From ba7353c561ca8cb423efc7b6e01508d6d19f408d Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 8 Aug 2011 15:04:38 -0400 Subject: [PATCH] Updated IntegrationTests to use the new type free format for VCF files --- .../commandline/ArgumentTypeDescriptor.java | 2 +- .../VariantAnnotatorIntegrationTest.java | 4 +- ...astaAlternateReferenceIntegrationTest.java | 2 +- .../UnifiedGenotyperPerformanceTest.java | 2 +- ...RealignerTargetCreatorIntegrationTest.java | 2 +- ...ergeAndMatchHaplotypesIntegrationTest.java | 4 +- .../phasing/MergeMNPsIntegrationTest.java | 2 +- ...gatingAlternateAllelesIntegrationTest.java | 2 +- .../PhaseByTransmissionIntegrationTest.java | 2 +- .../ReadBackedPhasingIntegrationTest.java | 2 +- .../RecalibrationWalkersPerformanceTest.java | 4 +- .../VariantEvalIntegrationTest.java | 68 +++++++++---------- ...ntRecalibrationWalkersIntegrationTest.java | 10 +-- .../CombineVariantsIntegrationTest.java | 16 ++--- 14 files changed, 61 insertions(+), 61 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java index d341b2cde..ebed68022 100644 --- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java +++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java @@ -333,7 +333,7 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor { FeatureManager.FeatureDescriptor featureDescriptor = manager.getByFiletype(file); if ( featureDescriptor != null ) { tribbleType = featureDescriptor.getName(); - logger.warn("Dynamically determined of " + file + " to be " + tribbleType); + logger.warn("Dynamically determined type of " + file + " to be " + tribbleType); if ( tags.getPositionalTags().size() == 1 ) { // -X:type style is a name when we can determine the type dynamically diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index fc50f67f2..09da337ce 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -102,7 +102,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testDBTagWithHapMap() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -B:compH3,VCF " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1, + baseTestString() + " -B:compH3 " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1, Arrays.asList("1bc01c5b3bd0b7aef75230310c3ce688")); executeTest("getting DB tag with HM3", spec); } @@ -110,7 +110,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testUsingExpression() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -B:foo,VCF " + validationDataLocation + "targetAnnotations.vcf -G \"Standard\" --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variants", 1, + baseTestString() + " -B:foo " + validationDataLocation + "targetAnnotations.vcf -G \"Standard\" --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variants", 1, Arrays.asList("e9c0d832dc6b4ed06c955060f830c140")); executeTest("using expression", spec); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java index be2f3cdaa..cedee826c 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java @@ -24,7 +24,7 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest { executeTest("testFastaReference", spec1b); WalkerTestSpec spec2 = new WalkerTestSpec( - "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B:indels,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 --snpmask:vcf " + b36dbSNP129 + " -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s", + "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B:indels " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 --snpmask:vcf " + b36dbSNP129 + " -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s", 1, Arrays.asList("0567b32ebdc26604ddf2a390de4579ac")); executeTest("testFastaAlternateReferenceIndels", spec2); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java index d271d78b1..132e6aeb7 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java @@ -15,7 +15,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest { " -glm BOTH" + " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + " -L chr1:1-50,000,000" + - " -B:dbsnp,VCF " + b36dbSNP129 + + " -B:dbsnp " + b36dbSNP129 + " -o /dev/null", 0, new ArrayList(0)); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java index aabf01415..8fa15700d 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java @@ -23,7 +23,7 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest { executeTest("test dbsnp", spec2); WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( - "-T RealignerTargetCreator -R " + b36KGReference + " -B:indels,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -BTI indels -o %s", + "-T RealignerTargetCreator -R " + b36KGReference + " -B:indels " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -BTI indels -o %s", 1, Arrays.asList("5206cee6c01b299417bf2feeb8b3dc96")); executeTest("test rods only", spec3); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java index 21435dd7d..d27c63759 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeAndMatchHaplotypesIntegrationTest.java @@ -16,8 +16,8 @@ public class MergeAndMatchHaplotypesIntegrationTest extends WalkerTest { buildCommandLine( "-T MergeAndMatchHaplotypes", "-R " + b37KGReference, - "-B:pbt,VCF " + fundamentalTestPBTVCF, - "-B:rbp,VCF " + fundamentalTestRBPVCF, + "-B:pbt " + fundamentalTestPBTVCF, + "-B:rbp " + fundamentalTestRBPVCF, "-o %s" ), 1, diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java index c88eac149..ef6fd0d7f 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java @@ -10,7 +10,7 @@ public class MergeMNPsIntegrationTest extends WalkerTest { public static String baseTestString(String reference, String VCF, int maxDistMNP) { return "-T MergeMNPs" + " -R " + reference + - " -B:variant,VCF " + validationDataLocation + VCF + + " -B:variant " + validationDataLocation + VCF + " --maxGenomicDistanceForMNP " + maxDistMNP + " -o %s" + " -NO_HEADER"; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesIntegrationTest.java index f855c1dd3..b9c291b61 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesIntegrationTest.java @@ -10,7 +10,7 @@ public class MergeSegregatingAlternateAllelesIntegrationTest extends WalkerTest public static String baseTestString(String reference, String VCF, int maxDist) { return "-T MergeSegregatingAlternateAlleles" + " -R " + reference + - " -B:variant,VCF " + validationDataLocation + VCF + + " -B:variant " + validationDataLocation + VCF + " --maxGenomicDistance " + maxDist + " -o %s" + " -NO_HEADER"; diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java index 59750e18f..4a205c85f 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java @@ -16,7 +16,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest { "-T PhaseByTransmission", "-NO_HEADER", "-R " + b37KGReference, - "-B:variant,VCF " + fundamentalTestVCF, + "-B:variant " + fundamentalTestVCF, "-f NA12892+NA12891=NA12878", "-o %s" ), diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java index 1bf3e579f..2b3122e77 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java @@ -11,7 +11,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest { return "-T ReadBackedPhasing" + " -R " + reference + " -I " + validationDataLocation + reads + - " -B:variant,VCF " + validationDataLocation + VCF + + " -B:variant " + validationDataLocation + VCF + " --cacheWindowSize " + cacheWindowSize + " --maxPhaseSites " + maxPhaseSites + " --phaseQualityThresh " + phaseQualityThresh + diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java index 43ea401f7..45d104862 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java @@ -16,7 +16,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest { " -L chr1:1-50,000,000" + " -standard" + " -OQ" + - " -B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132.hg18.vcf" + + " -B:dbsnp " + GATKDataLocation + "dbsnp_132.hg18.vcf" + " -recalFile /dev/null" + moreArgs, 0, new ArrayList(0)); @@ -31,7 +31,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest { " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" + " -standard" + " -OQ" + - " -B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132.hg18.vcf" + + " -B:dbsnp " + GATKDataLocation + "dbsnp_132.hg18.vcf" + " -recalFile /dev/null" + moreArgs, 0, new ArrayList(0)); diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index 8fa5f0c29..6bbaa266d 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -20,8 +20,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + b37dbSNP132, - "-B:eval,VCF " + fundamentalTestVCF, + "-B:dbsnp " + b37dbSNP132, + "-B:eval " + fundamentalTestVCF, "-noEV", "-EV CountVariants", "-noST", @@ -40,8 +40,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + b37dbSNP132, - "-B:eval,VCF " + fundamentalTestVCF, + "-B:dbsnp " + b37dbSNP132, + "-B:eval " + fundamentalTestVCF, "-noEV", "-EV CountVariants", "-noST", @@ -61,8 +61,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + b37dbSNP132, - "-B:eval,VCF " + fundamentalTestVCF, + "-B:dbsnp " + b37dbSNP132, + "-B:eval " + fundamentalTestVCF, "-noEV", "-EV CountVariants", "-noST", @@ -83,8 +83,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + b37dbSNP132, - "-B:eval,VCF " + fundamentalTestVCF, + "-B:dbsnp " + b37dbSNP132, + "-B:eval " + fundamentalTestVCF, "-noEV", "-EV CountVariants", "-noST", @@ -104,8 +104,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + b37dbSNP132, - "-B:eval,VCF " + fundamentalTestVCF, + "-B:dbsnp " + b37dbSNP132, + "-B:eval " + fundamentalTestVCF, "-noEV", "-EV CountVariants", "-noST", @@ -125,8 +125,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + b37dbSNP132, - "-B:eval,VCF " + fundamentalTestVCF, + "-B:dbsnp " + b37dbSNP132, + "-B:eval " + fundamentalTestVCF, "-noEV", "-EV CountVariants", "-noST", @@ -146,8 +146,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + b37dbSNP132, - "-B:eval,VCF " + fundamentalTestVCF, + "-B:dbsnp " + b37dbSNP132, + "-B:eval " + fundamentalTestVCF, "-noEV", "-EV CountVariants", "-noST", @@ -167,8 +167,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + b37dbSNP132, - "-B:eval,VCF " + fundamentalTestVCF, + "-B:dbsnp " + b37dbSNP132, + "-B:eval " + fundamentalTestVCF, "-noEV", "-EV CountVariants", "-noST", @@ -190,8 +190,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + b37dbSNP132, - "-B:eval,VCF " + fundamentalTestVCF, + "-B:dbsnp " + b37dbSNP132, + "-B:eval " + fundamentalTestVCF, "-noEV", "-EV CountVariants", "-noST", @@ -215,7 +215,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:eval,VCF " + fundamentalTestVCF, + "-B:eval " + fundamentalTestVCF, "-noEV", "-EV CountVariants", "-noST", @@ -232,7 +232,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { public void testSelect1() { String extraArgs = "-L 1:1-10,000,000"; String tests = cmdRoot + - " -B:dbsnp,VCF " + b36dbSNP129 + + " -B:dbsnp " + b36dbSNP129 + " -B:eval,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" + " -B:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf"; WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s", @@ -280,8 +280,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { String extraArgs = "-T VariantEval -R " + b37KGReference + " -L 20" + - " -B:dbsnp,VCF " + b37dbSNP132 + - " -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" + + " -B:dbsnp " + b37dbSNP132 + + " -B:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" + " -noST -ST Novelty -o %s"; WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("0897dfba2f4a245faddce38000555cce")); executeTestParallel("testEvalTrackWithoutGenotypes",spec); @@ -291,9 +291,9 @@ public class VariantEvalIntegrationTest extends WalkerTest { public void testMultipleEvalTracksWithoutGenotypes() { String extraArgs = "-T VariantEval -R " + b37KGReference + " -L 20" + - " -B:dbsnp,VCF " + b37dbSNP132 + - " -B:evalBI,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" + - " -B:evalBC,VCF " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" + + " -B:dbsnp " + b37dbSNP132 + + " -B:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" + + " -B:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" + " -noST -ST Novelty -o %s"; WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("ead3602e14ec2944b5d9e4dacc08c819")); executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec); @@ -305,9 +305,9 @@ public class VariantEvalIntegrationTest extends WalkerTest { String extraArgs = "-T VariantEval" + " -R " + b37KGReference + - " -B:comp,VCF " + validationDataLocation + "/VariantEval/ALL.phase1.chr20.broad.snps.genotypes.subset.vcf" + - " -B:eval,VCF " + validationDataLocation + "/VariantEval/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.subset.vcf" + - " -B:dbsnp,VCF " + dbsnp + + " -B:comp " + validationDataLocation + "/VariantEval/ALL.phase1.chr20.broad.snps.genotypes.subset.vcf" + + " -B:eval " + validationDataLocation + "/VariantEval/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.subset.vcf" + + " -B:dbsnp " + dbsnp + " -L 20:10000000-10100000" + " -noST -noEV -ST Novelty -EV CompOverlap" + " -o %s"; @@ -324,8 +324,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + b37dbSNP132, - "-B:eval,VCF " + fundamentalTestSNPsVCF, + "-B:dbsnp " + b37dbSNP132, + "-B:eval " + fundamentalTestSNPsVCF, "-noEV", "-EV CompOverlap", "-sn HG00625", @@ -342,8 +342,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + b37dbSNP132, - "-B:eval,VCF " + fundamentalTestSNPsOneSampleVCF, + "-B:dbsnp " + b37dbSNP132, + "-B:eval " + fundamentalTestSNPsOneSampleVCF, "-noEV", "-EV CompOverlap", "-noST", @@ -363,8 +363,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + b37dbSNP132, - "-B:eval,VCF " + fundamentalTestSNPsVCF, + "-B:dbsnp " + b37dbSNP132, + "-B:eval " + fundamentalTestSNPsVCF, "-noEV", "-EV CountVariants", "-noST", diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java index 3ac7e3785..f6c858135 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java @@ -41,11 +41,11 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { //System.out.printf("PARAMS FOR %s is %s%n", vcf, clusterFile); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b37KGReference + - " -B:dbsnp,VCF,known=true,training=false,truth=false,prior=10.0 " + GATKDataLocation + "dbsnp_132_b37.leftAligned.vcf" + - " -B:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 " + comparisonDataLocation + "Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf" + - " -B:omni,VCF,known=false,training=true,truth=true,prior=12.0 " + comparisonDataLocation + "Validated/Omni2.5_chip/Omni25_sites_1525_samples.b37.vcf" + + " -B:dbsnp,known=true,training=false,truth=false,prior=10.0 " + GATKDataLocation + "dbsnp_132_b37.leftAligned.vcf" + + " -B:hapmap,known=false,training=true,truth=true,prior=15.0 " + comparisonDataLocation + "Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf" + + " -B:omni,known=false,training=true,truth=true,prior=12.0 " + comparisonDataLocation + "Validated/Omni2.5_chip/Omni25_sites_1525_samples.b37.vcf" + " -T VariantRecalibrator" + - " -B:input,VCF " + params.inVCF + + " -B:input " + params.inVCF + " -L 20:1,000,000-40,000,000" + " -an QD -an HaplotypeScore -an HRun" + " -percentBad 0.07" + @@ -64,7 +64,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { " -T ApplyRecalibration" + " -L 20:12,000,000-30,000,000" + " -NO_HEADER" + - " -B:input,VCF " + params.inVCF + + " -B:input " + params.inVCF + " -o %s" + " -tranchesFile " + MD5DB.getMD5FilePath(params.tranchesMD5, null) + " -recalFile " + MD5DB.getMD5FilePath(params.recalMD5, null), diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java index d27ab34a0..6dfbc1723 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java @@ -63,8 +63,8 @@ public class CombineVariantsIntegrationTest extends WalkerTest { String file2 = "hapmap_3.3.b37.sites.vcf"; WalkerTestSpec spec = new WalkerTestSpec( "-T CombineVariants -NO_HEADER -o %s -R " + b37KGReference - + " -L 1:1-10,000,000 -V:omni,VCF " + validationDataLocation + file1 - + " -V:hm3,VCF " + validationDataLocation + file2 + args, + + " -L 1:1-10,000,000 -V:omni " + validationDataLocation + file1 + + " -V:hm3 " + validationDataLocation + file2 + args, 1, Arrays.asList(md5)); executeTest("combineSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec); @@ -91,10 +91,10 @@ public class CombineVariantsIntegrationTest extends WalkerTest { @Test public void threeWayWithRefs() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString(" -V:NA19240_BGI,VCF "+validationDataLocation+"NA19240.BGI.RG.vcf" + - " -V:NA19240_ILLUMINA,VCF "+validationDataLocation+"NA19240.ILLUMINA.RG.vcf" + - " -V:NA19240_WUGSC,VCF "+validationDataLocation+"NA19240.WUGSC.RG.vcf" + - " -V:denovoInfo,VCF "+validationDataLocation+"yri_merged_validation_data_240610.annotated.b36.vcf" + + baseTestString(" -V:NA19240_BGI "+validationDataLocation+"NA19240.BGI.RG.vcf" + + " -V:NA19240_ILLUMINA "+validationDataLocation+"NA19240.ILLUMINA.RG.vcf" + + " -V:NA19240_WUGSC "+validationDataLocation+"NA19240.WUGSC.RG.vcf" + + " -V:denovoInfo "+validationDataLocation+"yri_merged_validation_data_240610.annotated.b36.vcf" + " -setKey centerSet" + " -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED" + " -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" + @@ -110,8 +110,8 @@ public class CombineVariantsIntegrationTest extends WalkerTest { String file2 = "combine.2.vcf"; WalkerTestSpec spec = new WalkerTestSpec( "-T CombineVariants -NO_HEADER -o %s -R " + b37KGReference - + " -V:one,VCF " + validationDataLocation + file1 - + " -V:two,VCF " + validationDataLocation + file2 + args, + + " -V:one " + validationDataLocation + file1 + + " -V:two " + validationDataLocation + file2 + args, 1, Arrays.asList(md5)); executeTest("combineComplexSites 1:" + new File(file1).getName() + " 2:" + new File(file2).getName() + " args = " + args, spec);