From badee667d763e5bfee1f6b7a8894fb442b945e4c Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 29 Apr 2024 04:29:48 +0000 Subject: [PATCH 1/6] Updating tools/pairtools from version 1.0.3 to 1.1.0 --- tools/pairtools/macros.xml | 2 +- tools/pairtools/parse.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/pairtools/macros.xml b/tools/pairtools/macros.xml index 09ebf6e06e3..1234d1869f5 100644 --- a/tools/pairtools/macros.xml +++ b/tools/pairtools/macros.xml @@ -1,5 +1,5 @@ - 1.0.3 + 1.1.0 0 diff --git a/tools/pairtools/parse.xml b/tools/pairtools/parse.xml index 9c78ac223b8..db89509c6d0 100644 --- a/tools/pairtools/parse.xml +++ b/tools/pairtools/parse.xml @@ -1,4 +1,4 @@ - + Find ligation pairs in alignments and create pairs. macros.xml From 1a898326cdc85ae5c1233a75b7a8e873c12774a8 Mon Sep 17 00:00:00 2001 From: Saim Momin Date: Mon, 29 Apr 2024 15:47:52 +0200 Subject: [PATCH 2/6] Updated test data and minor changes as per new release --- tools/pairtools/dedup.xml | 2 +- .../test-data/output_dedup_pairs.pairsam | 8 +- .../test-data/output_dedup_pairs.stats | 443 +++++++++++------ .../output_dedup_pairs_markdups.pairsam | 8 +- .../output_dups_pairs_markdups.pairsam | 8 +- .../test-data/output_parsed_pairs.stats | 449 +++++++++++------ .../test-data/output_parsed_pairs_bam.pairs | 8 +- .../output_parsed_pairs_bam_5unique.pairs | 8 +- .../output_parsed_pairs_bam_min_mapq_40.pairs | 8 +- ...tput_parsed_pairs_bam_readid_dropped.pairs | 8 +- ..._parsed_pairs_bam_readid_dropped_seq.pairs | 66 +-- .../test-data/output_parsed_pairs_sam.pairs | 48 +- ...output_parsed_pairs_sam_assemblyname.pairs | 48 +- tools/pairtools/test-data/pairs_output.stats | 443 +++++++++++------ .../test-data/pairs_output_merged.stats | 457 ++++++++++++------ .../pairs_output_with_chromsize.stats | 443 +++++++++++------ .../test-data/pairs_output_yaml.stats | 212 +++++++- 17 files changed, 1823 insertions(+), 844 deletions(-) diff --git a/tools/pairtools/dedup.xml b/tools/pairtools/dedup.xml index 363c9603011..4ef6bac3e12 100644 --- a/tools/pairtools/dedup.xml +++ b/tools/pairtools/dedup.xml @@ -20,7 +20,7 @@ ]]> - + diff --git a/tools/pairtools/test-data/output_dedup_pairs.pairsam b/tools/pairtools/test-data/output_dedup_pairs.pairsam index 367efff7761..fbefa6d2fad 100644 --- a/tools/pairtools/test-data/output_dedup_pairs.pairsam +++ b/tools/pairtools/test-data/output_dedup_pairs.pairsam @@ -39,20 +39,20 @@ #samheader: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz #samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa VN:1.0.2 #samheader: @PG ID:pairtools_sort-1.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-1.2 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs.pairsam output_sorted_pairs.pairsam PP:pairtools_sort-1.3 VN:1.0.2 +#samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/2/1/3/dataset_21372a8a-66a4-4ab8-8a38-a1e4d87d5048.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/2/outputs/dataset_b7034ba7-f57e-4752-a341-425fdb4da81e.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-1.3 VN:1.1.0 #samheader: @PG ID:bwa-2CCE5976 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz #samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-2CCE5976 VN:1.0.2 #samheader: @PG ID:pairtools_sort-2.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-2.2 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs.pairsam output_sorted_pairs.pairsam PP:pairtools_sort-2.3 VN:1.0.2 +#samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/2/1/3/dataset_21372a8a-66a4-4ab8-8a38-a1e4d87d5048.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/2/outputs/dataset_b7034ba7-f57e-4752-a341-425fdb4da81e.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-2.3 VN:1.1.0 #samheader: @PG ID:bwa-3CAFD9D9 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz #samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-3CAFD9D9 VN:1.0.2 #samheader: @PG ID:pairtools_sort-3.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-3.2 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs.pairsam output_sorted_pairs.pairsam PP:pairtools_sort-3.3 VN:1.0.2 +#samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/2/1/3/dataset_21372a8a-66a4-4ab8-8a38-a1e4d87d5048.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/2/outputs/dataset_b7034ba7-f57e-4752-a341-425fdb4da81e.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-3.3 VN:1.1.0 #samheader: @PG ID:bwa-4548A671 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz #samheader: @PG ID:samtools PN:samtools PP:bwa-4548A671 VN:1.19.2 CL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam #samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:samtools VN:1.0.2 #samheader: @PG ID:pairtools_sort-4.4 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-4.3 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs.pairsam output_sorted_pairs.pairsam PP:pairtools_sort-4.4 VN:1.0.2 +#samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/2/1/3/dataset_21372a8a-66a4-4ab8-8a38-a1e4d87d5048.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/2/outputs/dataset_b7034ba7-f57e-4752-a341-425fdb4da81e.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-4.4 VN:1.1.0 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2 HWI-ST560:29:B0A7LABXX:2:1101:15566:24141 chrI 3199 chrI 3399 + - UU HWI-ST560:29:B0A7LABXX:2:1101:15566:2414197chrI31996015S35M=3350201CTTAGACAATAAGCTAGCTTTCAAGATATAAGATACGAAATAGGGGTTGA111442422223232232EGDD?BFIIIIGBHCJIJIHFIHFHGHGGC<2GHGHFDEGDD?BFIIIIGBHCJIJIHFIHFHGHGGC<2GHGHFD332224D=:1NM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU HWUSI-EAS1533_0033_FC:1:1:2403:20808 chrIV 497939 chrIV 498215 + - DD HWUSI-EAS1533_0033_FC:1:1:2403:2080897chrIV4979396036M=498180277CGCTTTCATTACTCGAATCCGTCAAAGACGCTTCTT4544588888C@@CC@CCC@@@C@@@C@CCC@C@CCNM:i:1MD:Z:0A35AS:i:35XS:i:0Yt:Z:UU HWUSI-EAS1533_0033_FC:1:1:2403:20808145chrIV4981806036M=497939-277GGCTGGTGAAGGAGTATTATTTACAATTCTAAAGCN@@C@@@@CC@CC@CC22C@@@CCCCC888886666)NM:i:1MD:Z:35T0AS:i:35XS:i:0Yt:Z:UU diff --git a/tools/pairtools/test-data/output_parsed_pairs.stats b/tools/pairtools/test-data/output_parsed_pairs.stats index dbf06e8809b..d14bad141d5 100644 --- a/tools/pairtools/test-data/output_parsed_pairs.stats +++ b/tools/pairtools/test-data/output_parsed_pairs.stats @@ -6,16 +6,14 @@ total_dups 0 total_nodups 308 cis 308 trans 0 -pair_types/MU 88 +pair_types/MU 95 pair_types/UU 293 pair_types/MM 49 pair_types/UR 8 pair_types/MR 26 pair_types/NR 110 pair_types/RU 7 -pair_types/nM 3 -pair_types/Mu 7 -pair_types/NM 1 +pair_types/NM 4 cis_1kb+ 15 cis_2kb+ 14 cis_4kb+ 14 @@ -31,6 +29,33 @@ summary/frac_cis_20kb+ 0.02922077922077922 summary/frac_cis_40kb+ 0.02922077922077922 summary/frac_dups 0.0 summary/complexity_naive nan +summary/dist_freq_convergence/convergence_dist 177828 +summary/dist_freq_convergence/strands_w_max_convergence_dist ++ +summary/dist_freq_convergence/convergence_rel_diff_threshold 0.05 +summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/++ 4 +summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/-- 2 +summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/-+ 1 +summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/+- 301 +summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist_all_strands 308 +summary/dist_freq_convergence/n_cis_pairs_above_convergence_dist_all_strands 0 +summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/++ 0.012987012987012988 +summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/-- 0.006493506493506494 +summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/-+ 0.003246753246753247 +summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/+- 0.9772727272727273 +summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist_all_strands 1.0 +summary/dist_freq_convergence/frac_cis_in_cis_above_convergence_dist_all_strands 0.0 +summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/++ 0.012987012987012988 +summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/-- 0.006493506493506494 +summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/-+ 0.003246753246753247 +summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/+- 0.9772727272727273 +summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist_all_strands 1.0 +summary/dist_freq_convergence/frac_total_mapped_in_cis_above_convergence_dist_all_strands 0.0 +summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/++ 0.012987012987012988 +summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/-- 0.006493506493506494 +summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/-+ 0.003246753246753247 +summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/+- 0.9772727272727273 +summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist_all_strands 1.0 +summary/dist_freq_convergence/frac_total_nodups_in_cis_above_convergence_dist_all_strands 0.0 chrom_freq/Test_seq/Test_seq 308 dist_freq/0-1/+- 0 dist_freq/0-1/-+ 0 @@ -44,143 +69,279 @@ dist_freq/2-3/+- 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+dist_freq/749894209-1000000000/++ 0 +dist_freq/1000000000+/+- 0 +dist_freq/1000000000+/-+ 0 +dist_freq/1000000000+/-- 0 +dist_freq/1000000000+/++ 0 diff --git a/tools/pairtools/test-data/output_parsed_pairs_bam.pairs b/tools/pairtools/test-data/output_parsed_pairs_bam.pairs index 83f16f389dd..d0142aee458 100644 --- a/tools/pairtools/test-data/output_parsed_pairs_bam.pairs +++ b/tools/pairtools/test-data/output_parsed_pairs_bam.pairs @@ -37,14 +37,14 @@ #samheader: @SQ SN:chrXV LN:1091291 #samheader: @SQ SN:chrXVI LN:948066 #samheader: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz -#samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa VN:1.0.3 +#samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/b/e/9/dataset_be9fce34-5096-400c-9efd-1f189da7f40a.dat -c /tmp/tmpchj83off/files/1/4/3/dataset_143017f3-646f-4cc1-b3d6-fc5d73287981.dat -o /tmp/tmpchj83off/job_working_directory/000/7/outputs/dataset_3348ea1d-0460-452f-aafb-dbde21a7b812.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa VN:1.1.0 #samheader: @PG ID:bwa-2CCE5976 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz -#samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-2CCE5976 VN:1.0.3 +#samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/b/e/9/dataset_be9fce34-5096-400c-9efd-1f189da7f40a.dat -c /tmp/tmpchj83off/files/1/4/3/dataset_143017f3-646f-4cc1-b3d6-fc5d73287981.dat -o /tmp/tmpchj83off/job_working_directory/000/7/outputs/dataset_3348ea1d-0460-452f-aafb-dbde21a7b812.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-2CCE5976 VN:1.1.0 #samheader: @PG ID:bwa-3CAFD9D9 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz -#samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-3CAFD9D9 VN:1.0.3 +#samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/b/e/9/dataset_be9fce34-5096-400c-9efd-1f189da7f40a.dat -c /tmp/tmpchj83off/files/1/4/3/dataset_143017f3-646f-4cc1-b3d6-fc5d73287981.dat -o /tmp/tmpchj83off/job_working_directory/000/7/outputs/dataset_3348ea1d-0460-452f-aafb-dbde21a7b812.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-3CAFD9D9 VN:1.1.0 #samheader: @PG ID:bwa-4548A671 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz #samheader: @PG ID:samtools PN:samtools PP:bwa-4548A671 VN:1.19.2 CL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam -#samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:samtools VN:1.0.3 +#samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/b/e/9/dataset_be9fce34-5096-400c-9efd-1f189da7f40a.dat -c /tmp/tmpchj83off/files/1/4/3/dataset_143017f3-646f-4cc1-b3d6-fc5d73287981.dat -o /tmp/tmpchj83off/job_working_directory/000/7/outputs/dataset_3348ea1d-0460-452f-aafb-dbde21a7b812.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:samtools VN:1.1.0 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2 HWI-ST560:29:B0A7LABXX:2:1101:5084:4188 ! 0 ! 0 - - NM HWI-ST560:29:B0A7LABXX:2:1101:5084:4188133chrI24200*=24200GGAACCGTAAAGGTTTATCGCGGTAGTAGTTTTTCACACGATTCGATAAA?<@DFDFD=FBHHCBHGGIJIIG:C@DGD??DDH?FHGHIJJDGCGEGG;AS:i:0XS:i:0Yt:Z:NM HWI-ST560:29:B0A7LABXX:2:1101:5084:418873chrI242009S41M=24200TTGATAGACTTCGTATGTGGAGTACTGTTTTATGGCGCTTATGTGTATTC11144222222322< Date: Mon, 29 Apr 2024 15:52:28 +0200 Subject: [PATCH 3/6] Version bump --- tools/pairtools/macros.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/pairtools/macros.xml b/tools/pairtools/macros.xml index 1234d1869f5..8d5263017bc 100644 --- a/tools/pairtools/macros.xml +++ b/tools/pairtools/macros.xml @@ -1,6 +1,6 @@ 1.1.0 - 0 + 1 topic_1381 From 206b30907028a99e706de346fd9841262caecb67 Mon Sep 17 00:00:00 2001 From: Saim Momin Date: Mon, 29 Apr 2024 16:45:34 +0200 Subject: [PATCH 4/6] Updated test data for sort and split --- .../test-data/output_dedup_sorted.pairsam | 16 ++++++++-------- .../test-data/output_pairs_split.bam | Bin 92044 -> 92148 bytes .../test-data/output_pairs_split.pairs | 16 ++++++++-------- .../test-data/output_sorted_pairs.pairs | 16 ++++++++-------- 4 files changed, 24 insertions(+), 24 deletions(-) diff --git a/tools/pairtools/test-data/output_dedup_sorted.pairsam b/tools/pairtools/test-data/output_dedup_sorted.pairsam index d3f2741de66..c4819f4cc02 100644 --- a/tools/pairtools/test-data/output_dedup_sorted.pairsam +++ b/tools/pairtools/test-data/output_dedup_sorted.pairsam @@ -39,24 +39,24 @@ #samheader: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz #samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa VN:1.0.2 #samheader: @PG ID:pairtools_sort-1.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-1.2 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-1.3 VN:1.0.2 -#samheader: @PG ID:pairtools_sort-1.5 PN:pairtools_sort CL:/usr/local/bin/pairtools sort /tmp/tmpwmd1r52h/files/c/1/c/dataset_c1c8eade-049e-4209-b8f9-a97c31df8468.dat -o /tmp/tmpwmd1r52h/job_working_directory/000/4/outputs/dataset_22fb7731-5e54-4b91-9180-5373e3456c9c.dat --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-1.4 VN:1.0.3 +#samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-1.3 VN:1.1.0 +#samheader: @PG ID:pairtools_sort-1.5 PN:pairtools_sort CL:/usr/local/bin/pairtools sort /tmp/tmptyq9evah/files/c/7/1/dataset_c7168a6f-71cc-4fb2-a696-c540bb977254.dat -o /tmp/tmptyq9evah/job_working_directory/000/4/outputs/dataset_d8a3cf41-0319-4df0-bc9f-d88012565c7e.dat --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-1.4 VN:1.1.0 #samheader: @PG ID:bwa-2CCE5976 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz #samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-2CCE5976 VN:1.0.2 #samheader: @PG ID:pairtools_sort-2.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-2.2 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-2.3 VN:1.0.2 -#samheader: @PG ID:pairtools_sort-2.5 PN:pairtools_sort CL:/usr/local/bin/pairtools sort /tmp/tmpwmd1r52h/files/c/1/c/dataset_c1c8eade-049e-4209-b8f9-a97c31df8468.dat -o /tmp/tmpwmd1r52h/job_working_directory/000/4/outputs/dataset_22fb7731-5e54-4b91-9180-5373e3456c9c.dat --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-2.4 VN:1.0.3 +#samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-2.3 VN:1.1.0 +#samheader: @PG ID:pairtools_sort-2.5 PN:pairtools_sort CL:/usr/local/bin/pairtools sort /tmp/tmptyq9evah/files/c/7/1/dataset_c7168a6f-71cc-4fb2-a696-c540bb977254.dat -o /tmp/tmptyq9evah/job_working_directory/000/4/outputs/dataset_d8a3cf41-0319-4df0-bc9f-d88012565c7e.dat --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-2.4 VN:1.1.0 #samheader: @PG ID:bwa-3CAFD9D9 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz #samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-3CAFD9D9 VN:1.0.2 #samheader: @PG ID:pairtools_sort-3.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-3.2 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-3.3 VN:1.0.2 -#samheader: @PG ID:pairtools_sort-3.5 PN:pairtools_sort CL:/usr/local/bin/pairtools sort /tmp/tmpwmd1r52h/files/c/1/c/dataset_c1c8eade-049e-4209-b8f9-a97c31df8468.dat -o /tmp/tmpwmd1r52h/job_working_directory/000/4/outputs/dataset_22fb7731-5e54-4b91-9180-5373e3456c9c.dat --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-3.4 VN:1.0.3 +#samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-3.3 VN:1.1.0 +#samheader: @PG ID:pairtools_sort-3.5 PN:pairtools_sort CL:/usr/local/bin/pairtools sort /tmp/tmptyq9evah/files/c/7/1/dataset_c7168a6f-71cc-4fb2-a696-c540bb977254.dat -o /tmp/tmptyq9evah/job_working_directory/000/4/outputs/dataset_d8a3cf41-0319-4df0-bc9f-d88012565c7e.dat --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-3.4 VN:1.1.0 #samheader: @PG ID:bwa-4548A671 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz #samheader: @PG ID:samtools PN:samtools PP:bwa-4548A671 VN:1.19.2 CL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam #samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:samtools VN:1.0.2 #samheader: @PG ID:pairtools_sort-4.4 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-4.3 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-4.4 VN:1.0.2 -#samheader: @PG ID:pairtools_sort-4.6 PN:pairtools_sort CL:/usr/local/bin/pairtools sort /tmp/tmpwmd1r52h/files/c/1/c/dataset_c1c8eade-049e-4209-b8f9-a97c31df8468.dat -o /tmp/tmpwmd1r52h/job_working_directory/000/4/outputs/dataset_22fb7731-5e54-4b91-9180-5373e3456c9c.dat --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-4.5 VN:1.0.3 +#samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-4.4 VN:1.1.0 +#samheader: @PG ID:pairtools_sort-4.6 PN:pairtools_sort CL:/usr/local/bin/pairtools sort /tmp/tmptyq9evah/files/c/7/1/dataset_c7168a6f-71cc-4fb2-a696-c540bb977254.dat -o /tmp/tmptyq9evah/job_working_directory/000/4/outputs/dataset_d8a3cf41-0319-4df0-bc9f-d88012565c7e.dat --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-4.5 VN:1.1.0 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2 HWI-ST560:29:B0A7LABXX:2:1101:15566:24141 chrI 3199 chrI 3399 + - UU HWI-ST560:29:B0A7LABXX:2:1101:15566:2414197chrI31996015S35M=3350201CTTAGACAATAAGCTAGCTTTCAAGATATAAGATACGAAATAGGGGTTGA111442422223232232EGDD?BFIIIIGBHCJIJIHFIHFHGHGGC<2GHGHFD?U~PW+e8${w?ipSVM-Yeoq=K4 zKY*3?m$Xt&4Jj~Yn&1+~^9Rrq-1tMdGLkLD za-7(m% zvqu>5c*|Vb8F5{T=k2}HOdLjh#^&w)($1OhdGqRfmAE5>KWD5Y9N~Im{)xS5egYGh zw9J*AU?2M&w;h$oajDDaQ>ii$+!4;aPQMCvUDqRS%RG}89ucDLs60O9oVA6j{DsF^ zs{;MrEKfrHR)73-VLtb;>)w0R{c5Z8csrQLt?qvHr?+}rt14znXU_?B2hnP_5RY!NGxrZ~CKPaA)oNG9XF zNYkMiWHL7z5sQ|IEtt!sY@>2ns3SWJbtaS8*avA;On+pqZJ9`wCZS}uPEL)zx6>Wy zYupC*dbp&#>)$P`sMJ#O5^W`&XULazzcJ)f@bri4EnX6qnY|2snmZQt-S}tJO zUSGVRP>16T5sSB1RGF(KjZJP3QzeHBxmFR-E=F1TlaW&q$c)=jJk-W!wy=FWl!Y|9 z7%<^SSYeJBqdwvk6XXX>A*PsgT`ja$+zMs2^nY`L&(dHpN%P}4IUIy>u2qrdFKmpl z?b_2?nC3xlT>@$udUk8pieGnSS{1}Df?A%ejS^^G}j!!%! zHFgkJkw#vme8ja<4soTH5t${BWO=GkoIuhH(s2PvdkdTMR_!3M@RB2$4dXJ#SvZrW z`G3+KtRkBAj?5r@USK)fLC+56cF+raA)_Eft`Hb;6>#JQ5kXO?gck%#V;RlXH7n-y znx7NDxR~@@F+=HNmyi$zI3$R3p^(%rL6I+&AY6nF3EK}X?}s(hDev>zWj?zFi**hr z64Bk=FC1UE*UxgYg5_ilmeUQ(FJbxF=6|h#I(?&{PS=1s-9Y^YL!GVxb-IE2m7z{A zfI8dV`SP*<*uQ3|(-kl1biEgJwt@O(P;WMG1=QIa1$DLt)Y%5=HyG+{4XCpX)UOP6 zb^+A6!@V6>kn4v!SpoHBZ|X*ls-(+o&OUeBnNFACTeM8Bj)JGLoVxhdcWRYA@ZmSN z>Ol`Ydv&*t>vh1>PjAwsW#AN&u@ru}V+8vp F{$j;JfI9#H delta 1183 zcmV;Q1YrC0&jpOn1%Drl2m}BC000301^_}s0sw~u?U+q+<3tq4dx~L*12qiAA`6P5 z4?wrnANtBFApy$NBzOqr^3JrRcC3jlDQY=prdUwL88`q7IKr$s0JDM}2VqOKY{`~m z$DT?S4C6&&_y4{A>-BrmuT=i*@Z{c$Jpc~Qo;1!*_k(`cY=1mH-KWf?#NC}!3)v-% zxV$D8IwQ7C&3V18WnwYnF*dJvw9c95y7TTQg}LQ8-kexiSdQ&F^H*$7>T^tDlbT%U z#Pm#$oAp2uv21Gd`BI8X9Bw(*yicb{wr$%bc1@nzJ1%jYdZ37Slyg=$D(ZJ!&T1X# zw5N3v>eccm2Y>UpYufhiLF>y#^LXDMi$?3T_-LQ*o7lm`LKz|4Y#cq-G91bwL^*UJ zx`GU%vldh$IFcE|J%P`k!;`~r#USmA?l%MvL@Wt5O-yi4sQhweoL2F&kW@rjo+Ja+ zO+}_8BADvJ7GzzNp@K~0LEi{NnTj}4##z$K$0C!4h<`HMIdB}0W$k@sOPRgNt5pt*U=!2p?NdpXBZ67Ids@AV=4qd~-sxr4j^e)<-rQGxfMv5@eV|Z= zqZAR$>nAGYyEsx|GCtERqedNVizL0gJQYt>Ghmt@ubc;3Iug_((V4 zBi-`x)_kNZ_{fe9zc}`ey*uV3UGv&VH+yYlTRz^z$7*KC%t?$leq_vJLpi zwtT!bAK3~%a*Ml%wnOfok7NxWm%TqKF@G$I*450ux9XJ^#~>c2y0|h6UPW>Yk%A^B z5cv=tK(6m{HS(35G_0h{Dj4%cifmzA!nm5n8W8hEZ2hM}%x`4R1abLzVX_FmWk01%_~$O6pMM6?HBY+ElfJqqTj$AM-IK5L)PHy1 z8qW^^0B-{T^e^k+tDoKi52lMI__6;Uc&A)7!5@F!uYzsx@ppUGssmat9+WO8;KQ%) zm5Vlb`f{htYd67@PwtnN?Pe4F@arS6Q!Sg|&!2b7ogJ_z-Ys`_n&9_OcgvlfW)u9P xs+}FZ^Zkz=&cbc*@}Jq>Hu(FuM-Nr7-30#lA@~>3HiiAQ7=!Kvx9$W124e+HQhWda diff --git a/tools/pairtools/test-data/output_pairs_split.pairs b/tools/pairtools/test-data/output_pairs_split.pairs index 85bfcf2a629..8f21c21c79f 100644 --- a/tools/pairtools/test-data/output_pairs_split.pairs +++ b/tools/pairtools/test-data/output_pairs_split.pairs @@ -39,24 +39,24 @@ #samheader: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz #samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa VN:1.0.2 #samheader: @PG ID:pairtools_sort-1.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-1.2 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-1.3 VN:1.0.2 -#samheader: @PG ID:pairtools_split-1.5 PN:pairtools_split CL:/usr/local/bin/pairtools split /tmp/tmpnt_hb134/files/7/4/2/dataset_7420fb9f-e3dd-4326-8cef-1e023c2b5e85.dat --output-pairs /tmp/tmpnt_hb134/job_working_directory/000/2/outputs/dataset_ba891b58-22e9-49f5-83f9-063b56eda346.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-1.4 VN:1.0.3 +#samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-1.3 VN:1.1.0 +#samheader: @PG ID:pairtools_split-1.5 PN:pairtools_split CL:/usr/local/bin/pairtools split /tmp/tmpms_dxt0a/files/8/b/9/dataset_8b97afbd-6770-4cb4-8bf1-fdc78bbce0af.dat --output-pairs /tmp/tmpms_dxt0a/job_working_directory/000/2/outputs/dataset_da90611d-b0d1-447c-ae61-f9ac7147d51d.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-1.4 VN:1.1.0 #samheader: @PG ID:bwa-2CCE5976 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz #samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-2CCE5976 VN:1.0.2 #samheader: @PG ID:pairtools_sort-2.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-2.2 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-2.3 VN:1.0.2 -#samheader: @PG ID:pairtools_split-2.5 PN:pairtools_split CL:/usr/local/bin/pairtools split /tmp/tmpnt_hb134/files/7/4/2/dataset_7420fb9f-e3dd-4326-8cef-1e023c2b5e85.dat --output-pairs /tmp/tmpnt_hb134/job_working_directory/000/2/outputs/dataset_ba891b58-22e9-49f5-83f9-063b56eda346.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-2.4 VN:1.0.3 +#samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-2.3 VN:1.1.0 +#samheader: @PG ID:pairtools_split-2.5 PN:pairtools_split CL:/usr/local/bin/pairtools split /tmp/tmpms_dxt0a/files/8/b/9/dataset_8b97afbd-6770-4cb4-8bf1-fdc78bbce0af.dat --output-pairs /tmp/tmpms_dxt0a/job_working_directory/000/2/outputs/dataset_da90611d-b0d1-447c-ae61-f9ac7147d51d.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-2.4 VN:1.1.0 #samheader: @PG ID:bwa-3CAFD9D9 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz #samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-3CAFD9D9 VN:1.0.2 #samheader: @PG ID:pairtools_sort-3.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-3.2 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-3.3 VN:1.0.2 -#samheader: @PG ID:pairtools_split-3.5 PN:pairtools_split CL:/usr/local/bin/pairtools split /tmp/tmpnt_hb134/files/7/4/2/dataset_7420fb9f-e3dd-4326-8cef-1e023c2b5e85.dat --output-pairs /tmp/tmpnt_hb134/job_working_directory/000/2/outputs/dataset_ba891b58-22e9-49f5-83f9-063b56eda346.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-3.4 VN:1.0.3 +#samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-3.3 VN:1.1.0 +#samheader: @PG ID:pairtools_split-3.5 PN:pairtools_split CL:/usr/local/bin/pairtools split /tmp/tmpms_dxt0a/files/8/b/9/dataset_8b97afbd-6770-4cb4-8bf1-fdc78bbce0af.dat --output-pairs /tmp/tmpms_dxt0a/job_working_directory/000/2/outputs/dataset_da90611d-b0d1-447c-ae61-f9ac7147d51d.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-3.4 VN:1.1.0 #samheader: @PG ID:bwa-4548A671 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz #samheader: @PG ID:samtools PN:samtools PP:bwa-4548A671 VN:1.19.2 CL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam #samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:samtools VN:1.0.2 #samheader: @PG ID:pairtools_sort-4.4 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-4.3 VN:1.0.2 -#samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs_markdups.pairsam --mark-dups --output-stats output_dedup_pairs.stats output_sorted_pairs.pairsam PP:pairtools_sort-4.4 VN:1.0.2 -#samheader: @PG ID:pairtools_split-4.6 PN:pairtools_split CL:/usr/local/bin/pairtools split /tmp/tmpnt_hb134/files/7/4/2/dataset_7420fb9f-e3dd-4326-8cef-1e023c2b5e85.dat --output-pairs /tmp/tmpnt_hb134/job_working_directory/000/2/outputs/dataset_ba891b58-22e9-49f5-83f9-063b56eda346.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-4.5 VN:1.0.3 +#samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/3/7/9/dataset_379f0c04-3329-4201-9b3c-3c3a66e7eec4.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_6f9ee270-56fb-4c2e-92f4-509340f9eb58.dat --mark-dups --output-stats /tmp/tmpp1v7bap4/job_working_directory/000/6/outputs/dataset_653a5918-ae05-4cfe-8fc9-4ecc516aeaf1.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-4.4 VN:1.1.0 +#samheader: @PG ID:pairtools_split-4.6 PN:pairtools_split CL:/usr/local/bin/pairtools split /tmp/tmpms_dxt0a/files/8/b/9/dataset_8b97afbd-6770-4cb4-8bf1-fdc78bbce0af.dat --output-pairs /tmp/tmpms_dxt0a/job_working_directory/000/2/outputs/dataset_da90611d-b0d1-447c-ae61-f9ac7147d51d.dat --output-sam ./output.bam --nproc-in 1 --nproc-out 1 PP:pairtools_dedup-4.5 VN:1.1.0 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type HWI-ST560:29:B0A7LABXX:2:1101:15566:24141 chrI 3199 chrI 3399 + - UU HWI-ST560:29:B0A7LABXX:2:1101:18861:21891 chrI 35431 chrI 35703 + - UU diff --git a/tools/pairtools/test-data/output_sorted_pairs.pairs b/tools/pairtools/test-data/output_sorted_pairs.pairs index 71fb26e05c3..92829f232bb 100644 --- a/tools/pairtools/test-data/output_sorted_pairs.pairs +++ b/tools/pairtools/test-data/output_sorted_pairs.pairs @@ -38,18 +38,18 @@ #samheader: @SQ SN:chrXV LN:1091291 #samheader: @SQ SN:chrXVI LN:948066 #samheader: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz -#samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa VN:1.0.3 -#samheader: @PG ID:pairtools_sort-1.3 PN:pairtools_sort CL:/usr/local/bin/pairtools sort /tmp/tmpwmd1r52h/files/d/5/c/dataset_d5c01101-89f1-4667-9536-e0a8f57684e3.dat -o /tmp/tmpwmd1r52h/job_working_directory/000/2/outputs/dataset_b446f275-b840-40de-9fb8-08bd13d19337.dat --nproc-in 1 --nproc-out 1 PP:pairtools_parse-1.2 VN:1.0.3 +#samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/b/e/9/dataset_be9fce34-5096-400c-9efd-1f189da7f40a.dat -c /tmp/tmpchj83off/files/1/4/3/dataset_143017f3-646f-4cc1-b3d6-fc5d73287981.dat -o /tmp/tmpchj83off/job_working_directory/000/7/outputs/dataset_3348ea1d-0460-452f-aafb-dbde21a7b812.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa VN:1.1.0 +#samheader: @PG ID:pairtools_sort-1.3 PN:pairtools_sort CL:/usr/local/bin/pairtools sort /tmp/tmptyq9evah/files/8/6/3/dataset_863ae21a-b207-4ba9-b94f-54406023b20a.dat -o /tmp/tmptyq9evah/job_working_directory/000/2/outputs/dataset_de1b3c74-45c1-408a-bb81-f91bacfb79cd.dat --nproc-in 1 --nproc-out 1 PP:pairtools_parse-1.2 VN:1.1.0 #samheader: @PG ID:bwa-2CCE5976 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz -#samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-2CCE5976 VN:1.0.3 -#samheader: @PG ID:pairtools_sort-2.3 PN:pairtools_sort CL:/usr/local/bin/pairtools sort /tmp/tmpwmd1r52h/files/d/5/c/dataset_d5c01101-89f1-4667-9536-e0a8f57684e3.dat -o /tmp/tmpwmd1r52h/job_working_directory/000/2/outputs/dataset_b446f275-b840-40de-9fb8-08bd13d19337.dat --nproc-in 1 --nproc-out 1 PP:pairtools_parse-2.2 VN:1.0.3 +#samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/b/e/9/dataset_be9fce34-5096-400c-9efd-1f189da7f40a.dat -c /tmp/tmpchj83off/files/1/4/3/dataset_143017f3-646f-4cc1-b3d6-fc5d73287981.dat -o /tmp/tmpchj83off/job_working_directory/000/7/outputs/dataset_3348ea1d-0460-452f-aafb-dbde21a7b812.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-2CCE5976 VN:1.1.0 +#samheader: @PG ID:pairtools_sort-2.3 PN:pairtools_sort CL:/usr/local/bin/pairtools sort /tmp/tmptyq9evah/files/8/6/3/dataset_863ae21a-b207-4ba9-b94f-54406023b20a.dat -o /tmp/tmptyq9evah/job_working_directory/000/2/outputs/dataset_de1b3c74-45c1-408a-bb81-f91bacfb79cd.dat --nproc-in 1 --nproc-out 1 PP:pairtools_parse-2.2 VN:1.1.0 #samheader: @PG ID:bwa-3CAFD9D9 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz -#samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-3CAFD9D9 VN:1.0.3 -#samheader: @PG ID:pairtools_sort-3.3 PN:pairtools_sort CL:/usr/local/bin/pairtools sort /tmp/tmpwmd1r52h/files/d/5/c/dataset_d5c01101-89f1-4667-9536-e0a8f57684e3.dat -o /tmp/tmpwmd1r52h/job_working_directory/000/2/outputs/dataset_b446f275-b840-40de-9fb8-08bd13d19337.dat --nproc-in 1 --nproc-out 1 PP:pairtools_parse-3.2 VN:1.0.3 +#samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/b/e/9/dataset_be9fce34-5096-400c-9efd-1f189da7f40a.dat -c /tmp/tmpchj83off/files/1/4/3/dataset_143017f3-646f-4cc1-b3d6-fc5d73287981.dat -o /tmp/tmpchj83off/job_working_directory/000/7/outputs/dataset_3348ea1d-0460-452f-aafb-dbde21a7b812.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:bwa-3CAFD9D9 VN:1.1.0 +#samheader: @PG ID:pairtools_sort-3.3 PN:pairtools_sort CL:/usr/local/bin/pairtools sort /tmp/tmptyq9evah/files/8/6/3/dataset_863ae21a-b207-4ba9-b94f-54406023b20a.dat -o /tmp/tmptyq9evah/job_working_directory/000/2/outputs/dataset_de1b3c74-45c1-408a-bb81-f91bacfb79cd.dat --nproc-in 1 --nproc-out 1 PP:pairtools_parse-3.2 VN:1.1.0 #samheader: @PG ID:bwa-4548A671 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz #samheader: @PG ID:samtools PN:samtools PP:bwa-4548A671 VN:1.19.2 CL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam -#samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpvtvmbj0m/files/5/c/9/dataset_5c90f563-7928-4455-84af-6129feb92ffc.dat -c /tmp/tmpvtvmbj0m/files/4/9/a/dataset_49af402e-cee9-4737-bf5e-15a04f62c1d8.dat -o /tmp/tmpvtvmbj0m/job_working_directory/000/7/outputs/dataset_461ac430-f019-4ae5-9b37-796f7c45fa35.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:samtools VN:1.0.3 -#samheader: @PG ID:pairtools_sort-4.4 PN:pairtools_sort CL:/usr/local/bin/pairtools sort /tmp/tmpwmd1r52h/files/d/5/c/dataset_d5c01101-89f1-4667-9536-e0a8f57684e3.dat -o /tmp/tmpwmd1r52h/job_working_directory/000/2/outputs/dataset_b446f275-b840-40de-9fb8-08bd13d19337.dat --nproc-in 1 --nproc-out 1 PP:pairtools_parse-4.3 VN:1.0.3 +#samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/usr/local/bin/pairtools parse /tmp/tmpchj83off/files/b/e/9/dataset_be9fce34-5096-400c-9efd-1f189da7f40a.dat -c /tmp/tmpchj83off/files/1/4/3/dataset_143017f3-646f-4cc1-b3d6-fc5d73287981.dat -o /tmp/tmpchj83off/job_working_directory/000/7/outputs/dataset_3348ea1d-0460-452f-aafb-dbde21a7b812.dat --min-mapq 1 --max-molecule-size 750 --walks-policy mask --max-inter-align-gap 20 --nproc-in 1 --nproc-out 1 PP:samtools VN:1.1.0 +#samheader: @PG ID:pairtools_sort-4.4 PN:pairtools_sort CL:/usr/local/bin/pairtools sort /tmp/tmptyq9evah/files/8/6/3/dataset_863ae21a-b207-4ba9-b94f-54406023b20a.dat -o /tmp/tmptyq9evah/job_working_directory/000/2/outputs/dataset_de1b3c74-45c1-408a-bb81-f91bacfb79cd.dat --nproc-in 1 --nproc-out 1 PP:pairtools_parse-4.3 VN:1.1.0 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2 HWUSI-EAS1533_0033_FC:1:1:1193:16038 ! 0 ! 0 - - MM HWUSI-EAS1533_0033_FC:1:1:1193:1603881chrIV1529635036MchrIX187220AATTGACATTAAGCAATTGATGATGGTGATCATGCT@@@@@@C@@C@C@@CCCCC@@CC@CC7777832324NM:i:0MD:Z:36AS:i:36XS:i:36Yt:Z:MM HWUSI-EAS1533_0033_FC:1:1:1193:16038161chrIX18722036MchrIV15296350NAAGTAAATTTACGATCTGGAAGGAGTGCTGTATGT&,,,,22032@@@@@@@@@@@@@@@@@@@@@@@@@@NM:i:2MD:Z:0A11G23AS:i:30XS:i:30XA:Z:chrX,+18705,36M,2;chrXV,+24474,36M,2;Yt:Z:MM HWUSI-EAS1533_0033_FC:1:1:2292:14294 ! 0 ! 0 - - MM HWUSI-EAS1533_0033_FC:1:1:2292:1429481chrVII1001809036M=1001598-247ATCGAAGATCCATTTGCTGAAGATGACTGGGAAGCT7@@@@@C@@@C@C@CC@@@@C@C@C@778771111-NM:i:0MD:Z:36AS:i:36XS:i:36XA:Z:chrVIII,-452209,36M,0;Yt:Z:MM HWUSI-EAS1533_0033_FC:1:1:2292:14294161chrVII1001598036M=1001809247NGCTTTGGACTTGATTGTTGACGCTATCAAGGCTGC)333377777@C@@@C@CCC@@@@C@C@@CC@@@@@NM:i:1MD:Z:0A35AS:i:35XS:i:35XA:Z:chrVIII,+451998,36M,1;Yt:Z:MM From c12d457acae903a0381c1f670e42d4833b7f2e96 Mon Sep 17 00:00:00 2001 From: Saim Momin <64724322+SaimMomin12@users.noreply.github.com> Date: Tue, 30 Apr 2024 10:40:57 +0200 Subject: [PATCH 5/6] Updated Suffix Version MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- tools/pairtools/macros.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/pairtools/macros.xml b/tools/pairtools/macros.xml index 8d5263017bc..1234d1869f5 100644 --- a/tools/pairtools/macros.xml +++ b/tools/pairtools/macros.xml @@ -1,6 +1,6 @@ 1.1.0 - 1 + 0 topic_1381 From 5bd5f2af23de3faf46488b9ee1383fd5a9c84534 Mon Sep 17 00:00:00 2001 From: Saim Momin <64724322+SaimMomin12@users.noreply.github.com> Date: Tue, 30 Apr 2024 11:06:33 +0200 Subject: [PATCH 6/6] Minor change MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Björn Grüning --- tools/pairtools/parse.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/pairtools/parse.xml b/tools/pairtools/parse.xml index db89509c6d0..a1e97ca373a 100644 --- a/tools/pairtools/parse.xml +++ b/tools/pairtools/parse.xml @@ -1,4 +1,4 @@ - + Find ligation pairs in alignments and create pairs. macros.xml