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Addition of serotypes O15 and O17 #5

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merged 6 commits into from
Aug 19, 2024
Merged

Addition of serotypes O15 and O17 #5

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8cba2c8
Added serotypes O15 and O17
sverwimp Aug 14, 2024
3c28bb7
Tests after addition O15 and O17 serotypes
sverwimp Aug 14, 2024
21ca9f2
Merge branch 'rpetit3:main' into new_serotypes
sverwimp Aug 14, 2024
a18a7d8
Added tests for O15 and O17O
sverwimp Aug 14, 2024
185fc37
Added O15 and O17 reference genomes to list
sverwimp Aug 14, 2024
79bd116
Merge branch 'rpetit3:main' into new_serotypes
sverwimp Aug 19, 2024
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468 changes: 468 additions & 0 deletions data/pa-osa.fasta
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6 changes: 6 additions & 0 deletions data/pa-osa.yaml
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Expand Up @@ -27,6 +27,8 @@ targets:
- "O11"
- "O12"
- "O13"
- "O15"
- "O17"
- "wzyB"

# types includes the final typing designations based on targets and aliases
Expand Down Expand Up @@ -56,3 +58,7 @@ types:
targets: ["O12"]
- name: "O13"
targets: ["O13"]
- name: "O15"
targets: ["O15"]
- name: "O17"
targets: ["O17"]
2 changes: 2 additions & 0 deletions test/README.md
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Expand Up @@ -52,3 +52,5 @@ serogroups. Below is a table of each serogroup and the corresponding reference g
| O11 | [GCF_001444955.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_001444955.1/)|
| O12 | [GCF_001444975.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_001444975.1/)|
| O13 | [GCF_001444995.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_001444995.1/)|
| O15 | [GCF_001444865.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_001444865.1/)|
| O17 | [GCA_001444915.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_001444915.1/)|
Binary file added test/data/O15-GCF_001444865.fna.gz
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Binary file added test/data/O17-GCF_001444915.fna.gz
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26 changes: 14 additions & 12 deletions test/expected-results/NT-GCF_000292685/NT-GCF_000292685.details.tsv
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sample type status targets missing coverage hits schema schema_version camlhmp_version params comment
NT-GCF_000292685 O1 False O1 0.00 0 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O2 False O2,wzyB 0.00,0.00 0,0 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O3 False O3 0.00 0 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O4 False O4 0.00 0 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O5 False O2 0.00 0 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O6 False O6 0.00 0 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O7 False O7 0.00 0 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O9 False O9 0.00 0 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O10 False O10 0.00 0 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O11 False O11 0.00 0 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O12 False O12 0.00 0 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O13 False O13 0.00 0 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O1 False O1 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O2 False O2,wzyB 0.00,0.00 0,0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O3 False O3 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O4 False O4 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O5 False O2 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O6 False O6 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O7 False O7 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O9 False O9 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O10 False O10 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O11 False O11 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O12 False O12 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O13 False O13 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O15 False O15 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
NT-GCF_000292685 O17 False O17 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
2 changes: 1 addition & 1 deletion test/expected-results/NT-GCF_000292685/NT-GCF_000292685.tsv
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sample type targets coverage hits schema schema_version camlhmp_version params comment
NT-GCF_000292685 - pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 A type could not be determined
NT-GCF_000292685 - pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 A type could not be determined
1 change: 1 addition & 0 deletions test/expected-results/O1-GCF_001420225/O1-GCF_001420225.blastn.tsv
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Expand Up @@ -20,3 +20,4 @@ O12 NZ_LJNU01000023.1 90.449 9 25864 73203 1916 1733 183 0 23949 25864 37732 396
O12 NZ_LJNU01000023.1 95.455 9 25864 73203 330 315 11 3 1 328 21280 21607 3.82e-147 523
O13 NZ_LJNU01000023.1 97.767 15 14316 73203 1926 1883 43 0 1 1926 39647 37722 0.0 3319
O13 NZ_LJNU01000023.1 99.650 15 14316 73203 286 285 1 0 14031 14316 21565 21280 2.11e-147 523
O17 NZ_LJNU01000009.1 78.426 5 21521 148102 1029 807 202 18 1053 2071 124065 123047 0.0 652
26 changes: 14 additions & 12 deletions test/expected-results/O1-GCF_001420225/O1-GCF_001420225.details.tsv
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sample type status targets missing coverage hits schema schema_version camlhmp_version params comment
O1-GCF_001420225 O1 True O1 100.00 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O1-GCF_001420225 O2 False O2,wzyB 9.86,0.00 2,0 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 O2:Coverage based on 2 hits
O1-GCF_001420225 O3 False O3 11.21 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O1-GCF_001420225 O4 False O4 14.36 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O1-GCF_001420225 O5 False O2 9.86 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O1-GCF_001420225 O6 False O6 14.07 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O1-GCF_001420225 O7 False O7 11.55 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O1-GCF_001420225 O9 False O9 36.67 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O1-GCF_001420225 O10 False O10 12.52 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O1-GCF_001420225 O11 False O11 15.85 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O1-GCF_001420225 O12 False O12 1.27 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O1-GCF_001420225 O13 False O13 15.45 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O1-GCF_001420225 O1 True O1 100.00 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O1-GCF_001420225 O2 False O2,wzyB 9.86,0.00 2,0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 O2:Coverage based on 2 hits
O1-GCF_001420225 O3 False O3 11.21 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O1-GCF_001420225 O4 False O4 14.36 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O1-GCF_001420225 O5 False O2 9.86 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O1-GCF_001420225 O6 False O6 14.07 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O1-GCF_001420225 O7 False O7 11.55 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O1-GCF_001420225 O9 False O9 36.67 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O1-GCF_001420225 O10 False O10 12.52 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O1-GCF_001420225 O11 False O11 15.85 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O1-GCF_001420225 O12 False O12 1.27 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O1-GCF_001420225 O13 False O13 15.45 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O1-GCF_001420225 O15 False O15 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O1-GCF_001420225 O17 False O17 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
2 changes: 1 addition & 1 deletion test/expected-results/O1-GCF_001420225/O1-GCF_001420225.tsv
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sample type targets coverage hits schema schema_version camlhmp_version params comment
O1-GCF_001420225 O1 O1 100.00 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O1-GCF_001420225 O1 O1 100.00 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
1 change: 1 addition & 0 deletions test/expected-results/O10-GCF_001444835/O10-GCF_001444835.blastn.tsv
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Expand Up @@ -26,3 +26,4 @@ O12 NZ_LJZD01000126.1 90.245 9 25864 72524 1917 1730 187 0 23948 25864 37004 389
O12 NZ_LJZD01000126.1 97.902 9 25864 72524 286 280 6 0 1 286 21286 21571 7.98e-139 496
O13 NZ_LJZD01000126.1 98.121 16 14316 72524 1916 1880 36 0 1 1916 38920 37005 0.0 3339
O13 NZ_LJZD01000126.1 95.224 16 14316 72524 335 319 6 6 13989 14316 21617 21286 7.28e-147 521
O17 NZ_LJZD01000124.1 78.328 5 21521 75204 1029 806 203 19 1053 2071 18233 19251 0.0 647
26 changes: 14 additions & 12 deletions test/expected-results/O10-GCF_001444835/O10-GCF_001444835.details.tsv
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sample type status targets missing coverage hits schema schema_version camlhmp_version params comment
O10-GCF_001444835 O1 False O1 12.02 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O10-GCF_001444835 O2 False O2,wzyB 9.81,0.00 2,0 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 O2:Coverage based on 2 hits
O10-GCF_001444835 O3 False O3 9.90 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O10-GCF_001444835 O4 False O4 13.86 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O10-GCF_001444835 O5 False O2 9.81 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O10-GCF_001444835 O6 False O6 14.06 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O10-GCF_001444835 O7 False O7 10.20 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O10-GCF_001444835 O9 False O9 12.76 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O10-GCF_001444835 O10 True O10 100.00 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O10-GCF_001444835 O11 False O11 15.86 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O10-GCF_001444835 O12 False O12 1.11 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O10-GCF_001444835 O13 False O13 15.67 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O10-GCF_001444835 O1 False O1 12.02 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O10-GCF_001444835 O2 False O2,wzyB 9.81,0.00 2,0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 O2:Coverage based on 2 hits
O10-GCF_001444835 O3 False O3 9.90 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O10-GCF_001444835 O4 False O4 13.86 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O10-GCF_001444835 O5 False O2 9.81 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O10-GCF_001444835 O6 False O6 14.06 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O10-GCF_001444835 O7 False O7 10.20 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O10-GCF_001444835 O9 False O9 12.76 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O10-GCF_001444835 O10 True O10 100.00 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O10-GCF_001444835 O11 False O11 15.86 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O10-GCF_001444835 O12 False O12 1.11 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O10-GCF_001444835 O13 False O13 15.67 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O10-GCF_001444835 O15 False O15 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O10-GCF_001444835 O17 False O17 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
2 changes: 1 addition & 1 deletion test/expected-results/O10-GCF_001444835/O10-GCF_001444835.tsv
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sample type targets coverage hits schema schema_version camlhmp_version params comment
O10-GCF_001444835 O10 O10 100.00 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O10-GCF_001444835 O10 O10 100.00 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
1 change: 1 addition & 0 deletions test/expected-results/O11-GCF_001444955/O11-GCF_001444955.blastn.tsv
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Expand Up @@ -29,3 +29,4 @@ O12 NZ_LJZE01000173.1 87.287 11 25864 68726 2643 2307 310 13 23227 25864 36184 3
O12 NZ_LJZE01000173.1 97.509 11 25864 68726 281 274 7 0 1 281 47430 47150 2.31e-134 481
O13 NZ_LJZE01000173.1 95.905 15 14316 68726 1929 1850 79 0 1 1929 33563 35491 0.0 3125
O13 NZ_LJZE01000173.1 99.288 15 14316 68726 281 279 2 0 14036 14316 47150 47430 5.87e-143 508
O17 NZ_LJZE01000232.1 78.134 5 21521 126170 1029 804 205 19 1053 2071 121971 120953 0.0 636
26 changes: 14 additions & 12 deletions test/expected-results/O11-GCF_001444955/O11-GCF_001444955.details.tsv
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sample type status targets missing coverage hits schema schema_version camlhmp_version params comment
O11-GCF_001444955 O1 False O1 11.56 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O11-GCF_001444955 O2 False O2,wzyB 9.85,0.00 4,0 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 O2:Coverage based on 4 hits;O2:There were one or more overlapping hits
O11-GCF_001444955 O3 False O3 10.85 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O11-GCF_001444955 O4 False O4 1.81 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O11-GCF_001444955 O5 False O2 9.85 4 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 4 hits;There were one or more overlapping hits
O11-GCF_001444955 O6 False O6 14.05 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O11-GCF_001444955 O7 False O7 11.17 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O11-GCF_001444955 O9 False O9 12.35 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O11-GCF_001444955 O10 False O10 12.46 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O11-GCF_001444955 O11 True O11 100.00 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O11-GCF_001444955 O12 False O12 1.09 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O11-GCF_001444955 O13 False O13 15.44 2 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O11-GCF_001444955 O1 False O1 11.56 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O11-GCF_001444955 O2 False O2,wzyB 9.85,0.00 4,0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 O2:Coverage based on 4 hits;O2:There were one or more overlapping hits
O11-GCF_001444955 O3 False O3 10.85 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O11-GCF_001444955 O4 False O4 1.81 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O11-GCF_001444955 O5 False O2 9.85 4 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 4 hits;There were one or more overlapping hits
O11-GCF_001444955 O6 False O6 14.05 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O11-GCF_001444955 O7 False O7 11.17 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O11-GCF_001444955 O9 False O9 12.35 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O11-GCF_001444955 O10 False O10 12.46 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O11-GCF_001444955 O11 True O11 100.00 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O11-GCF_001444955 O12 False O12 1.09 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O11-GCF_001444955 O13 False O13 15.44 2 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95 Coverage based on 2 hits
O11-GCF_001444955 O15 False O15 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O11-GCF_001444955 O17 False O17 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
2 changes: 1 addition & 1 deletion test/expected-results/O11-GCF_001444955/O11-GCF_001444955.tsv
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sample type targets coverage hits schema schema_version camlhmp_version params comment
O11-GCF_001444955 O11 O11 100.00 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O11-GCF_001444955 O11 O11 100.00 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
1 change: 1 addition & 0 deletions test/expected-results/O12-GCF_001444975/O12-GCF_001444975.blastn.tsv
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Expand Up @@ -22,3 +22,4 @@ O11 NZ_LJZF01000047.1 97.509 21 13868 75294 281 274 7 0 1 281 54078 53798 1.20e-
O12 NZ_LJZF01000047.1 100.000 100 25864 75294 25864 25864 0 0 1 25864 54078 28215 0.0 47762
O13 NZ_LJZF01000047.1 90.900 15 14316 75294 1901 1728 173 0 1 1901 28215 30115 0.0 2553
O13 NZ_LJZF01000047.1 98.270 15 14316 75294 289 284 5 0 14028 14316 53790 54078 2.05e-142 507
O17 NZ_LJZF01000203.1 78.410 5 21521 64295 1019 799 204 16 1053 2063 38882 39892 0.0 649
26 changes: 14 additions & 12 deletions test/expected-results/O12-GCF_001444975/O12-GCF_001444975.details.tsv
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sample type status targets missing coverage hits schema schema_version camlhmp_version params comment
O12-GCF_001444975 O1 False O1 1.79 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O2 False O2,wzyB 0.00,0.00 0,0 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O3 False O3 1.42 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O4 False O4 1.81 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O5 False O2 0.00 0 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O6 False O6 1.85 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O7 False O7 1.46 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O9 False O9 1.93 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O10 False O10 1.62 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O11 False O11 2.03 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O12 True O12 100.00 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O13 False O13 2.02 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O1 False O1 1.79 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O2 False O2,wzyB 0.00,0.00 0,0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O3 False O3 1.42 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O4 False O4 1.81 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O5 False O2 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O6 False O6 1.85 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O7 False O7 1.46 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O9 False O9 1.93 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O10 False O10 1.62 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O11 False O11 2.03 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O12 True O12 100.00 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O13 False O13 2.02 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O15 False O15 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O17 False O17 0.00 0 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
2 changes: 1 addition & 1 deletion test/expected-results/O12-GCF_001444975/O12-GCF_001444975.tsv
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sample type targets coverage hits schema schema_version camlhmp_version params comment
O12-GCF_001444975 O12 O12 100.00 1 pasty 1.0.0 0.2.1 min-coverage=95;min-pident=95
O12-GCF_001444975 O12 O12 100.00 1 pasty 2.0.0 0.3.1 min-coverage=95;min-pident=95
1 change: 1 addition & 0 deletions test/expected-results/O13-GCF_001444995/O13-GCF_001444995.blastn.tsv
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Expand Up @@ -28,3 +28,4 @@ O11 NZ_LJZG01000080.1 99.288 16 13868 69130 281 279 2 0 1 281 21285 21565 5.57e-
O12 NZ_LJZG01000080.1 90.710 9 25864 69130 1916 1738 178 0 23949 25864 33685 35600 0.0 2553
O12 NZ_LJZG01000080.1 98.270 9 25864 69130 289 284 5 0 1 289 21285 21573 3.74e-142 507
O13 NZ_LJZG01000080.1 100.000 100 14316 69130 14316 14316 0 0 1 14316 35600 21285 0.0 26437
O17 NZ_LJZG01000036.1 78.058 5 21521 158873 1030 804 206 19 1053 2072 115305 114286 4.92e-180 632
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