From 43056d01882894df4579c79aad4b7e6803997796 Mon Sep 17 00:00:00 2001 From: kiran Date: Mon, 7 Mar 2011 20:25:57 +0000 Subject: [PATCH] Fixed integration test to reflect changes regarding when comp tracks got subset to fewer samples and whether no-call sites would get pulled in for comp tracks. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5393 348d0f76-0448-11de-a6fe-93d51630548a --- .../VariantEvalIntegrationTest.java | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index 4fceb3f4c..10c22c20f 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -334,7 +334,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { String extraArgs = "-L 1:1-10,000,000"; for (String tests : testsEnumerations) { WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s", - 1, Arrays.asList("4ae87d76a3b39cf0b80221f3bd681839")); + 1, Arrays.asList("9e74d649fcf1c884b324f0818e1d7395")); executeTestParallel("testSelect1", spec); //executeTest("testSelect1", spec); } @@ -355,7 +355,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { for (String vcfFile : vcfFiles) { WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG -B:eval,VCF " + validationDataLocation + vcfFile + " -B:comp,VCF " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s", 1, - Arrays.asList("1387fcf8d5c53ff2c820fe79cc999bcf")); + Arrays.asList("86de930ab857e27717c80b11594808f3")); executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec); //executeTest("testVEGenotypeConcordance" + vcfFile, spec); } @@ -365,8 +365,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { @Test public void testVESimple() { HashMap expectations = new HashMap(); - expectations.put("-L 1:1-10,000,000 -ST CpG", "b82f1ad442d354a5ed3c18ecef93553e"); - expectations.put("-L 1:1-10,000,000 -ST CpG -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "dc3d34f5a03890217d1f548027a82028"); + expectations.put("-L 1:1-10,000,000 -ST CpG", "9784b1fc319e856ad84678b6c8a4c15c"); + expectations.put("-L 1:1-10,000,000 -ST CpG -family NA19238+NA19239=NA19240 -mvq 0 -EV MendelianViolationEvaluator", "374c06e9ba8ca3496698b3f95e241b82"); for ( Map.Entry entry : expectations.entrySet() ) { String extraArgs = entry.getKey(); @@ -389,9 +389,9 @@ public class VariantEvalIntegrationTest extends WalkerTest { " -B:comp_hapmap,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf"; - expectations.put("", "c3936ef2e7af52019ade05461fbf4180"); - expectations.put(" -knownName comp_hapmap -knownName dbsnp", "e19bd1bc89463e558fa3b83e65f55ca5"); - expectations.put(" -knownName comp_hapmap", "831d69ec830836f7d2ac8310713f1691"); + expectations.put("", "48fcd7d9f3c8e347c70d7692c4b3cbff"); + expectations.put(" -knownName comp_hapmap -knownName dbsnp", "308948e0e227425d73e35a6702bfefcb"); + expectations.put(" -knownName comp_hapmap", "6f1383f3ea5b741215e8f7cbfcb47fb1"); for (String tests : testsEnumerations) { for (Map.Entry entry : expectations.entrySet()) { String extraArgs2 = entry.getKey(); @@ -409,7 +409,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { @Test public void testCompVsEvalAC() { String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance -B:evalYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF /humgen/gsa-hpprojects/GATK/data/Validation_Data/yri.trio.gatk.fake.genotypes.ac.test.vcf"; - WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("132e0825d1ed6e54963da94784cf7803")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("3199177faa347fe3a78de17b83afd909")); executeTestParallel("testCompVsEvalAC",spec); //executeTest("testCompVsEvalAC",spec); } @@ -429,7 +429,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { @Test public void testCompOverlap() { String extraArgs = "-T VariantEval -R " + b37KGReference + " -L " + validationDataLocation + "VariantEval/pacbio.hg19.intervals -B:comphapmap,vcf " + comparisonDataLocation + "Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf -B:eval,vcf " + validationDataLocation + "VariantEval/pacbio.ts.recalibrated.vcf -noEV -EV CompOverlap -sn NA12878 -noST -ST Novelty -o %s"; - WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("e8b5561eb60ea98a9be4a45abee00e07")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("70aa420929de7f888a6f48c2d01bbcda")); executeTestParallel("testCompOverlap",spec); //executeTest("testCompOverlap",spec); } @@ -444,7 +444,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { " -D " + dbsnp + " -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" + " -noST -ST Novelty -o %s"; - WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("5d0d89c7cbcc7887e34447cee70c5bae")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("2ea5334cf0b004e0a6119a5b653bde4c")); executeTestParallel("testEvalTrackWithoutGenotypes",spec); } @@ -458,7 +458,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { " -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" + " -B:evalBC,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" + " -noST -ST Novelty -o %s"; - WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("8dec8f384852876ba8ec4943ff953d2d")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("50fb57dddf7040a62e3befba30c5cb22")); executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec); }