From f8ad91b16fc019f95a2aa7385588dd6e5f8584dc Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 8 Aug 2011 16:57:38 -0400 Subject: [PATCH] Reverting a bunch of bad -B type drops --- .../phasing/ReadBackedPhasingWalker.java | 19 +++-- .../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 +- .../RecalibrationWalkersIntegrationTest.java | 4 +- .../RecalibrationWalkersPerformanceTest.java | 4 +- .../VariantEvalIntegrationTest.java | 76 +++++++++---------- ...ntRecalibrationWalkersIntegrationTest.java | 10 +-- .../VariantContextIntegrationTest.java | 4 +- 15 files changed, 71 insertions(+), 68 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java index 8e62999b5..7df55b4cd 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java @@ -23,9 +23,7 @@ */ package org.broadinstitute.sting.gatk.walkers.phasing; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Hidden; -import org.broadinstitute.sting.commandline.Output; +import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.datasources.sample.Sample; @@ -64,6 +62,13 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr public class ReadBackedPhasingWalker extends RodWalker { private static final boolean DEBUG = false; + /** + * The VCF file we are phasing variants from. + * + * All heterozygous variants found in this VCF file will be phased, where possible + */ + @Input(fullName="variants", shortName = "V", doc="Phase variants from this VCF file", required=true) + public RodBinding variants; @Output(doc = "File to which variants should be written", required = true) protected VCFWriter writer = null; @@ -98,8 +103,6 @@ public class ReadBackedPhasingWalker extends RodWalker rodNameToHeader = getVCFHeadersFromRods(getToolkit(), Arrays.asList(rodName)); - Set samples = new TreeSet(samplesToPhase == null ? rodNameToHeader.get(rodName).getGenotypeSamples() : samplesToPhase); + Map rodNameToHeader = getVCFHeadersFromRods(getToolkit(), Arrays.asList(variants.getName())); + Set samples = new TreeSet(samplesToPhase == null ? rodNameToHeader.get(variants.getName()).getGenotypeSamples() : samplesToPhase); writer.writeHeader(new VCFHeader(hInfo, samples)); } @@ -204,7 +207,7 @@ public class ReadBackedPhasingWalker extends RodWalker unprocessedList = new LinkedList(); - for (VariantContext vc : tracker.getValues(VariantContext.class, rodName, context.getLocation())) { + for (VariantContext vc : tracker.getValues(variants, context.getLocation())) { if (samplesToPhase != null) vc = reduceVCToSamples(vc, samplesToPhase); if (ReadBackedPhasingWalker.processVariantInPhasing(vc)) { 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 09da337ce..fc50f67f2 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 " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1, + baseTestString() + " -B:compH3,VCF " + 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 " + validationDataLocation + "targetAnnotations.vcf -G \"Standard\" --variants:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variants", 1, + baseTestString() + " -B:foo,VCF " + 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 cedee826c..be2f3cdaa 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 " + 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,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", 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 132e6aeb7..d271d78b1 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 " + b36dbSNP129 + + " -B:dbsnp,VCF " + 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 8fa15700d..aabf01415 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 " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -BTI indels -o %s", + "-T RealignerTargetCreator -R " + b36KGReference + " -B:indels,VCF " + 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 d27c63759..21435dd7d 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 " + fundamentalTestPBTVCF, - "-B:rbp " + fundamentalTestRBPVCF, + "-B:pbt,VCF " + fundamentalTestPBTVCF, + "-B:rbp,VCF " + 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 ef6fd0d7f..c88eac149 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 " + validationDataLocation + VCF + + " -B:variant,VCF " + 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 b9c291b61..f855c1dd3 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 " + validationDataLocation + VCF + + " -B:variant,VCF " + 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 4a205c85f..59750e18f 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 " + fundamentalTestVCF, + "-B:variant,VCF " + 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 2b3122e77..1bf3e579f 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 " + validationDataLocation + VCF + + " -B:variant,VCF " + validationDataLocation + VCF + " --cacheWindowSize " + cacheWindowSize + " --maxPhaseSites " + maxPhaseSites + " --phaseQualityThresh " + phaseQualityThresh + diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java index 8334c99ec..74f803ac6 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java @@ -236,7 +236,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b36KGReference + - " -B:dbsnp " + validationDataLocation + "vcfexample3.vcf" + + " -B:dbsnp,VCF3 " + validationDataLocation + "vcfexample3.vcf" + " -T CountCovariates" + " -I " + bam + " -L 1:10,000,000-10,200,000" + @@ -284,7 +284,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R " + b36KGReference + - " -B:anyNameABCD " + validationDataLocation + "vcfexample3.vcf" + + " -B:anyNameABCD,VCF3 " + validationDataLocation + "vcfexample3.vcf" + " -T CountCovariates" + " -I " + bam + " -B:dbsnp,vcf " + b36dbSNP129 + 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 45d104862..43ea401f7 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 " + GATKDataLocation + "dbsnp_132.hg18.vcf" + + " -B:dbsnp,VCF " + 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 " + GATKDataLocation + "dbsnp_132.hg18.vcf" + + " -B:dbsnp,VCF " + 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 401fecb44..8fa5f0c29 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 " + b37dbSNP132, - "-B:eval " + fundamentalTestVCF, + "-B:dbsnp,VCF " + b37dbSNP132, + "-B:eval,VCF " + fundamentalTestVCF, "-noEV", "-EV CountVariants", "-noST", @@ -40,8 +40,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp " + b37dbSNP132, - "-B:eval " + fundamentalTestVCF, + "-B:dbsnp,VCF " + b37dbSNP132, + "-B:eval,VCF " + fundamentalTestVCF, "-noEV", "-EV CountVariants", "-noST", @@ -61,8 +61,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp " + b37dbSNP132, - "-B:eval " + fundamentalTestVCF, + "-B:dbsnp,VCF " + b37dbSNP132, + "-B:eval,VCF " + fundamentalTestVCF, "-noEV", "-EV CountVariants", "-noST", @@ -83,8 +83,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp " + b37dbSNP132, - "-B:eval " + fundamentalTestVCF, + "-B:dbsnp,VCF " + b37dbSNP132, + "-B:eval,VCF " + fundamentalTestVCF, "-noEV", "-EV CountVariants", "-noST", @@ -104,8 +104,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp " + b37dbSNP132, - "-B:eval " + fundamentalTestVCF, + "-B:dbsnp,VCF " + b37dbSNP132, + "-B:eval,VCF " + fundamentalTestVCF, "-noEV", "-EV CountVariants", "-noST", @@ -125,8 +125,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp " + b37dbSNP132, - "-B:eval " + fundamentalTestVCF, + "-B:dbsnp,VCF " + b37dbSNP132, + "-B:eval,VCF " + fundamentalTestVCF, "-noEV", "-EV CountVariants", "-noST", @@ -146,8 +146,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp " + b37dbSNP132, - "-B:eval " + fundamentalTestVCF, + "-B:dbsnp,VCF " + b37dbSNP132, + "-B:eval,VCF " + fundamentalTestVCF, "-noEV", "-EV CountVariants", "-noST", @@ -167,8 +167,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp " + b37dbSNP132, - "-B:eval " + fundamentalTestVCF, + "-B:dbsnp,VCF " + b37dbSNP132, + "-B:eval,VCF " + fundamentalTestVCF, "-noEV", "-EV CountVariants", "-noST", @@ -190,8 +190,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp " + b37dbSNP132, - "-B:eval " + fundamentalTestVCF, + "-B:dbsnp,VCF " + b37dbSNP132, + "-B:eval,VCF " + fundamentalTestVCF, "-noEV", "-EV CountVariants", "-noST", @@ -215,7 +215,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:eval " + fundamentalTestVCF, + "-B:eval,VCF " + fundamentalTestVCF, "-noEV", "-EV CountVariants", "-noST", @@ -232,9 +232,9 @@ public class VariantEvalIntegrationTest extends WalkerTest { public void testSelect1() { String extraArgs = "-L 1:1-10,000,000"; String tests = cmdRoot + - " -B:dbsnp " + b36dbSNP129 + - " -B:eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" + - " -B:comp_genotypes " + validationDataLocation + "yri.trio.gatk.ug.head.vcf"; + " -B:dbsnp,VCF " + 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", 1, Arrays.asList("14054badcd89b24c2375e1d09918f681")); executeTestParallel("testSelect1", spec); @@ -244,7 +244,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { public void testVEGenotypeConcordance() { String vcfFile = "GenotypeConcordanceEval.vcf"; - WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG -B:eval " + validationDataLocation + vcfFile + " -B:comp " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s", + WalkerTestSpec spec = new WalkerTestSpec(cmdRoot + " -ST CpG -B:eval,VCF3 " + validationDataLocation + vcfFile + " -B:comp,VCF3 " + validationDataLocation + "GenotypeConcordanceComp.vcf -noEV -EV GenotypeConcordance -o %s", 1, Arrays.asList("96f27163f16bb945f19c6623cd6db34e")); executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec); @@ -252,7 +252,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { @Test public void testCompVsEvalAC() { - String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance -B:evalYRI " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf"; + String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance -B:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf -B:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf"; WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("d1932be3748fcf6da77dc51aec323710")); executeTestParallel("testCompVsEvalAC",spec); } @@ -280,8 +280,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { String extraArgs = "-T VariantEval -R " + b37KGReference + " -L 20" + - " -B:dbsnp " + b37dbSNP132 + - " -B:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" + + " -B:dbsnp,VCF " + b37dbSNP132 + + " -B:evalBI,VCF " + 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 " + b37dbSNP132 + - " -B:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" + - " -B:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" + + " -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" + " -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 " + 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 + + " -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 + " -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 " + b37dbSNP132, - "-B:eval " + fundamentalTestSNPsVCF, + "-B:dbsnp,VCF " + b37dbSNP132, + "-B:eval,VCF " + fundamentalTestSNPsVCF, "-noEV", "-EV CompOverlap", "-sn HG00625", @@ -342,8 +342,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp " + b37dbSNP132, - "-B:eval " + fundamentalTestSNPsOneSampleVCF, + "-B:dbsnp,VCF " + b37dbSNP132, + "-B:eval,VCF " + fundamentalTestSNPsOneSampleVCF, "-noEV", "-EV CompOverlap", "-noST", @@ -363,8 +363,8 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp " + b37dbSNP132, - "-B:eval " + fundamentalTestSNPsVCF, + "-B:dbsnp,VCF " + b37dbSNP132, + "-B:eval,VCF " + 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 f6c858135..3ac7e3785 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,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" + + " -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" + " -T VariantRecalibrator" + - " -B:input " + params.inVCF + + " -B:input,VCF " + 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 " + params.inVCF + + " -B:input,VCF " + 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/utils/variantcontext/VariantContextIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java index 9655b514a..7cdb6af95 100755 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java @@ -16,7 +16,7 @@ public class VariantContextIntegrationTest extends WalkerTest { private static String root = cmdRoot + " -L 1:1-1,000,000 -B:dbsnp,vcf " + b36dbSNP129 + - " -B:vcf " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf"; + " -B:vcf,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf"; private static final class VCITTest extends TestDataProvider { String args, md5; @@ -58,7 +58,7 @@ public class VariantContextIntegrationTest extends WalkerTest { public void testToVCF() { // this really just tests that we are seeing the same number of objects over all of chr1 - WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -NO_HEADER -B:vcf " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s", + WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -NO_HEADER -B:vcf,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s", 2, // just one output file Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "ff91731213fd0bbdc200ab6fd1c93e63")); executeTest("testToVCF", spec);