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Merge pull request #317 from PolinaBevad/integration_tests_validator
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Integration tests updates
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@pcingola
pcingola authored Sep 8, 2020
2 parents cfcb765 + 8080f32 commit a630412
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Showing 6 changed files with 13 additions and 6 deletions.
2 changes: 1 addition & 1 deletion VarDict
Submodule VarDict updated 3 files
+5 −4 var2vcf_paired.pl
+1 −1 var2vcf_valid.pl
+1 −1 vardict.pl
2 changes: 1 addition & 1 deletion build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ plugins {
id 'jacoco'
}

version = '1.8.0'
version = '1.8.1'

repositories {
mavenCentral()
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2 changes: 2 additions & 0 deletions tests/integration/config.sh
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Expand Up @@ -4,6 +4,8 @@ set -o pipefail
#---
# Paths
#---
# Validation of VCF files with EBIvariation vcf-validator, must be on the PATH
VCF_VALIDATOR="vcf_validator"

WORKSPACE="$HOME/IdeaProjects"
WORKSPACE="$HOME/workspace"
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6 changes: 3 additions & 3 deletions tests/integration/expected/vardict.paired.vcf
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@@ -1,5 +1,5 @@
##fileformat=VCFv4.3
##source=VarDict_v1.8.0
##source=VarDict_v1.8.1
##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)">
##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
Expand All @@ -15,7 +15,7 @@
##INFO=<ID=RSEQ,Number=1,Type=String,Description="3' flanking seq">
##INFO=<ID=STATUS,Number=1,Type=String,Description="Somatic or germline status">
##INFO=<ID=P0.01Likely,Number=0,Type=Flag,Description="Likely candidate but p-value > 0.01/5**vd2 (means the evidence in tumor sample might be weak, e.g. small diff in AF)">
##INFO=<ID=IndelLikely,Number=0,Type=Flag,Description="Likely indels more than 2bp are not considered somatic (weak evidence of presence in normal samples)">
##INFO=<ID=InDelLikely,Number=0,Type=Flag,Description="Likely indels more than 2bp are not considered somatic (weak evidence of presence in normal samples)">
##FILTER=<ID=q22.5,Description="Mean Base Quality Below 22.5">
##FILTER=<ID=Q0,Description="Mean Mapping Quality Below 0">
##FILTER=<ID=p8,Description="Mean Position in Reads Less than 8">
Expand Down Expand Up @@ -3141,7 +3141,7 @@
20 33501567 . C A 30 v3;f0.02 STATUS=StrongSomatic;SAMPLE=abc;TYPE=SNV;DP=993;VD=2;AF=0.002;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.4306;SOR=0;LSEQ=CTTCCCTAGTTTGCAGGCTT;RSEQ=TCTTCAGAGTCTCTATGTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:993:2:0,2:485,503:988,2:0.002:2,0:17:1:30.8:1:0.4997:0:60:4:0.0021:0.001:1 0/0:520:0:0,0:270,250:520,0:0:2,0:18.6:1:34.2:1:1:0:59:19.8:1:0:0.1
20 33501572 . C A 49 f0.02 STATUS=StrongSomatic;SAMPLE=abc;TYPE=SNV;DP=948;VD=3;AF=0.0032;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.27515;SOR=0;LSEQ=CTAGTTTGCAGGCTTCTCTT;RSEQ=AGAGTCTCTATGTGAACGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:948:3:2,1:407,538:945,3:0.0032:2,2:25:1:31:1:0.58105:2.64:60:6:0.0033:0:1 0/0:509:0:0,0:247,261:508,0:0:2,0:18.9:1:34.1:1:1:0:59:11.39:1:0:0.1
20 33501579 . T A 35 f0.02 STATUS=LikelySomatic;SAMPLE=abc;TYPE=SNV;DP=928;VD=3;AF=0.0032;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=0.55239;SOR=0.77206;LSEQ=GCAGGCTTCTCTTCAGAGTC;RSEQ=CTATGTGAACGGATCTTGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:928:3:1,2:357,566:923,3:0.0032:2,2:15.3:1:22.7:1:1:1.26115:50:2:0.0022:0:1 0/0:478:2:0,2:204,269:473,2:0.0042:2,0:15:1:17.5:1:0.50891:0:60:0:0:0:1.5
20 33502196 . A C 81 Bias;Bias STATUS=AFDiff;SAMPLE=abc;TYPE=SNV;DP=49;VD=14;AF=0.2857;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07586;SOR=0.47487;LSEQ=AGCTCGGCATGGGTGACTCC;RSEQ=CCAGCCAGTCCCCCCCAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:14:0,14:29,6:35,14:0.2857:2,1:10.7:1:23.7:1:0:0:33:2.5:0.25:0:4 0/1:37:17:1,16:15,5:20,17:0.4595:2,1:15.8:1:20:1:0.00003:41.60206:44:0.7:0.2692:0.1622:2.5
20 33502196 . A C 81 Bias STATUS=AFDiff;SAMPLE=abc;TYPE=SNV;DP=49;VD=14;AF=0.2857;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.07586;SOR=0.47487;LSEQ=AGCTCGGCATGGGTGACTCC;RSEQ=CCAGCCAGTCCCCCCCAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:49:14:0,14:29,6:35,14:0.2857:2,1:10.7:1:23.7:1:0:0:33:2.5:0.25:0:4 0/1:37:17:1,16:15,5:20,17:0.4595:2,1:15.8:1:20:1:0.00003:41.60206:44:0.7:0.2692:0.1622:2.5
20 33508401 . G T 34 v3;f0.02 STATUS=StrongSomatic;SAMPLE=abc;TYPE=SNV;DP=230;VD=2;AF=0.0087;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=0.44639;SOR=0;LSEQ=GCCACAACCTTCAAGTATGT;RSEQ=TTTGACTTCCATGCAGAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:230:2:1,1:106,122:228,2:0.0087:2,2:11:1:34.5:1:1:1.15:60:4:0.0091:0.0043:1 0/0:114:0:0,0:55,59:114,0:0:2,0:16:1:35.3:1:1:0:59:56:1:0:0.4
20 33508470 . C A 26 v3;f0.02 STATUS=StrongLOH;SAMPLE=abc;TYPE=SNV;DP=153;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.12272;SOR=0;LSEQ=TGGATCACTGGTCATTCCTA;RSEQ=GTCACCTATGGGCCACTGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:153:0:0,0:47,106:153,0:0:2,0:17.3:1:30.7:1:1:0:59:14.3:1:0:0.2 0/1:83:2:2,0:19,62:81,2:0.0241:2,0:13.5:1:26.8:1:0.06171:0:60:4:0.029:0.012:1.5
20 33508814 . G T 27 v3;f0.02 STATUS=StrongSomatic;SAMPLE=abc;TYPE=SNV;DP=523;VD=2;AF=0.0038;SHIFT3=3;MSI=4.000;MSILEN=1;SSF=0.42181;SOR=0;LSEQ=GCCTTCATGGGTCAGTTTGA;RSEQ=GGGATTCCCACATATCCGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:523:2:1,1:291,230:521,2:0.0038:2,2:19.5:1:27.5:1:1:1.26464:60:4:0.0041:0:1.5 0/0:282:0:0,0:170,112:282,0:0:2,0:18:1:35.8:1:1:0:59:39.286:1:0:0.2
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2 changes: 1 addition & 1 deletion tests/integration/expected/vardict.simple.vcf
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@@ -1,5 +1,5 @@
##fileformat=VCFv4.3
##source=VarDict_v1.8.0
##source=VarDict_v1.8.1
##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)">
##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
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5 changes: 5 additions & 0 deletions tests/integration/tests_integration.sh
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@@ -1,6 +1,7 @@
#!/bin/bash -eu
set -o pipefail

# Needs EBIvariation vcf-validator to be installed on path to validate VCF files
#---
# Config variables
#---
Expand Down Expand Up @@ -244,6 +245,10 @@ function vcf_testing {
echo Running paired mode VCF integration testing
cat $RAWVARDICT_PAIRED | $VARDICTPERL_R_PAIRED | $VARDICTPERL_VAR_PAIRED > $VARDICT_VCF_PAIRED
diff_results "VCF_paired" $VARDICT_VCF_PAIRED_EXP $VARDICT_VCF_PAIRED

echo Running validation of VCF files
$VCF_VALIDATOR -i $VARDICT_VCF_SIMPLE
$VCF_VALIDATOR -i $VARDICT_VCF_PAIRED
}

download_files
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