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Merge pull request #5 from StefaanVerwimp/new_serotypes
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Addition of serotypes O15 and O17
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@rpetit3
rpetit3 authored Aug 19, 2024
2 parents dd60940 + 79bd116 commit 23fea68
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Showing 52 changed files with 815 additions and 195 deletions.
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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@@ -1,13 +1,15 @@
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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Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
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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Original file line number Diff line number Diff line change
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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