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..38a852eb5 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 @@ -4,8 +4,6 @@ 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"; @@ -16,27 +14,13 @@ public class VariantEvalIntegrationTest extends WalkerTest { 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:dbsnp,VCF " + b37dbSNP132, "-B:eval,VCF " + fundamentalTestVCF, "-noEV", "-EV CountVariants", @@ -45,7 +29,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { "-o %s" ), 1, - Arrays.asList("48b8417c1f8bd74ff7b9808580abd2a2") + Arrays.asList("bced1842c78fbabb089dd12b7087050d") ); executeTest("testFundamentalsCountVariantsSNPsandIndels", spec); } @@ -56,7 +40,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", + "-B:dbsnp,VCF " + b37dbSNP132, "-B:eval,VCF " + fundamentalTestVCF, "-noEV", "-EV CountVariants", @@ -66,7 +50,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { "-o %s" ), 1, - Arrays.asList("86d45ecefdf5849c55b3ca8f82a3d525") + Arrays.asList("06510bd37ffaa39e817ca0dcaf8f8ac2") ); executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNovelty", spec); } @@ -77,7 +61,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", + "-B:dbsnp,VCF " + b37dbSNP132, "-B:eval,VCF " + fundamentalTestVCF, "-noEV", "-EV CountVariants", @@ -88,7 +72,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { "-o %s" ), 1, - Arrays.asList("3d18901ec1766aa2e748eac913f5ddcd") + Arrays.asList("19c5b1b6396921c5b1059a2849ae4fcc") ); executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNoveltyAndFilter", spec); } @@ -99,7 +83,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", + "-B:dbsnp,VCF " + b37dbSNP132, "-B:eval,VCF " + fundamentalTestVCF, "-noEV", "-EV CountVariants", @@ -109,7 +93,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { "-o %s" ), 1, - Arrays.asList("677fe398643e62a10d6739d36a720a12") + Arrays.asList("a71f8d81cf166cd97ac628092650964a") ); executeTest("testFundamentalsCountVariantsSNPsandIndelsWithCpG", spec); } @@ -120,7 +104,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", + "-B:dbsnp,VCF " + b37dbSNP132, "-B:eval,VCF " + fundamentalTestVCF, "-noEV", "-EV CountVariants", @@ -130,7 +114,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { "-o %s" ), 1, - Arrays.asList("5fb44fd7cb00941c986a9941e43e44cd") + Arrays.asList("4dabe0658232f6174188515db6dfe112") ); executeTest("testFundamentalsCountVariantsSNPsandIndelsWithFunctionalClass", spec); } @@ -141,7 +125,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", + "-B:dbsnp,VCF " + b37dbSNP132, "-B:eval,VCF " + fundamentalTestVCF, "-noEV", "-EV CountVariants", @@ -151,7 +135,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { "-o %s" ), 1, - Arrays.asList("daaca7ef3b7313e5af217cbc6f37c9e2") + Arrays.asList("3340587f10ceff83e5567ddfd1a9a60e") ); executeTest("testFundamentalsCountVariantsSNPsandIndelsWithDegeneracy", spec); } @@ -162,7 +146,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", + "-B:dbsnp,VCF " + b37dbSNP132, "-B:eval,VCF " + fundamentalTestVCF, "-noEV", "-EV CountVariants", @@ -172,7 +156,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { "-o %s" ), 1, - Arrays.asList("97c466f8ffd0fcf2c30ef08669d213d9") + Arrays.asList("c730c7ee31c8138cef6efd8dd04fbbfc") ); executeTest("testFundamentalsCountVariantsSNPsandIndelsWithSample", spec); } @@ -183,7 +167,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", + "-B:dbsnp,VCF " + b37dbSNP132, "-B:eval,VCF " + fundamentalTestVCF, "-noEV", "-EV CountVariants", @@ -195,7 +179,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { "-o %s" ), 1, - Arrays.asList("df8cdfcf3d0c2fc795812c6eae6a76f8") + Arrays.asList("2559ca8f454b03e81561f6947f79df18") ); executeTest("testFundamentalsCountVariantsSNPsandIndelsWithJexlExpression", spec); } @@ -206,7 +190,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", + "-B:dbsnp,VCF " + b37dbSNP132, "-B:eval,VCF " + fundamentalTestVCF, "-noEV", "-EV CountVariants", @@ -220,7 +204,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { "-o %s" ), 1, - Arrays.asList("c7aed12265e2b2311d17a0cc8a29f6aa") + Arrays.asList("23aa5f97641d2fd033095f21c51d2f37") ); executeTest("testFundamentalsCountVariantsSNPsandIndelsWithMultipleJexlExpressions", spec); } @@ -239,7 +223,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { "-o %s" ), 1, - Arrays.asList("d44c8f44384189a09eea85a8e89d7299") + Arrays.asList("a69dd3f06903b3f374c6d6f010c653e0") ); executeTest("testFundamentalsCountVariantsNoCompRod", spec); } @@ -247,11 +231,13 @@ public class VariantEvalIntegrationTest extends WalkerTest { @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); - } + String tests = cmdRoot + + " -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("db95c8af8ba549d38ca6741a59fd6892")); + executeTestParallel("testSelect1", spec); } @Test @@ -260,14 +246,14 @@ public class VariantEvalIntegrationTest extends WalkerTest { 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")); + Arrays.asList("96f27163f16bb945f19c6623cd6db34e")); 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")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("d1932be3748fcf6da77dc51aec323710")); executeTestParallel("testCompVsEvalAC",spec); } @@ -278,14 +264,14 @@ public class VariantEvalIntegrationTest extends WalkerTest { @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")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("984df6e94a546294fc7e0846cbac2dfe")); 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")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("462d4784dd55294ef9d5118217b157a5")); executeTestParallel("testCompOverlap",spec); } @@ -294,10 +280,10 @@ public class VariantEvalIntegrationTest extends WalkerTest { String extraArgs = "-T VariantEval -R " + b37KGReference + " -L 20" + - " -B:dbsnp,vcf " + b37dbSNP132 + + " -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")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("61c36fb6cc75172e2b22a44edeae85e0")); executeTestParallel("testEvalTrackWithoutGenotypes",spec); } @@ -305,11 +291,11 @@ public class VariantEvalIntegrationTest extends WalkerTest { public void testMultipleEvalTracksWithoutGenotypes() { String extraArgs = "-T VariantEval -R " + b37KGReference + " -L 20" + - " -B:dbsnp,vcf " + b37dbSNP132 + + " -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")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("79089484097614b7ab81bbc3ad3a892a")); executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec); } @@ -326,19 +312,19 @@ public class VariantEvalIntegrationTest extends WalkerTest { " -noST -noEV -ST Novelty -EV CompOverlap" + " -o %s"; - WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("20332902ae36a84b2fd80405410815f1")); + WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("9f906c04a4553d649b51ae67e0a25113")); executeTestParallel("testMultipleCompTracks",spec); } @Test public void testPerSampleAndSubsettedSampleHaveSameResults() { - String md5 = "9d61f6e2c8592dcf616712a2c587b2af"; + String md5 = "97a16a99a43d2384cfabc39d36647419"; WalkerTestSpec spec = new WalkerTestSpec( buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", + "-B:dbsnp,VCF " + b37dbSNP132, "-B:eval,VCF " + fundamentalTestSNPsVCF, "-noEV", "-EV CompOverlap", @@ -356,7 +342,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", + "-B:dbsnp,VCF " + b37dbSNP132, "-B:eval,VCF " + fundamentalTestSNPsOneSampleVCF, "-noEV", "-EV CompOverlap", @@ -377,7 +363,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { buildCommandLine( "-T VariantEval", "-R " + b37KGReference, - "-B:dbsnp,VCF " + GATKDataLocation + "dbsnp_132_b37.vcf", + "-B:dbsnp,VCF " + b37dbSNP132, "-B:eval,VCF " + fundamentalTestSNPsVCF, "-noEV", "-EV CountVariants", @@ -387,7 +373,7 @@ public class VariantEvalIntegrationTest extends WalkerTest { "-o %s" ), 1, - Arrays.asList("bf324e4c87fe0d21170fcd2a67a20371") + Arrays.asList("44464fe7c89a56cf128a932ef640f7da") ); executeTest("testAlleleCountStrat", spec); }