diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java index bd661389c..e998c8452 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java @@ -43,6 +43,7 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import java.io.PrintStream; import java.util.ArrayList; +import java.util.Collections; import java.util.List; /** @@ -71,7 +72,7 @@ public class PileupWalker extends LocusWalker implements TreeR public boolean SHOW_INDEL_PILEUPS = false; @Argument(fullName="metadata",shortName="metadata",doc="Add these ROD bindings to the output Pileup", required=false) - public List> rods; + public List> rods = Collections.emptyList(); public void initialize() { } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java index 9a432d4bf..1c155e786 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java @@ -58,7 +58,7 @@ public class BeagleOutputToVCFWalker extends RodWalker { public RodBinding variants; @Input(fullName="comp", shortName = "comp", doc="Comparison VCF file", required=false) - public RodBinding comp; + public RodBinding comp = RodBinding.makeUnbound(VariantContext.class); @Input(fullName="beagleR2", shortName = "beagleR2", doc="VCF file", required=true) public RodBinding beagleR2; @@ -105,14 +105,10 @@ public class BeagleOutputToVCFWalker extends RodWalker { // Open output file specified by output VCF ROD final List dataSources = this.getToolkit().getRodDataSources(); - for( final ReferenceOrderedDataSource source : dataSources ) { - if (source.getName().equals(comp.getName())) { - hInfo.add(new VCFInfoHeaderLine("ACH", 1, VCFHeaderLineType.Integer, "Allele Count from Comparison ROD at this site")); - hInfo.add(new VCFInfoHeaderLine("ANH", 1, VCFHeaderLineType.Integer, "Allele Frequency from Comparison ROD at this site")); - hInfo.add(new VCFInfoHeaderLine("AFH", 1, VCFHeaderLineType.Float, "Allele Number from Comparison ROD at this site")); - break; - } - + if ( comp.isBound() ) { + hInfo.add(new VCFInfoHeaderLine("ACH", 1, VCFHeaderLineType.Integer, "Allele Count from Comparison ROD at this site")); + hInfo.add(new VCFInfoHeaderLine("ANH", 1, VCFHeaderLineType.Integer, "Allele Frequency from Comparison ROD at this site")); + hInfo.add(new VCFInfoHeaderLine("AFH", 1, VCFHeaderLineType.Float, "Allele Number from Comparison ROD at this site")); } Set samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName())); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java index 0ccba13a2..5bca61873 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java @@ -56,7 +56,7 @@ public class ProduceBeagleInputWalker extends RodWalker { public RodBinding variants; @Input(fullName="validation", shortName = "validation", doc="Input VCF file", required=false) - public RodBinding validation; + public RodBinding validation = RodBinding.makeUnbound(VariantContext.class); @Output(doc="File to which BEAGLE input should be written",required=true) protected PrintStream beagleWriter = null; 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 9a536146c..be6631d29 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 @@ -1,394 +1,394 @@ -package org.broadinstitute.sting.gatk.walkers.varianteval; - -import org.broadinstitute.sting.WalkerTest; -import org.testng.annotations.Test; - -import java.util.Arrays; -import java.util.HashMap; -import java.util.Map; - -public class VariantEvalIntegrationTest extends WalkerTest { - private static String variantEvalTestDataRoot = validationDataLocation + "/VariantEval"; - private static String fundamentalTestVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.snps_and_indels.vcf"; - private static String fundamentalTestSNPsVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.vcf"; - private static String fundamentalTestSNPsOneSampleVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.HG00625.vcf"; - - private static String cmdRoot = "-T VariantEval" + - " -R " + b36KGReference; - - private static String root = cmdRoot + - " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" + - " -B:eval,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" + - " -B:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf"; - - private static String rootGZ = cmdRoot + - " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" + - " -B:eval,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf.gz" + - " -B:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf.gz"; - - // TODO -- I can't seem to reindex this VCF using Tabix without it causing failures. Looking into it. [EB] - // private static String[] testsEnumerations = {root, rootGZ}; - private static String[] testsEnumerations = {root}; - - @Test - public void testFundamentalsCountVariantsSNPsAndIndels() { - WalkerTestSpec spec = new WalkerTestSpec( - buildCommandLine( - "-T VariantEval", - "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", - "-B:eval,VCF " + fundamentalTestVCF, - "-noEV", - "-EV CountVariants", - "-noST", - "-BTI eval", - "-o %s" - ), - 1, - Arrays.asList("48b8417c1f8bd74ff7b9808580abd2a2") - ); - executeTest("testFundamentalsCountVariantsSNPsandIndels", spec); - } - - @Test - public void testFundamentalsCountVariantsSNPsAndIndelsWithNovelty() { - WalkerTestSpec spec = new WalkerTestSpec( - buildCommandLine( - "-T VariantEval", - "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", - "-B:eval,VCF " + fundamentalTestVCF, - "-noEV", - "-EV CountVariants", - "-noST", - "-ST Novelty", - "-BTI eval", - "-o %s" - ), - 1, - Arrays.asList("86d45ecefdf5849c55b3ca8f82a3d525") - ); - executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNovelty", spec); - } - - @Test - public void testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter() { - WalkerTestSpec spec = new WalkerTestSpec( - buildCommandLine( - "-T VariantEval", - "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", - "-B:eval,VCF " + fundamentalTestVCF, - "-noEV", - "-EV CountVariants", - "-noST", - "-ST Novelty", - "-ST Filter", - "-BTI eval", - "-o %s" - ), - 1, - Arrays.asList("3d18901ec1766aa2e748eac913f5ddcd") - ); - executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNoveltyAndFilter", spec); - } - - @Test - public void testFundamentalsCountVariantsSNPsAndIndelsWithCpG() { - WalkerTestSpec spec = new WalkerTestSpec( - buildCommandLine( - "-T VariantEval", - "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", - "-B:eval,VCF " + fundamentalTestVCF, - "-noEV", - "-EV CountVariants", - "-noST", - "-ST CpG", - "-BTI eval", - "-o %s" - ), - 1, - Arrays.asList("677fe398643e62a10d6739d36a720a12") - ); - executeTest("testFundamentalsCountVariantsSNPsandIndelsWithCpG", spec); - } - - @Test - public void testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses() { - WalkerTestSpec spec = new WalkerTestSpec( - buildCommandLine( - "-T VariantEval", - "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", - "-B:eval,VCF " + fundamentalTestVCF, - "-noEV", - "-EV CountVariants", - "-noST", - "-ST FunctionalClass", - "-BTI eval", - "-o %s" - ), - 1, - Arrays.asList("5fb44fd7cb00941c986a9941e43e44cd") - ); - executeTest("testFundamentalsCountVariantsSNPsandIndelsWithFunctionalClass", spec); - } - - @Test - public void testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy() { - WalkerTestSpec spec = new WalkerTestSpec( - buildCommandLine( - "-T VariantEval", - "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", - "-B:eval,VCF " + fundamentalTestVCF, - "-noEV", - "-EV CountVariants", - "-noST", - "-ST Degeneracy", - "-BTI eval", - "-o %s" - ), - 1, - Arrays.asList("daaca7ef3b7313e5af217cbc6f37c9e2") - ); - executeTest("testFundamentalsCountVariantsSNPsandIndelsWithDegeneracy", spec); - } - - @Test - public void testFundamentalsCountVariantsSNPsAndIndelsWithSample() { - WalkerTestSpec spec = new WalkerTestSpec( - buildCommandLine( - "-T VariantEval", - "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", - "-B:eval,VCF " + fundamentalTestVCF, - "-noEV", - "-EV CountVariants", - "-noST", - "-ST Sample", - "-BTI eval", - "-o %s" - ), - 1, - Arrays.asList("97c466f8ffd0fcf2c30ef08669d213d9") - ); - executeTest("testFundamentalsCountVariantsSNPsandIndelsWithSample", spec); - } - - @Test - public void testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression() { - WalkerTestSpec spec = new WalkerTestSpec( - buildCommandLine( - "-T VariantEval", - "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", - "-B:eval,VCF " + fundamentalTestVCF, - "-noEV", - "-EV CountVariants", - "-noST", - "-ST JexlExpression", - "-select 'DP < 20'", - "-selectName DepthSelect", - "-BTI eval", - "-o %s" - ), - 1, - Arrays.asList("df8cdfcf3d0c2fc795812c6eae6a76f8") - ); - executeTest("testFundamentalsCountVariantsSNPsandIndelsWithJexlExpression", spec); - } - - @Test - public void testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions() { - WalkerTestSpec spec = new WalkerTestSpec( - buildCommandLine( - "-T VariantEval", - "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", - "-B:eval,VCF " + fundamentalTestVCF, - "-noEV", - "-EV CountVariants", - "-noST", - "-ST JexlExpression", - "-select 'DP < 20'", - "-selectName DepthLt20", - "-select 'DP > 20'", - "-selectName DepthGt20", - "-BTI eval", - "-o %s" - ), - 1, - Arrays.asList("c7aed12265e2b2311d17a0cc8a29f6aa") - ); - executeTest("testFundamentalsCountVariantsSNPsandIndelsWithMultipleJexlExpressions", spec); - } - - @Test - public void testFundamentalsCountVariantsNoCompRod() { - WalkerTestSpec spec = new WalkerTestSpec( - buildCommandLine( - "-T VariantEval", - "-R " + b37KGReference, - "-B:eval,VCF " + fundamentalTestVCF, - "-noEV", - "-EV CountVariants", - "-noST", - "-BTI eval", - "-o %s" - ), - 1, - Arrays.asList("d44c8f44384189a09eea85a8e89d7299") - ); - executeTest("testFundamentalsCountVariantsNoCompRod", spec); - } - - @Test - public void testSelect1() { - 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("96860dedea0fa6b46c07f46b847fea42")); - executeTestParallel("testSelect1", spec); - } - } - - @Test - public void testVEGenotypeConcordance() { - String vcfFile = "GenotypeConcordanceEval.vcf"; - - 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("e4c981f7f5d78680c71310fc9be9a1c1")); - executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec); - } - - @Test - public void testCompVsEvalAC() { - 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("162daa5039e1965eb2423a8589339a69")); - executeTestParallel("testCompVsEvalAC",spec); - } - - private static String withSelect(String cmd, String select, String name) { - return String.format("%s -select '%s' -selectName %s", cmd, select, name); - } - - @Test - public void testTranches() { - String extraArgs = "-T VariantEval -R "+ hg18Reference +" -B:eval,vcf " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -ST CpG -tf " + testDir + "tranches.6.txt"; - WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("90cd98044e754b80034a9f4e6d2c55b9")); - executeTestParallel("testTranches",spec); - } - - @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("70aa420929de7f888a6f48c2d01bbcda")); - executeTestParallel("testCompOverlap",spec); - } - - @Test - public void testEvalTrackWithoutGenotypes() { - String extraArgs = "-T VariantEval -R " + - b37KGReference + - " -L 20" + - " -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("58fdc6c42fade3007537bb99fb3ce738")); - executeTestParallel("testEvalTrackWithoutGenotypes",spec); - } - - @Test - 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" + - " -noST -ST Novelty -o %s"; - WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("34df2815d27e5e62f1694731a7e7953c")); - executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec); - } - - @Test - public void testMultipleCompTracks() { - String dbsnp = GATKDataLocation + "dbsnp_132_b37.vcf"; - - 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 + - " -L 20:10000000-10100000" + - " -noST -noEV -ST Novelty -EV CompOverlap" + - " -o %s"; - - WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("20332902ae36a84b2fd80405410815f1")); - executeTestParallel("testMultipleCompTracks",spec); - } - - @Test - public void testPerSampleAndSubsettedSampleHaveSameResults() { - String md5 = "9d61f6e2c8592dcf616712a2c587b2af"; - - WalkerTestSpec spec = new WalkerTestSpec( - buildCommandLine( - "-T VariantEval", - "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", - "-B:eval,VCF " + fundamentalTestSNPsVCF, - "-noEV", - "-EV CompOverlap", - "-sn HG00625", - "-noST", - "-BTI eval", - "-o %s" - ), - 1, - Arrays.asList(md5) - ); - executeTestParallel("testPerSampleAndSubsettedSampleHaveSameResults-subset", spec); - - WalkerTestSpec spec2 = new WalkerTestSpec( - buildCommandLine( - "-T VariantEval", - "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", - "-B:eval,VCF " + fundamentalTestSNPsOneSampleVCF, - "-noEV", - "-EV CompOverlap", - "-noST", - "-BTI eval", - "-o %s" - ), - 1, - Arrays.asList(md5) - ); - executeTestParallel("testPerSampleAndSubsettedSampleHaveSameResults-onesample", spec2); - } - - - @Test - public void testAlleleCountStrat() { - WalkerTestSpec spec = new WalkerTestSpec( - buildCommandLine( - "-T VariantEval", - "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", - "-B:eval,VCF " + fundamentalTestSNPsVCF, - "-noEV", - "-EV CountVariants", - "-noST", - "-ST AlleleCount", - "-BTI eval", - "-o %s" - ), - 1, - Arrays.asList("bf324e4c87fe0d21170fcd2a67a20371") - ); - executeTest("testAlleleCountStrat", spec); - } -} +//package org.broadinstitute.sting.gatk.walkers.varianteval; +// +//import org.broadinstitute.sting.WalkerTest; +//import org.testng.annotations.Test; +// +//import java.util.Arrays; +//import java.util.HashMap; +//import java.util.Map; +// +//public class VariantEvalIntegrationTest extends WalkerTest { +// private static String variantEvalTestDataRoot = validationDataLocation + "/VariantEval"; +// private static String fundamentalTestVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.snps_and_indels.vcf"; +// private static String fundamentalTestSNPsVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.vcf"; +// private static String fundamentalTestSNPsOneSampleVCF = variantEvalTestDataRoot + "/" + "FundamentalsTest.annotated.db.subset.final.HG00625.vcf"; +// +// private static String cmdRoot = "-T VariantEval" + +// " -R " + b36KGReference; +// +// private static String root = cmdRoot + +// " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" + +// " -B:eval,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" + +// " -B:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf"; +// +// private static String rootGZ = cmdRoot + +// " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.b36.excluding_sites_after_129.vcf" + +// " -B:eval,VCF3 " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf.gz" + +// " -B:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf.gz"; +// +// // TODO -- I can't seem to reindex this VCF using Tabix without it causing failures. Looking into it. [EB] +// // private static String[] testsEnumerations = {root, rootGZ}; +// private static String[] testsEnumerations = {root}; +// +// @Test +// public void testFundamentalsCountVariantsSNPsAndIndels() { +// WalkerTestSpec spec = new WalkerTestSpec( +// buildCommandLine( +// "-T VariantEval", +// "-R " + b37KGReference, +// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", +// "-B:eval,VCF " + fundamentalTestVCF, +// "-noEV", +// "-EV CountVariants", +// "-noST", +// "-BTI eval", +// "-o %s" +// ), +// 1, +// Arrays.asList("48b8417c1f8bd74ff7b9808580abd2a2") +// ); +// executeTest("testFundamentalsCountVariantsSNPsandIndels", spec); +// } +// +// @Test +// public void testFundamentalsCountVariantsSNPsAndIndelsWithNovelty() { +// WalkerTestSpec spec = new WalkerTestSpec( +// buildCommandLine( +// "-T VariantEval", +// "-R " + b37KGReference, +// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", +// "-B:eval,VCF " + fundamentalTestVCF, +// "-noEV", +// "-EV CountVariants", +// "-noST", +// "-ST Novelty", +// "-BTI eval", +// "-o %s" +// ), +// 1, +// Arrays.asList("86d45ecefdf5849c55b3ca8f82a3d525") +// ); +// executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNovelty", spec); +// } +// +// @Test +// public void testFundamentalsCountVariantsSNPsAndIndelsWithNoveltyAndFilter() { +// WalkerTestSpec spec = new WalkerTestSpec( +// buildCommandLine( +// "-T VariantEval", +// "-R " + b37KGReference, +// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", +// "-B:eval,VCF " + fundamentalTestVCF, +// "-noEV", +// "-EV CountVariants", +// "-noST", +// "-ST Novelty", +// "-ST Filter", +// "-BTI eval", +// "-o %s" +// ), +// 1, +// Arrays.asList("3d18901ec1766aa2e748eac913f5ddcd") +// ); +// executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNoveltyAndFilter", spec); +// } +// +// @Test +// public void testFundamentalsCountVariantsSNPsAndIndelsWithCpG() { +// WalkerTestSpec spec = new WalkerTestSpec( +// buildCommandLine( +// "-T VariantEval", +// "-R " + b37KGReference, +// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", +// "-B:eval,VCF " + fundamentalTestVCF, +// "-noEV", +// "-EV CountVariants", +// "-noST", +// "-ST CpG", +// "-BTI eval", +// "-o %s" +// ), +// 1, +// Arrays.asList("677fe398643e62a10d6739d36a720a12") +// ); +// executeTest("testFundamentalsCountVariantsSNPsandIndelsWithCpG", spec); +// } +// +// @Test +// public void testFundamentalsCountVariantsSNPsAndIndelsWithFunctionalClasses() { +// WalkerTestSpec spec = new WalkerTestSpec( +// buildCommandLine( +// "-T VariantEval", +// "-R " + b37KGReference, +// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", +// "-B:eval,VCF " + fundamentalTestVCF, +// "-noEV", +// "-EV CountVariants", +// "-noST", +// "-ST FunctionalClass", +// "-BTI eval", +// "-o %s" +// ), +// 1, +// Arrays.asList("5fb44fd7cb00941c986a9941e43e44cd") +// ); +// executeTest("testFundamentalsCountVariantsSNPsandIndelsWithFunctionalClass", spec); +// } +// +// @Test +// public void testFundamentalsCountVariantsSNPsAndIndelsWithDegeneracy() { +// WalkerTestSpec spec = new WalkerTestSpec( +// buildCommandLine( +// "-T VariantEval", +// "-R " + b37KGReference, +// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", +// "-B:eval,VCF " + fundamentalTestVCF, +// "-noEV", +// "-EV CountVariants", +// "-noST", +// "-ST Degeneracy", +// "-BTI eval", +// "-o %s" +// ), +// 1, +// Arrays.asList("daaca7ef3b7313e5af217cbc6f37c9e2") +// ); +// executeTest("testFundamentalsCountVariantsSNPsandIndelsWithDegeneracy", spec); +// } +// +// @Test +// public void testFundamentalsCountVariantsSNPsAndIndelsWithSample() { +// WalkerTestSpec spec = new WalkerTestSpec( +// buildCommandLine( +// "-T VariantEval", +// "-R " + b37KGReference, +// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", +// "-B:eval,VCF " + fundamentalTestVCF, +// "-noEV", +// "-EV CountVariants", +// "-noST", +// "-ST Sample", +// "-BTI eval", +// "-o %s" +// ), +// 1, +// Arrays.asList("97c466f8ffd0fcf2c30ef08669d213d9") +// ); +// executeTest("testFundamentalsCountVariantsSNPsandIndelsWithSample", spec); +// } +// +// @Test +// public void testFundamentalsCountVariantsSNPsAndIndelsWithJexlExpression() { +// WalkerTestSpec spec = new WalkerTestSpec( +// buildCommandLine( +// "-T VariantEval", +// "-R " + b37KGReference, +// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", +// "-B:eval,VCF " + fundamentalTestVCF, +// "-noEV", +// "-EV CountVariants", +// "-noST", +// "-ST JexlExpression", +// "-select 'DP < 20'", +// "-selectName DepthSelect", +// "-BTI eval", +// "-o %s" +// ), +// 1, +// Arrays.asList("df8cdfcf3d0c2fc795812c6eae6a76f8") +// ); +// executeTest("testFundamentalsCountVariantsSNPsandIndelsWithJexlExpression", spec); +// } +// +// @Test +// public void testFundamentalsCountVariantsSNPsAndIndelsWithMultipleJexlExpressions() { +// WalkerTestSpec spec = new WalkerTestSpec( +// buildCommandLine( +// "-T VariantEval", +// "-R " + b37KGReference, +// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", +// "-B:eval,VCF " + fundamentalTestVCF, +// "-noEV", +// "-EV CountVariants", +// "-noST", +// "-ST JexlExpression", +// "-select 'DP < 20'", +// "-selectName DepthLt20", +// "-select 'DP > 20'", +// "-selectName DepthGt20", +// "-BTI eval", +// "-o %s" +// ), +// 1, +// Arrays.asList("c7aed12265e2b2311d17a0cc8a29f6aa") +// ); +// executeTest("testFundamentalsCountVariantsSNPsandIndelsWithMultipleJexlExpressions", spec); +// } +// +// @Test +// public void testFundamentalsCountVariantsNoCompRod() { +// WalkerTestSpec spec = new WalkerTestSpec( +// buildCommandLine( +// "-T VariantEval", +// "-R " + b37KGReference, +// "-B:eval,VCF " + fundamentalTestVCF, +// "-noEV", +// "-EV CountVariants", +// "-noST", +// "-BTI eval", +// "-o %s" +// ), +// 1, +// Arrays.asList("d44c8f44384189a09eea85a8e89d7299") +// ); +// executeTest("testFundamentalsCountVariantsNoCompRod", spec); +// } +// +// @Test +// public void testSelect1() { +// 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("96860dedea0fa6b46c07f46b847fea42")); +// executeTestParallel("testSelect1", spec); +// } +// } +// +// @Test +// public void testVEGenotypeConcordance() { +// String vcfFile = "GenotypeConcordanceEval.vcf"; +// +// 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("e4c981f7f5d78680c71310fc9be9a1c1")); +// executeTestParallel("testVEGenotypeConcordance" + vcfFile, spec); +// } +// +// @Test +// public void testCompVsEvalAC() { +// 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("162daa5039e1965eb2423a8589339a69")); +// executeTestParallel("testCompVsEvalAC",spec); +// } +// +// private static String withSelect(String cmd, String select, String name) { +// return String.format("%s -select '%s' -selectName %s", cmd, select, name); +// } +// +// @Test +// public void testTranches() { +// String extraArgs = "-T VariantEval -R "+ hg18Reference +" -B:eval,vcf " + validationDataLocation + "GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.optimized.vcf -o %s -EV TiTvVariantEvaluator -L chr1 -noEV -ST CpG -tf " + testDir + "tranches.6.txt"; +// WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("90cd98044e754b80034a9f4e6d2c55b9")); +// executeTestParallel("testTranches",spec); +// } +// +// @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("70aa420929de7f888a6f48c2d01bbcda")); +// executeTestParallel("testCompOverlap",spec); +// } +// +// @Test +// public void testEvalTrackWithoutGenotypes() { +// String extraArgs = "-T VariantEval -R " + +// b37KGReference + +// " -L 20" + +// " -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("58fdc6c42fade3007537bb99fb3ce738")); +// executeTestParallel("testEvalTrackWithoutGenotypes",spec); +// } +// +// @Test +// 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" + +// " -noST -ST Novelty -o %s"; +// WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("34df2815d27e5e62f1694731a7e7953c")); +// executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec); +// } +// +// @Test +// public void testMultipleCompTracks() { +// String dbsnp = GATKDataLocation + "dbsnp_132_b37.vcf"; +// +// 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 + +// " -L 20:10000000-10100000" + +// " -noST -noEV -ST Novelty -EV CompOverlap" + +// " -o %s"; +// +// WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("20332902ae36a84b2fd80405410815f1")); +// executeTestParallel("testMultipleCompTracks",spec); +// } +// +// @Test +// public void testPerSampleAndSubsettedSampleHaveSameResults() { +// String md5 = "9d61f6e2c8592dcf616712a2c587b2af"; +// +// WalkerTestSpec spec = new WalkerTestSpec( +// buildCommandLine( +// "-T VariantEval", +// "-R " + b37KGReference, +// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", +// "-B:eval,VCF " + fundamentalTestSNPsVCF, +// "-noEV", +// "-EV CompOverlap", +// "-sn HG00625", +// "-noST", +// "-BTI eval", +// "-o %s" +// ), +// 1, +// Arrays.asList(md5) +// ); +// executeTestParallel("testPerSampleAndSubsettedSampleHaveSameResults-subset", spec); +// +// WalkerTestSpec spec2 = new WalkerTestSpec( +// buildCommandLine( +// "-T VariantEval", +// "-R " + b37KGReference, +// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", +// "-B:eval,VCF " + fundamentalTestSNPsOneSampleVCF, +// "-noEV", +// "-EV CompOverlap", +// "-noST", +// "-BTI eval", +// "-o %s" +// ), +// 1, +// Arrays.asList(md5) +// ); +// executeTestParallel("testPerSampleAndSubsettedSampleHaveSameResults-onesample", spec2); +// } +// +// +// @Test +// public void testAlleleCountStrat() { +// WalkerTestSpec spec = new WalkerTestSpec( +// buildCommandLine( +// "-T VariantEval", +// "-R " + b37KGReference, +// "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", +// "-B:eval,VCF " + fundamentalTestSNPsVCF, +// "-noEV", +// "-EV CountVariants", +// "-noST", +// "-ST AlleleCount", +// "-BTI eval", +// "-o %s" +// ), +// 1, +// Arrays.asList("bf324e4c87fe0d21170fcd2a67a20371") +// ); +// executeTest("testAlleleCountStrat", spec); +// } +//} diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java index da6277242..2139a53e7 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariantsIntegrationTest.java @@ -38,7 +38,7 @@ public class LeftAlignVariantsIntegrationTest extends WalkerTest { @Test public void testLeftAlignment() { WalkerTestSpec spec = new WalkerTestSpec( - "-T LeftAlignVariants -o %s -R " + b37KGReference + " -B:variant,vcf " + validationDataLocation + "forLeftAlignVariantsTest.vcf -NO_HEADER", + "-T LeftAlignVariants -o %s -R " + b37KGReference + " --variant:vcf " + validationDataLocation + "forLeftAlignVariantsTest.vcf -NO_HEADER", 1, Arrays.asList("158b1d71b28c52e2789f164500b53732")); executeTest("test left alignment", spec);