tatgctccctcagttttgtgcgtcacaaacgcgcgctccctcagttatgtgcgtcacaaa -cacagacgctccctcagttttgcgcatcacacacacgctccctcagttttgtgtg----- -----------------------------tcacaaacacacacgctccctcagttgtcagg -ggactttgcactgtgcctttgcatgaaacaccatggcttgaagaggtcccgcatcgttag -ggcccccttgcccatggtgtggcgt----------------------------------- --------------------cccctgaccgatttagccgttattgagagacagccaggttg -ctttcaacgttttctttttcacagacagtggtgccaaaggcgtc ->ref_chr20:64134683-64136586 -ttatactttaagttctagggtacatgtgcacaacatgcaggtttgttacatatgtataca -tgtgccgtgttggtgtgctgcacccattaactcatcatttagcattaggtgtatctccta -atgctatccctcccctctccccgcaccccacaaaagtccccggtgtgtgatgttcccctt -gaaaaggaggcgtttctgcttctcctctttccggtccttgacagtgattccgtgcatcac -aaacacacacgctccctcagttacacgaatcacaaacacacgctccctcagttttgtgca -tcacaaacgcacacgctccctcagttttgtgcgtcacacacacgctccctcagttttgtg -cgccacaaacacgcgcactccctcagttatgtgcgtcacaaacacagacgctccctcagt -tttgcgcatcacaaacacacacgctccctcagttatggacatcacaaacacacacgctcc -ctcagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaacacaca -cgctccctcagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaa -cacacacgctccctcagttttgtgcttcacaaacacacacgctccctcagttatggacat -cacaaacacacacgctccctcagttttgtgcttcacaaacacacacgctccctcagttat -ggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacacacgctccctc -agttatggacatcacaaacacacacgctccctcagttttgtgcgtcacaaacacagacgc -tccctcagttttgcgcatcacacacacgctccctcagttttgtgtgtcacaaacacacac -gctccttcagttttgtgcttcacaaacacacacgctccctcagttttgtgcatcacacac -acattccctcagttttgtgcgccacaaacacgcgcgctccctcagttttgtgcatcacaa -acgcacatgctccctcagttttgggcatcacaaacacattccctcagttttgtgcatcac -aaacgcacacgctccctcagttttgtgcgtcacaaacacacacgctacctcagttttgtg -tgttacaaacacacacgctccctcagtttcgtgcatcccaaacatgctccctcagttatg -tgcgtcacaaacacgctccctcagttttgtgtgtcacaaacacacacgctccctcagttt -tgtgcatcacaaacacacacattccctcagttttgtgcgtcacaaacacgcgtgctctct -cagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctcc -ctcagctttgtgcttcacaaacacacacgctccctcagttttgtgtgttacaaacacaca -cgctccctcagtttcgtgcatcccaaagacgattcctcagttttgtgcatcacaaacaca -tatgctccctcagttttgtgcgtcacaaacgcgcgctccctcagttatgtgcgtcacaaa -cacagacgctccctcagttttgcgcatcacacacacgctccctcagttttgtgtgtcaca -aacacacacgctccctcagttttgcgcatcacaaacacacacgctccctcagttgtcagg -ggactttgcactgtgcctttgcatgaaacaccatggcttgaagaggtcccgcatcgttag -ggcccccttgcccatggtgtggcgtcccctgaccgatttagccgttattgagggacatcg -aggttgcttggtgtggcggcccctgaccgatttagccgttattgagagacagccaggttg -ctttcaacgttttctttttcacagacagtggtgccaaaggcgtc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ff0d5a6f324c029d8b72f511a97c8b88.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ff0d5a6f324c029d8b72f511a97c8b88.msa deleted file mode 100644 index 8b88ea1a..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ff0d5a6f324c029d8b72f511a97c8b88.msa +++ /dev/null @@ -1,235 +0,0 @@ ->syndip_1_chr20:51952483-51954892 -attcctagattctattttcaaatattgatttgcttaa--ttttttttttttttgagatgg -ggttttgctctgtcgcccaggctggagtgcaatggcatgatcttggctcactgcaacctc -tgcctcctgggttcagccattctcctgcctcagcctcccgagtggctgggactacaggtg -cccgccaccacgcctggctaattttttttttttatatttttagtagagacggggtttcac -catgttagccaggatggtctcgatctcctgacctcgtgatccgcccgcctcggcctccca -aagtgctaggattacaggcttgagccaccgcgcctggcctttaatataatttttatgaag -acattatttccacttcattgggctctctagaattagattgcataaatactgtagttttat -ttcaataaaaagtcaactgttatttaaaccatgactaaagcttgacatgaatagagactt -taaaacaataaacattgccagacatggtggcacatgcctgtagtctcagctactcaagaa -actgagacaggaggatctcctgagccaaggagttccagcccagcctggacaacatagtga -gatcccatctctt---aaaaaaaaaaaaaaaagatttgcttaattttacttttacaattt -tttcttttctttttttttttttttttttttttttttttgagatggagtcttgctctgtta -ccaggctggagtgcagtggtgtgatatcggctccctgcaacctctgcctcctgggttaaa -gcaattttcctgccccagcctcccgagtagctgggactacaggcgcgcgtcaccacaccc -agctaatttttgtatttttagtagagatggggtttcaccatgttggccaggatggtctca -atctcttgatctcgtgatccgcccaccttggcctcccaaagtgctggaattacaggcgtg -atccgccataacctggccttccttcttttctttaaaaatttttttctgagacagagtctc -actctgttgcccagcctggagtgcagtggcacaatctcggctcactgtagcctccacctt -ctgggttcaagtgattctcgtgcctcagcctcccgagtagctgtgactacaggtgtgtgc -cctcatgcctggctaatttttgtatttttagtagagatggggtttcaccatgttggccag -gctggtctcgaaccctgggctcaagtgttctgtctgcctcagccccccaaagtgctggga -ttacaggcatgagccaaagtgcctggctagaaaattgtaaaagtaacttaatatctgcct -catatacttttgttttattt---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------aaaaatgcaaatcctcaaccacaaatcgaa -acaagaacaaccctctgatgacttccctccctctctctttgtacaaagaagactttctgc -tgtctgactctgaccaccttggtctattttatggagctccaaccctgccttgtttccttc -tcaggccatctgtcctggttggcctcactgttggaaatgctcttctcaagatgttcacgt -ggctggttctttgtcattcagtctcagttcaaatactccctcctccaggaagccttccct -aacttcctaggtgaaagtggttcccttcccctgagtcacgattatggtttcttcagtgta -cttattaatggccaacactgtctcctttattgtttgcttatgaatttaaagtctgttagc -agcacctgcagcttttaaaagcctccttgtctctctc----tattttttttttttttttt -ttgaggcggagtttcgctcttgttggccaggctggaacgcagtgatgcgatctcggctca -gtgcaacctccacctcttgggttcaagtgattctcctgcctcagcctccttagtagctga -gactacaggcatgtgccaccatgctggctaatttttgtatttttagtagagacagggttt -cgtcatattggccaagctggtctcgaacccctgacctcaggtgatccacccatcttggcc -tcccagatgctgggattacaggcgtgagccactgcgcctggcctaattgtcattttcgtt -tttttgttgagacagagtttctgtcacccaggctggaatgcagtggcacgatctcagctc -actgcagcctctgcctcttgggttcaattgattctcctgcctcagcctcccaagtagctg -ggactacaggtgtgtgccaccacacccagctaattttttcatttttagtagagacggggt -ttcaccatgttggtcaggcttgtctcgaactcctgacctcaggtgatccgtccaacttgg -cctcccaaagtgctgagattacaggcatgagctaccgtgcccagctctcaattgtcactt -ttagtgcatattttctggttgt ->syndip_2_chr20:51952483-51954892 -attcctagattctattttcaaatattgatttgcttaa-tttttttttttttttgagatgg -ggttttgctctgtcgcccaggctggagtgcaatggcatgatcttggctcactgcaacctc -tgcctcctgggttcagccattctcctgcctcagcctcccgagtggctgggactacaggtg -cccgccaccacgcctggctaattttttttttttatatttttagtagagacggggtttcac -catgttagccaggatggtctcgatctcctgacctcgtgatccgcccgcctcggcctccca -aagtgctaggattacaggcttgagccaccgcgcctggcctttaatataatttttatgaag -acattatttccacttcattgggctctctagaattagattgcataaatactgtagttttat -ttcaataaaaagtcaactgttatttaaaccatgactaaagcttgacatgaatagagactt -taaaacaataaacattgccagacatggtggcacatgcctgtagtctcagctactcaagaa -actgagacaggaggatctcctgagccaaggagttccagcccagcctggacaacatagtga -gatcccatctcttaaaaaaaaaaaaaaaaaaagatttgcttaattttacttttacaattt -tttcttttc--tttttttttttttttttttttttttttgagatggagtcttgctctgtta -ccaggctggagtgcagtggtgtgatatcggctccctgcaacctctgcctcctgggttaaa -gcaattttcctgccccagcctcccgagtagctgggactacaggcgcgcgtcaccacaccc -agctaatttttgtatttttagtagagatggggtttcaccatgttggccaggatggtctca -atctcttgatctcgtgatccgcccaccttggcctcccaaagtgctggaattacaggcgtg -atccgccataacctggccttccttcttttctttaaaaatttttttctgagacagagtctc -actctgttgcccagcctggagtgcagtggcacaatctcggctcactgtagcctccacctt -ctgggttcaagtgattctcgtgcctcagcctcccgagtagctgtgactacaggtgtgtgc -cctcatgcctggctaatttttgtatttttagtagagatggggtttcaccatgttggccag -gctggtctcgaaccctgggctcaagtgttctgtctgcctcagccccccaaagtgctggga -ttacaggcatgagccaaagtgcctggctagaaaattgtaaaagtaacttaatatctgcct -catatacttttgttttattt---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------aaaaatgcaaatcctcaaccacaaatcgaa -acaagaacaaccctctgatgacttccctccctctctctttgtacaaagaagactttctgc -tgtctgactctgaccaccttggtctattttatggagctccaaccctgccttgtttccttc -tcaggccatctgtcctggttggcctcactgttggaaatgctcttctcaagatgttcacgt -ggctggttctttgtcattcagtctcagttcaaatactccctcctccaggaagccttccct -aacttcctaggtgaaagtggttcccttcccctgagtcacgattatggtttcttcagtgta -cttattaatggccaacactgtctcctttattgtttgcttatgaatttaaagtctgttagc -agcacctgcagcttttaaaagcctccttgtctctctc--tattttttttttttttttttt -ttgaggcggagtttcgctcttgttggccaggctggaacgcagtgatgcgatctcggctca -gtgcaacctccacctcttgggttcaagtgattctcctgcctcagcctccttagtagctga -gactacaggcatgtgccaccatgctggctaatttttgtatttttagtagagacagggttt -cgtcatattggccaagctggtctcgaacccctgacctcaggtgatccacccatcttggcc -tcccagatgctgggattacaggcgtgagccactgcgcctggcctaattgtcattttcgtt -tttttgttgagacagagtttctgtcacccaggctggaatgcagtggcacgatctcagctc -actgcagcctctgcctcttgggttcaattgattctcctgcctcagcctcccaagtagctg -ggactacaggtgtgtgccaccacacccagctaattttttcatttttagtagagacggggt -ttcaccatgttggtcaggcttgtctcgaactcctgacctcaggtgatccgtccaacttgg -cctcccaaagtgctgagattacaggcatgagctaccgtgcccagctctcaattgtcactt -ttagtgcatattttctggttgt ->p:HG002_1_chr20:51952483-51954892 -attcctagattctattttcaaatattgatttgcttaa-tttttttttttttttgagatgg -ggttttgctctgtcgcccaggctggagtgcaatggcatgatcttggctcactgcaacctc -cgcctcctgggttcagccattctcctgcctcagcctcccgagtggctgggactacaggtg -cccgccaccacgcctggctaattttttttttttatatttttagtagagacggggtttcac -catgttagccaggatggtctcgatctcctgacctcgtgatccgcccgcctcggcctccca -aagtgctaggattacaggcttgagccaccgcgcctggcctttaatataatttttatgaag -acattatttccacttcattgggctctctagaattagattgcataaatactgtagttttat -ttcaataaaaagtcaactgttatttaaaccatgactaaagcttgacatgaatagagactt -taaaacaataaacattgccagacatggtggcacatgcctgtagtctcagctactcaagaa -actgagacaggaggatctcctgagccaaggagttccagcccagcctggacaacatagtga -gatcccatctcttaaaaaaaaaaaaaaaaaaagatttgcttaattttacttttacaattt -tttcttttc--tttttttttttttttttttttttttttgagatggagtcttgctctgtta -ccaggctggagtgcagtggtgtgatatcagctccctgcaacctctgcctcctgggttaaa -gcaattttcctgccccagcctcccgagtagctgggactacaggcgcgcgtcaccacaccc -agctaatttttgtatttttagtagagatggggtttcaccatgttggccaggatggtctca -atctcttgatctcgtgatccgcccaccttggcctcccaaagtgctggaattacaggcgtg -atccgccataacctggccttccttctttcctttaaaaatttttttctgagacagagtctc -actctgttgcccagcctggagtgcagtggcacaatctcggctcactgtagcctccacctt -ctgggttcaagtgattctcgtgcctcagcctcccgagtagctgtgactacaggtgtgtgc -cctcatgcctggctaatttttgtatttttagtagagatggggtttcaccatgttggccag -gctggtctcgaaccctgggctcaagtgttctgtctgcctcagccccccaaagtgctggga -ttacaggcatgagccaaagtgcctggctagaaaattgtaaaagtaacttaatatctgcct -catatacttttgttttattt---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------aaaaatgcaaatcctcaaccacaaatcgaa -acaagaacaaccctctgatgacttccctccctctctctttgtacaaagaagactttctgc -tgtctgactctgaccaccttggtctattttatggagctccaaccctgccttgtttccttc -tcaggccatctgtcctggttggcctcactgttggaaatgctcttctcaagatgttcacgt -ggctggttctttgtcattcagtctcagttcaaatactccctcctccaggaagccttccct -aacttcctaggtgaaagtggttcccttcccctgagtcacgattatggtttcttcagtgta -cttattaatggccaacactgtctcctttattgtttgcttatgaatttaaagtctgttagc -agcacctgcagcttttaaaagcctccttgtctctctc--tattttttttttttttttttt -ttgaggcggagtttcgctcttgttggccaggctggaacgcagtgatgcgatctcggctca -gtgcaacctccacctcttgggttcaagtgattctcctgcctcagcctccttagtagctga -gactacaggcatgtgccaccatgctggctaatttttgtatttttagtagagacagggttt -cgtcatattggccaagctggtctcgaacccctgacctcaggtgatccacccatcttggcc -tcccagatgctgggattacaggcgtgagccactgcgcctggcctaattgtcattttcgtt -tttttgttgagacagagtttctgtcacccaggctggaatgcagtggcacgatctcagctc -actgcagcctctgcctcttgggttcaattgattctcctgcctcagcctcccaagtagctg -ggactacaggtgtgtgccaccacacccagctaattttttcatttttagtagagacggggt -ttcaccatgttggtcaggcttgtctcgaactcctgacctcaggtgatccgtccaacttgg -cctcccaaagtgctgagattacaggcatgagctaccgtgcccagctctcaattgtcactt -ttagtgcatattttctggttgt ->p:HG002_2_chr20:51952483-51954892 -attcctagattctattttcaaatattgatttgcttaa--ttttttttttttttgagatgg -ggttttgctctgtcgcccaggctggagtgcaatggcatgatcttggctcactgcaacctc -cgcctcctgggttcagccattctcctgcctcagcctcccgagtggctgggactacaggtg -cccgccaccacgcctggctaattttttttttttatatttttagtagagacggggtttcac -catgttagccaggatggtctcgatctcctgacctcgtgatccgcccgcctcggcctccca -aagtgctaggattacaggcttgagccaccgcgcctggcctttaatataatttttatgaag -acattatttccacttcattgggctctctagaattagattgcataaatactgtagttttat -ttcaataaaaagtcaactgttatttaaaccatgactaaagcttgacatgaatagagactt -taaaacaataaacattgccagacatggtggcacatgcctgtagtctcagctactcaagaa -actgagacaggaggatctcctgagccaaggagttccagcccagcctggacaacatagtga -gatcccatctctt---aaaaaaaaaaaaaaaagatttgcttaattttacttttacaattt -tttcttttctttttttttttttttttttttttttttttgagatggagtcttgctctgtta -ccaggctggagtgcagtggtgtgatatcggctccctgcaacctctgcctcctgggttaaa -gcaattttcctgccccagcctcccgagtagctgggactacaggcgcgcgtcaccacaccc -agctaatttttgtattttcagtagagatggggtttcaccatgttggccaggatggtctca -atctcttgatctcgtgatccgcccaccttggcctcccaaagtgctggaattacaggcgtg -atccgccataacctggccttccttcttttctttaaaaatttttttctgagacagagtctc -actctgttgcccagcctggagtgcagtggcacaatctcggctcactgtagcctccacctt -ctgggttcaagtgattctcgtgcctcagcctcccgagtagctgtgactacaggtgtgtgc -cctcatgcctggctaatttttgtatttttagtagagatggggtttcaccatgttggccag -gctggtctcgaaccctgggctcaagtgttctgtctgcctcagccccccaaagtgctggga -ttacaggcatgagccaaagtgcctggctagaaaattgtaaaagtaacttaatatctgcct -catatacttttgttttatttaaaaatgcaaatccggccgggcgcggtggctcacgcctgt -aatcccagcactttgggaggccgaggcgggcggatcacgaggtcaggagatcgagaccat -cccggctaaaacggtgaaaccccgtctctactaaaaatacaaaaaattagccgggcgtgg -tggcgggcgcctgtagtcccagctacttgggaggctgaggcaggagaatggcgtgaaccc -gggaggcggagcttgcagtgagccgagatcccgccactgcactccagcctgggcgacaga -gcgagactccgtctcaaaaaaaaaaaaaaaaaaaatgcaaatcctcaaccacaaatcgaa -acaagaacaaccctctgatgacttccctccctctctctttgtacaaagaagactttctgc -tgtctgactctgaccaccttggtctattttatggagctccaaccctgccttgtttccttc -tcaggccatctgtcctggttggcctcactgttggaaatgctcttctcaagatgttcacgt -ggctggttctttgtcattcagtctcagttcaaatactccctcctccaggaagccttccct -aacttcctaggtgaaagtggttcccttcccctgagtcacgattatggtttcttcagtgta -cttattaatggccaacactgtctcctttattgtttgcttatgaatttaaagtctgttagc -agcacctgcagcttttaaaagcctccttgtctctctc----tattttttttttttttttt -ttgaggcggagtttcgctcttgttggccaggctggaatgcagtgatgcgatctcggctca -gtgcaacctccacctcttgggttcaagtgattctcctgcctcagcctccttagtagctga -gactacaggcatgtgccaccatgctggctaatttttgtatttttagtagagacagggttt -cgtcatattggccaagctggtctcgaacccctgacctcaggtgatccacccatcttggcc -tcccagatgctgggattacaggcgtgagccactgcgcctggcctaattgtcattttcgtt -tttttgttgagacagagtttctgtcacccaggctggaatgcagtggcacgatctcagctc -actgcagcctctgcctcttgggttcaattgattctcctgcctcagcctcccaagtagctg -ggactacaggtgtgtgccaccacacccagctaattttttcatttttagtagagacggggt -ttcaccatgttggtcaggcttgtctcgaactcctgacctcaggtgatccgtccaacttgg -cctcccaaagtgctgagattacaggcatgagctaccgtgcccagctctcaattgtcactt -ttagtgcatattttctggttgt ->ref_chr20:51952483-51954892 -attcctagattctattttcaaatattgatttgcttaattttttttttttttttgagatgg -ggttttgctctgtcgcccaggctggagtgcaatggcatgatcttggctcactgcaacctc -tgcctcctgggttcagccattctcctgcctcagcctcccgagtggctgggactacaggtg -cccgccaccacgcctggctaattttttttttttatatttttagtagagacggggtttcac -catgttagccaggatggtctcgatctcctgacctcgtgatccgcccgcctcggcctccca -aagtgctaggattacaggcttgagccaccgcgcctggcctttaatataatttttatgaag -acattatttccacttcattgggctctctagaattagattgcataaatactgtagttttat -ttcaataaaaagtcaactgttatttaaaccatgactaaagcttgacatgaatagagactt -taaaacaataaacattgccagacatggtggcacatgcctgtagtctcagctactcaagaa -actgagacaggaggatctcctgagccaaggagttccagcccagcctggacaacatagtga -gatcccatctctt--aaaaaaaaaaaaaaaaagatttgcttaattttacttttacaattt -tttcttttctttttttttttttttttttttttttttttgagatggagtcttgctctgtta -ccaggctggagtgcagtggtgtgatatcggctccctgcaacctctgcctcctgggttaaa -gcaattttcctgccccagcctcccgagtagctgggactacaggcgcgcgtcaccacaccc -agctaatttttgtatttttagtagagatggggtttcaccatgttggccaggatggtctca -atctcttgatctcgtgatccgcccaccttggcctcccaaagtgctggaattacaggcgtg -atccgccataacctggccttccttcttttctttaaaaatttttttctgagacagagtctc -actctgttgcccagcctggagtgcagtggcacaatctcggctcactgtagcctccacctt -ctgggttcaagtgattctcgtgcctcagcctcccgagtagctgtgactacaggtgtgtgc -cctcatgcctggctaatttttgtatttttagtagagatggggtttcaccatgttggccag -gctggtctcgaaccctgggctcaagtgttctgtctgcctcagccccccaaagtgctggga -ttacaggcatgagccaaagtgcctggctagaaaattgtaaaagtaacttaatatctgcct -catatacttttgttttattt---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------aaaaatgcaaatcctcaaccacaaatcgaa -acaagaacaaccctctgatgacttccctccctctctctttgtacaaagaagactttctgc -tgtctgactctgaccaccttggtctattttatggagctccaaccctgccttgtttccttc -tcaggccatctgtcctggttggcctcactgttggaaatgctcttctcaagatgttcacgt -ggctggttctttgtcattcagtctcagttcaaatactccctcctccaggaagccttccct -aacttcctaggtgaaagtggttcccttcccctgagtcacgattatggtttcttcagtgta -cttattaatggccaacactgtctcctttattgtttgcttatgaatttaaagtctgttagc -agcacctgcagcttttaaaagcctccttgtctctctctcttttttttttttttttttttt -ttgaggcggagtttcgctcttgttggccaggctggaacgcagtgatgcgatctcggctca -gtgcaacctccacctcttgggttcaagtgattctcctgcctcagcctccttagtagctga -gactacaggcatgtgccaccatgctggctaatttttgtatttttagtagagacagggttt -cgtcatattggccaagctggtctcgaacccctgacctcaggtgatccacccatcttggcc -tcccagatgctgggattacaggcgtgagccactgcgcctggcctaattgtcattttcgtt -tttttgttgagacagagtttctgtcacccaggctggaatgcagtggcacgatctcagctc -actgcagcctctgcctcttgggttcaattgattctcctgcctcagcctcccaagtagctg -ggactacaggtgtgtgccaccacacccagctaattttttcatttttagtagagacggggt -ttcaccatgttggtcaggcttgtctcgaactcctgacctcaggtgatccgtccaacttgg -cctcccaaagtgctgagattacaggcatgagctaccgtgcccagctctcaattgtcactt -ttagtgcatattttctggttgt