From 35a06879f1c8dd0fe795fe1858b11f17296b9551 Mon Sep 17 00:00:00 2001 From: Ron Levine Date: Tue, 26 Apr 2016 13:56:05 -0400 Subject: [PATCH] Move htsjdk and picard to version 2.3.0 --- .../genotyper/ConsensusAlleleCounter.java | 2 +- .../walkers/genotyper/GenotypingEngine.java | 6 +- .../walkers/genotyper/UnifiedGenotyper.java | 4 +- .../VariantAnnotatorIntegrationTest.java | 52 +++++++-------- .../cancer/m2/MuTect2IntegrationTest.java | 12 ++-- .../VariantFiltrationIntegrationTest.java | 2 +- .../UnifiedGenotyperEngineUnitTest.java | 2 +- ...perGeneralPloidySuite1IntegrationTest.java | 8 +-- ...perGeneralPloidySuite2IntegrationTest.java | 6 +- ...dGenotyperIndelCallingIntegrationTest.java | 22 +++---- .../UnifiedGenotyperIntegrationTest.java | 32 ++++----- ...GenotyperNormalCallingIntegrationTest.java | 16 ++--- ...lexAndSymbolicVariantsIntegrationTest.java | 10 +-- .../HaplotypeCallerGVCFIntegrationTest.java | 66 +++++++++---------- .../HaplotypeCallerIntegrationTest.java | 64 +++++++++--------- .../PhaseByTransmissionIntegrationTest.java | 2 +- .../ReadBackedPhasingIntegrationTest.java | 6 +- ...ntRecalibrationWalkersIntegrationTest.java | 6 +- ...lateGenotypePosteriorsIntegrationTest.java | 10 +-- .../CombineGVCFsIntegrationTest.java | 28 ++++---- .../CombineVariantsIntegrationTest.java | 2 +- .../GenotypeGVCFsIntegrationTest.java | 63 +++++++++--------- ...ftAlignAndTrimVariantsIntegrationTest.java | 10 +-- .../SelectVariantsIntegrationTest.java | 30 ++++----- ...SelectVariantsParallelIntegrationTest.java | 4 +- public/external-example/pom.xml | 2 +- .../engine/EngineFeaturesIntegrationTest.java | 8 +-- .../engine/arguments/CramIntegrationTest.java | 8 +-- .../arguments/IntervalIntegrationTest.java | 2 +- public/gatk-root/pom.xml | 10 +-- .../readutils/PrintReadsIntegrationTest.java | 2 +- .../variantutils/VCFIntegrationTest.java | 2 +- .../1.2-20140817/cofoja-1.2-20140817.pom | 4 +- 33 files changed, 251 insertions(+), 252 deletions(-) diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ConsensusAlleleCounter.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ConsensusAlleleCounter.java index 4bfd6cc89..feee51aea 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ConsensusAlleleCounter.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/ConsensusAlleleCounter.java @@ -278,7 +278,7 @@ public class ConsensusAlleleCounter { builder.noGenotypes(); if (doMultiAllelicCalls) { vcs.add(builder.make()); - if (vcs.size() >= GenotypeLikelihoods.MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED) + if (vcs.size() >= GenotypeLikelihoods.MAX_DIPLOID_ALT_ALLELES_THAT_CAN_BE_GENOTYPED) break; } else if (curCnt > maxAlleleCnt) { maxAlleleCnt = curCnt; diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java index a5e5d8a87..83c7ed533 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java @@ -407,14 +407,14 @@ public abstract class GenotypingEngine, Unif UAC.setSampleContamination(AlleleBiasedDownsamplingUtils.loadContaminationFile(UAC.CONTAMINATION_FRACTION_FILE, UAC.CONTAMINATION_FRACTION, sampleNameSet, logger)); // check for a bad max alleles value - if ( UAC.genotypeArgs.MAX_ALTERNATE_ALLELES > GenotypeLikelihoods.MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED) - throw new UserException.BadArgumentValue("max_alternate_alleles", "the maximum possible value is " + GenotypeLikelihoods.MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED); + if ( UAC.genotypeArgs.MAX_ALTERNATE_ALLELES > GenotypeLikelihoods.MAX_DIPLOID_ALT_ALLELES_THAT_CAN_BE_GENOTYPED) + throw new UserException.BadArgumentValue("max_alternate_alleles", "the maximum possible value is " + GenotypeLikelihoods.MAX_DIPLOID_ALT_ALLELES_THAT_CAN_BE_GENOTYPED); // warn the user for misusing EMIT_ALL_SITES if ( UAC.outputMode == OutputMode.EMIT_ALL_SITES && diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java index 94c3db651..0029f78a6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -99,7 +99,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("832861ecdc6344cfb7097d02903ffd4d")); + Arrays.asList("b63baada372925a76c3f279e16eb631d")); executeTest("test file has annotations, asking for annotations, #1", spec); } @@ -107,7 +107,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, - Arrays.asList("d584454019f21729757ed7685ff8d02c")); + Arrays.asList("6f5856bc2d31f8aae4131717e5ab0b16")); executeTest("test file has annotations, asking for annotations, #2", spec); } @@ -133,7 +133,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("95a4be70c46496fb6791fdd0c3bcf8a3")); + Arrays.asList("7ec5470f742f80cdfbfb203213bea8cc")); executeTest("test file doesn't have annotations, asking for annotations, #1", spec); } @@ -141,7 +141,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, - Arrays.asList("fe6a7fdd3f7c1c77b31c2676aeb0ed8d")); + Arrays.asList("afc47e4f253d0999961f26920be8e834")); executeTest("test file doesn't have annotations, asking for annotations, #2", spec); } @@ -150,7 +150,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testExcludeAnnotations() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + STANDARD_ANNOTATIONS + "-XA FisherStrand -XA ReadPosRankSumTest --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("4995f77bedf7f476a15d46b5a8a392bd")); + Arrays.asList("a8a87e2a67436e14ed32ce9d355a3440")); executeTest("test exclude annotations", spec); } @@ -183,7 +183,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testOverwritingHeader() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1, - Arrays.asList("de96b1e62f414b107430d179a154534d")); + Arrays.asList("fc7958261af93681fde73c1fc6b578a0")); executeTest("test overwriting header", spec); } @@ -191,7 +191,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoReads() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1, - Arrays.asList("489a09a8531d9c8ef683ad8cc81db3e8")); + Arrays.asList("2d535a48ec1c66aa9c707f6d498fc81d")); executeTest("not passing it any reads", spec); } @@ -199,7 +199,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testDBTagWithDbsnp() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --dbsnp " + b36dbSNP129 + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1, - Arrays.asList("a7af6774ea1f7622d999cae1b7f8ea32")); + Arrays.asList("a2a2f9ce8e6f9c933ad46906719ce402")); executeTest("getting DB tag with dbSNP", spec); } @@ -207,7 +207,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testMultipleIdsWithDbsnp() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --alwaysAppendDbsnpId --dbsnp " + b36dbSNP129 + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3withIDs.vcf -L " + privateTestDir + "vcfexample3withIDs.vcf", 1, - Arrays.asList("de8cfffe3b61b7c8832096a399e9d954")); + Arrays.asList("ed351765d63d92b1913784fa47b3d859")); executeTest("adding multiple IDs with dbSNP", spec); } @@ -215,7 +215,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testDBTagWithHapMap() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1, - Arrays.asList("25443af7099f7de184b8dcdfb659f62e")); + Arrays.asList("114d8300ec0fac613bb2e82f8951adc0")); executeTest("getting DB tag with HM3", spec); } @@ -223,7 +223,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testDBTagWithTwoComps() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf --comp:foo " + privateTestDir + "fakeHM3.vcf " + STANDARD_ANNOTATIONS + " --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1, - Arrays.asList("ea9b10d2b82a7846c01a017f6f3bb57e")); + Arrays.asList("af59185b6a03d4147d2755019dcc6bf9")); executeTest("getting DB tag with 2 comps", spec); } @@ -239,7 +239,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testUsingExpression() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty.vcf", 1, - Arrays.asList("f26d1f849cceca0ab115737f8db670ae")); + Arrays.asList("7bcbd8ad8388f371d1a990fde67d3273")); executeTest("using expression", spec); } @@ -247,7 +247,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testUsingExpressionAlleleMisMatch() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --resourceAlleleConcordance --resource:foo " + privateTestDir + "targetAnnotations.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty-mod.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty-mod.vcf", 1, - Arrays.asList("6f288c4b672ac3a22cb2385981f51d75")); + Arrays.asList("76f716569e33d88914e479b70e08ac88")); executeTest("using expression allele mismatch", spec); } @@ -255,7 +255,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testUsingExpressionMultiAllele() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations-multiAllele.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty-multiAllele.vcf -E foo.AF -E foo.AC -L " + privateTestDir + "vcfexample3empty-multiAllele.vcf", 1, - Arrays.asList("af92a439f092f45da10adac0f9c8fc8f")); + Arrays.asList("0e3fc86349f5fd28159d00d22d278e84")); executeTest("using expression with multi-alleles", spec); } @@ -264,7 +264,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { /* The order of filters in the output seems platform-dependent. May need to change htsjdk to make the order consistent across platforms. [Sato] */ WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --resource:foo " + privateTestDir + "annotationResourceWithFilter.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty-multiAllele.vcf -E foo.FILTER -L " + privateTestDir + "vcfexample3empty-multiAllele.vcf", 1, - Arrays.asList("d0a381375a407dd454637f78bb5b194f")); + Arrays.asList("6fe67e72232165a829fde7c3b12c2275")); executeTest("annotate a vcf with the FILTER field of another vcf", spec); } @@ -272,7 +272,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testUsingExpressionWithID() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf" + STANDARD_ANNOTATIONS + "--variant " + privateTestDir + "vcfexample3empty.vcf -E foo.ID -L " + privateTestDir + "vcfexample3empty.vcf", 1, - Arrays.asList("58a86fe8a34c92127eb33e36107941dd")); + Arrays.asList("94b03ee63604ab8d61aacfd3297c5dca")); executeTest("using expression with ID", spec); } @@ -300,7 +300,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { validationDataLocation + "1kg_exomes_unfiltered.AFR.unfiltered.vcf --snpEffFile " + validationDataLocation + "snpEff2.0.5.AFR.unfiltered.vcf -L 1:1-1,500,000 -L 2:232,325,429", 1, - Arrays.asList("6618f3ae9dc6d4ce6ebd4eb8f9495103") + Arrays.asList("db0c5f273583a54d0cefc4b3c01aae9a") ); executeTest("Testing SnpEff annotations", spec); } @@ -313,7 +313,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { "--snpEffFile " + privateTestDir + "snpEff_unsupported_version_gatk_mode.vcf " + "-L 1:10001292-10012424", 1, - Arrays.asList("7533645a3791ce30d7407f789e1ffbb0") + Arrays.asList("5f952cfcd25653edcffd3916d52e94ec") ); executeTest("Testing SnpEff annotations (unsupported version, GATK mode)", spec); } @@ -326,14 +326,14 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { "--snpEffFile " + privateTestDir + "snpEff_unsupported_version_no_gatk_mode.vcf " + "-L 1:10001292-10012424", 1, - Arrays.asList("0e201a91a2b2b130debcd5dd7d9328ab") + Arrays.asList("86fb28c2e3886eda194026b3b7d07c77") ); executeTest("Testing SnpEff annotations (unsupported version, no GATK mode)", spec); } @Test(enabled = true) public void testTDTAnnotation() { - final String MD5 = "9532ca341b52be650b35e32d7c765030"; + final String MD5 = "cf65fdfbcd822279e84326989b2f6378"; WalkerTestSpec spec = new WalkerTestSpec( "-T VariantAnnotator -R " + b37KGReference + " -A TransmissionDisequilibriumTest --variant:vcf " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf" + " -L " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + privateTestDir + "ug.random50000.family.ped -o %s", 1, @@ -344,7 +344,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test(enabled = true) public void testChromosomeCountsPed() { - final String MD5 = "4ab0b4245ba2c5c62424775879f51379"; + final String MD5 = "71045f20e4cd9f5fdaa367f6d7324e59"; WalkerTestSpec spec = new WalkerTestSpec( "-T VariantAnnotator -R " + b37KGReference + " -A ChromosomeCounts --variant:vcf " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf" + " -L " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + privateTestDir + "ug.random50000.family.ped -o %s", 1, @@ -354,7 +354,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test(enabled = true) public void testInbreedingCoeffPed() { - final String MD5 = "5cbf01dc895bff5a8dd9f6c46e0958c6"; + final String MD5 = "0cf7c115316950abc0213935b20a653a"; WalkerTestSpec spec = new WalkerTestSpec( "-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf" + " -L " + privateTestDir + "ug.random50000.subset300bp.chr1.family.vcf --no_cmdline_in_header -ped " + privateTestDir + "ug.random50000.family.ped -o %s", 1, @@ -364,7 +364,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test(enabled = true) public void testAlleleTrimming() { - final String MD5 = "90f9ee6c34c0820435dce7a0d63b4c1e"; + final String MD5 = "5db0cd72ad0ffc711afb95df58de31fa"; WalkerTestSpec spec = new WalkerTestSpec( "-T VariantAnnotator -R " + b37KGReference + " -A InbreedingCoeff --variant:vcf " + privateTestDir + "alleleTrim.vcf.gz" + " -L 1:26608870-26608875 -no_cmdline_in_header --resource:exac " + privateTestDir + "exacAlleleTrim.vcf.gz -E exac.AC_Adj" + @@ -423,7 +423,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testStrandAlleleCountsBySample() { - final String MD5 = "dca6c2b416076ca89769a322cae65bb8"; + final String MD5 = "564aeeefad92353d66dbb2a2222d5108"; final WalkerTestSpec spec = new WalkerTestSpec( "-T HaplotypeCaller --disableDithering " + String.format("-R %s -I %s ", REF, CEUTRIO_BAM) + @@ -510,7 +510,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T VariantAnnotator -R " + hg19ReferenceWithChrPrefixInChromosomeNames + " -A HomopolymerRun --variant:vcf " + privateTestDir + "problem_del.vcf " + "-U ALLOW_SEQ_DICT_INCOMPATIBILITY -L chr18:44382010-44384010 --reference_window_stop 59 --no_cmdline_in_header -o %s", 1, - Arrays.asList("bda55495578147b2390d850d7fb25a12")); + Arrays.asList("f3166721ef0380636590b3e860aa06af")); executeTest("Testing testHomopolymerRunWindow", spec); } @@ -519,7 +519,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T VariantAnnotator -R " + hg19ReferenceWithChrPrefixInChromosomeNames + " -A HomopolymerRun --variant:vcf " + privateTestDir + "problem_del.vcf " + "-U ALLOW_SEQ_DICT_INCOMPATIBILITY -L chr18:44382010-44384010 --no_cmdline_in_header -o %s", 1, - Arrays.asList("e20b12fd45f37a7bb31a2f2e91983477")); + Arrays.asList("3dba997d03779781c82a25ace69c838e")); executeTest("Testing HomopolymerRunTooBig", spec); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java index 8a7c54d35..bfd0e4911 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java @@ -121,7 +121,7 @@ public class MuTect2IntegrationTest extends WalkerTest { @Test public void testMicroRegression() { - M2Test(CCLE_MICRO_TUMOR_BAM, CCLE_MICRO_NORMAL_BAM, CCLE_MICRO_INTERVALS_FILE, "", "617054c6d056cad7448a463cb8d04a55"); + M2Test(CCLE_MICRO_TUMOR_BAM, CCLE_MICRO_NORMAL_BAM, CCLE_MICRO_INTERVALS_FILE, "", "a7658ccfb75bf1ce8d3d3cfbf3b552f0"); } /** @@ -131,7 +131,7 @@ public class MuTect2IntegrationTest extends WalkerTest { */ @Test public void testTruePositivesDream3() { - M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_TP_INTERVALS_FILE, "", "f856432679e43445d2939772be4326cf"); + M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_TP_INTERVALS_FILE, "", "91dee82a13275e5568f5d2e680e3162b"); } /** @@ -140,7 +140,7 @@ public class MuTect2IntegrationTest extends WalkerTest { @Test public void testTruePositivesDream3TrackedDropped() { M2TestWithDroppedReads(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, "21:10935369", "", - "ee4786de29532ffd745048c449a9772a", + "4f1337df1de5dd4468e2d389403ca785", "b536e76870326b4be01b8d6b83c1cf1c"); } @@ -150,7 +150,7 @@ public class MuTect2IntegrationTest extends WalkerTest { */ @Test public void testFalsePositivesDream3() { - M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_FP_INTERVALS_FILE, "", "11357aa543e7c6b2725cd330adba23a0"); + M2Test(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, DREAM3_FP_INTERVALS_FILE, "", "6be3fc318e2c22a28098f58b76c9a5a1"); } /** @@ -158,7 +158,7 @@ public class MuTect2IntegrationTest extends WalkerTest { */ @Test public void testContaminationCorrection() { - M2Test(CCLE_MICRO_TUMOR_BAM, CCLE_MICRO_NORMAL_BAM, CCLE_MICRO_INTERVALS_FILE, "-contamination 0.1", "1df41f2dd6d4715ae1b423bf295ec7c5"); + M2Test(CCLE_MICRO_TUMOR_BAM, CCLE_MICRO_NORMAL_BAM, CCLE_MICRO_INTERVALS_FILE, "-contamination 0.1", "b1010a6614b0332c41fd6da9d5f6b14e"); } /** @@ -166,7 +166,7 @@ public class MuTect2IntegrationTest extends WalkerTest { */ @Test public void testTumorOnly(){ - m2TumorOnlyTest(CCLE_MICRO_TUMOR_BAM, "2:166000000-167000000", "", "8439d9a673b3a57aa5893af600125d3b"); + m2TumorOnlyTest(CCLE_MICRO_TUMOR_BAM, "2:166000000-167000000", "", "bb0cddfdc29500fbea68a0913d6706a3"); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java index e594dce5b..61d92f0bb 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/filters/VariantFiltrationIntegrationTest.java @@ -189,7 +189,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference + " --filterExpression 'FS > 60.0' --filterName SNP_FS -V " + privateTestDir + "unfilteredForFiltering.vcf", 1, - Arrays.asList("0febd66699fcd7f521377d1d0d0016fb")); + Arrays.asList("b9fa012770831c984101d23420ef0c38")); executeTest("testUnfilteredBecomesFilteredAndPass", spec); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java index 9d0984c81..ff8d7f99a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java @@ -133,7 +133,7 @@ public class UnifiedGenotyperEngineUnitTest extends BaseTest { } final VariantContext vc = new VariantContextBuilder("test", "chr1", 1000, 1000, alleles).make(); final boolean result = ugEngine.hasTooManyAlternativeAlleles(vc); - Assert.assertTrue(result == (vc.getNAlleles() > GenotypeLikelihoods.MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED)); + Assert.assertTrue(result == (vc.getNAlleles() > GenotypeLikelihoods.MAX_DIPLOID_ALT_ALLELES_THAT_CAN_BE_GENOTYPED)); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java index 0f7f9fb67..6e21e96d1 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java @@ -69,17 +69,17 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe @Test(enabled = true) public void testSNP_ACS_Pools() { - executor.PC_LSV_Test_short("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES", "LSV_SNP_ACS", "SNP", "bf6012b6e7dec2d44b2bcb402c98c95e"); + executor.PC_LSV_Test_short("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES", "LSV_SNP_ACS", "SNP", "ebdf749d404aaef298780a53059a4f93"); } @Test(enabled = true) public void testBOTH_GGA_Pools() { - executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_BOTH_GGA", "BOTH", "1b834608171f67e52a4e7617458a3ba6"); + executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_BOTH_GGA", "BOTH", "c3826794a250e32b0497353ceb1deb26"); } @Test(enabled = true) public void testINDEL_GGA_Pools() { - executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_INDEL_GGA", "INDEL", "5b9e08bb141c48f826dc513066cb8a13"); + executor.PC_LSV_Test(String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_INDEL_GGA", "INDEL", "4eb0d8018da6612cd434491f338ed5a4"); } @Test(enabled = true) @@ -88,6 +88,6 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe //TODO the old MD5 is kept for the record. //TODO this should be revisit once we get into addressing inaccuracies by the independent allele approach. // executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "b5ff7530827f4b9039a58bdc8a3560d2"); - executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "988d421354869ec3b17f90bad695757a"); + executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "c2fb9b05027c2b0ac9e338d9ddda69b1"); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java index e683b34b7..51d7a5a65 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java @@ -63,16 +63,16 @@ public class UnifiedGenotyperGeneralPloidySuite2IntegrationTest extends WalkerTe @Test(enabled = true) public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() { - executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","1ad2b57af06e90679ce6476900d9cbbe"); + executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","e22846de4567f576e08e00edda2931d0"); } @Test(enabled = true) public void testMT_SNP_DISCOVERY_sp4() { - executor.PC_MT_Test(CEUTRIO_BAM, "-A AlleleCountBySample -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","b9f5d1db0d2f5eb00eeb72ea29130de6"); + executor.PC_MT_Test(CEUTRIO_BAM, "-A AlleleCountBySample -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","9757563c5e32f59cb47eb9b16f1016ac"); } @Test(enabled = true) public void testMT_SNP_GGA_sp10() { - executor.PC_MT_Test(CEUTRIO_BAM, String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "d90e41081b4a910a50116ff18c311245"); + executor.PC_MT_Test(CEUTRIO_BAM, String.format("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "37f8ccc683dc525c25dddc4f8dad505c"); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java index 79385a81f..9e524e347 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java @@ -78,7 +78,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("8893a0ef99744757333ec6a85c31b753")); + Arrays.asList("32bece91e170d623092817738faddb4e")); executeTest(String.format("test indel caller in SLX"), spec); } @@ -92,7 +92,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { " -minIndelCnt 1" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("7fca7fe87afba84c1bece29ce7a402ef")); + Arrays.asList("897c6063236fcd7242c2ff5982585648")); executeTest(String.format("test indel caller in SLX with low min allele count"), spec); } @@ -105,7 +105,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("343307f432d2026e3c4cc44f64aad06f")); + Arrays.asList("dd66e5f8a6e43be0e473251185a4f38a")); executeTest(String.format("test indel calling, multiple technologies"), spec); } @@ -115,7 +115,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("618d6cdd823c9f88c03b58fc7ebf47b4")); + Arrays.asList("aa56ed44e77162efce45c936c485769e")); executeTest("test MultiSample Pilot2 indels with alleles passed in", spec); } @@ -125,7 +125,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("889e43aa0d2c9ce07064817268c965a4")); + Arrays.asList("a4b6434c59c4b119e480ddafc86de234")); executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec); } @@ -140,7 +140,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L " + result.get(0).getAbsolutePath(), 1, - Arrays.asList("8052ee2044f3c5687859aadee2fe2a75")); + Arrays.asList("f9d848fe5e6e6762e0dd5b5d925f74f4")); executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2); } @@ -150,7 +150,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + privateTestDir + vcf + " -I " + validationDataLocation + "NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam -o %s -L " + validationDataLocation + vcf, 1, - Arrays.asList("6e8319e65fef1059c2092c05e6916257")); + Arrays.asList("41aa49e9c15198a006a1bc8e9638d6ec")); executeTest("test GENOTYPE_GIVEN_ALLELES with no evidence in reads", spec); } @@ -162,7 +162,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { " -o %s" + " -L 20:10,000,000-10,100,000", 1, - Arrays.asList("745eb3eefa93aca72f724aab4734c7ef")); + Arrays.asList("e883a8863bdd44c559c4440183c87078")); executeTest(String.format("test UG with base indel quality scores"), spec); } @@ -181,7 +181,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { public void testMinIndelFraction0() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 0.0", 1, - Arrays.asList("8861c367dd20505e120af174a9d4f9f4")); + Arrays.asList("2a82d1586b2148e8d902da5cf8538210")); executeTest("test minIndelFraction 0.0", spec); } @@ -189,7 +189,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { public void testMinIndelFraction25() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 0.25", 1, - Arrays.asList("a3bb6d95764d6f5a7d2f78e09699d4ef")); + Arrays.asList("3184a3f58b3aeafcd97280af708a04bb")); executeTest("test minIndelFraction 0.25", spec); } @@ -197,7 +197,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { public void testMinIndelFraction100() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 1", 1, - Arrays.asList("c7f190f7cea34a7f9c931cd8de110a48")); + Arrays.asList("990b838ef13b8ccf257eb6cbcc7c7741")); executeTest("test minIndelFraction 1.0", spec); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index 822be96b5..7d45eddb5 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -86,7 +86,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMinBaseQualityScore() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --min_base_quality_score 26", 1, - Arrays.asList("b4201a4d30b6ed5c6fc80248676be5ff")); + Arrays.asList("52a3064863b97e43d8df878edc29275c")); executeTest("test min_base_quality_score 26", spec); } @@ -94,7 +94,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testSLOD() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --computeSLOD --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1, - Arrays.asList("06d166ecf40563c234902d1b340a3ff1")); + Arrays.asList("31790ea2bd2fa7e5cec78e3ffbc98c81")); executeTest("test SLOD", spec); } @@ -102,7 +102,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testNDA() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " --annotateNDA -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1, - Arrays.asList("0538b7363d271f1f37d73dc3bd5b0071")); + Arrays.asList("2f2d7dd623446fc3cae62a44a016c16d")); executeTest("test NDA", spec); } @@ -110,7 +110,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testCompTrack() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -comp:FOO " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1, - Arrays.asList("f54dafe8e9ac1402d230e4d83766d6cf")); + Arrays.asList("7645a06b917efb1ee799bf21bdf08bc4")); executeTest("test using comp track", spec); } @@ -124,17 +124,17 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testOutputParameterSitesOnly() { - testOutputParameters("-sites_only", "dfd11f2f33dc4da50a2725bfb6f64dba"); + testOutputParameters("-sites_only", "3c0e109190cfbe41d24e7726cc8fe6e3"); } @Test public void testOutputParameterAllConfident() { - testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "a9c30d2bb179ea7a69dd0e7367fcd465"); + testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "f6937cc8ec068f2d38b5d277a92be34b"); } @Test public void testOutputParameterAllSites() { - testOutputParameters("--output_mode EMIT_ALL_SITES", "791fbabf4a8a7a1d0735d57c4c6b4a5a"); + testOutputParameters("--output_mode EMIT_ALL_SITES", "1cddd7b1e730765c2b7b55d8a1d69b4c"); } private void testOutputParameters(final String args, final String md5) { @@ -148,7 +148,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testConfidence() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1, - Arrays.asList("38a2f8e5542f78c324e89d09eb545f07")); + Arrays.asList("5c7d237e666439edb0ef8c697e37933c")); executeTest("test confidence 1", spec1); } @@ -156,7 +156,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testNoPrior() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 -inputPrior 0.33333 -inputPrior 0.33333", 1, - Arrays.asList("6f96d079f5889d8555880e6cb614a41d")); + Arrays.asList("24b550bbc3c9f0577e069b3fd3122d52")); executeTest("test no prior 1", spec1); } @@ -165,7 +165,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testUserPrior() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 -inputPrior 0.001 -inputPrior 0.495", 1, - Arrays.asList("6e48c44b58960954e7e49810d9e3b3ad")); + Arrays.asList("f60b6705daec1059ce3e533bf8e44c89")); executeTest("test user prior 1", spec1); } @@ -174,7 +174,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void emitPLsAtAllSites() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --output_mode EMIT_ALL_SITES -allSitePLs", 1, - Arrays.asList("04630efda71e0e804cfa4b2e7461c083")); + Arrays.asList("ae778a64323abe0da5194f0b936f48aa")); // GDA: TODO: BCF encoder/decoder doesn't seem to support non-standard values in genotype fields. IE even if there is a field defined in FORMAT and in the header the BCF2 encoder will still fail spec1.disableShadowBCF(); @@ -190,12 +190,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testHeterozyosity1() { - testHeterozosity( 0.01, "3e6328e822a92911e591733438fe023c" ); + testHeterozosity( 0.01, "6b8bdde9d303139806c5177fae53b1fd" ); } @Test public void testHeterozyosity2() { - testHeterozosity( 1.0 / 1850, "e87e2ad4a6d86ba9cc627b397af9c681" ); + testHeterozosity( 1.0 / 1850, "b1604d1ba68dfe2fcfb861ef6420a8ba" ); } private void testHeterozosity(final double arg, final String md5) { @@ -274,7 +274,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("9363de1caf569d565e0c377fe234f170")); + Arrays.asList("7ed55f70feeacf8ecc6b36f0d741dfc7")); executeTest(String.format("test multiple technologies"), spec); } @@ -293,7 +293,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -L 1:10,000,000-10,100,000" + " -baq CALCULATE_AS_NECESSARY", 1, - Arrays.asList("5e9d48c296d50d553ae13f283b75e1ee")); + Arrays.asList("90224ac1c9e2ce9b77fee8dd6e044efe")); executeTest(String.format("test calling with BAQ"), spec); } @@ -310,7 +310,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000 " + "-A SnpEff", 1, - Arrays.asList("52bac28a85b85d9596d668d3f934f792")); + Arrays.asList("e99f100fe71bb7f328b485204c16f14a")); executeTest("testSnpEffAnnotationRequestedWithoutRodBinding", spec); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java index 39bd498f2..bdd3eb5c0 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java @@ -70,7 +70,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testMultiSamplePilot1() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1, - Arrays.asList("46dd44e69ff078a48057ff08d278a293")); + Arrays.asList("c759b04ed0d948bda95008e29f3f5c2d")); executeTest("test MultiSample Pilot1", spec); } @@ -78,7 +78,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testWithAllelesPassedIn1() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, - Arrays.asList("a19e5f74606cd980c3083d41d23b4acb")); + Arrays.asList("c35cadefda8a9f13c497f84193f9f841")); executeTest("test MultiSample Pilot2 with alleles passed in", spec1); } @@ -86,7 +86,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testWithAllelesPassedIn2() { WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1, - Arrays.asList("fe3aec195ceb9180b6ffc474a4bb37b3")); + Arrays.asList("06b4ce476bf444305c8d76a765c5ddb6")); executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2); } @@ -94,7 +94,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testSingleSamplePilot2() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1, - Arrays.asList("4cc795e0e2ec1ce31fd6545fb24a850e")); + Arrays.asList("281db46f39e3367f207838c620a82bd2")); executeTest("test SingleSample Pilot2", spec); } @@ -102,7 +102,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testMultipleSNPAlleles() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1, - Arrays.asList("0de8363482204fe2aedbe612782d1049")); + Arrays.asList("94ca1e00d4fad9c5279271c2779ff797")); executeTest("test Multiple SNP alleles", spec); } @@ -110,7 +110,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testBadRead() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH -I " + privateTestDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1, - Arrays.asList("67dbab7d307d02b3d879eca8bd15a573")); + Arrays.asList("1d5c55b2df63eb24832de3486c020453")); executeTest("test bad read", spec); } @@ -118,7 +118,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testReverseTrim() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1, - Arrays.asList("e86ff5eb488f29aa77606309b2fd4fcb")); + Arrays.asList("87dbae957b1df41c1938906e23a88c5e")); executeTest("test reverse trim", spec); } @@ -126,7 +126,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testMismatchedPLs() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1, - Arrays.asList("d8b205bce4addb4ceff0b5a7ec36e3fe")); + Arrays.asList("c5aff2572ce09c413e7f5c9e1b3f92d6")); executeTest("test mismatched PLs", spec); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java index 9d09dd253..0a62bcdcb 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java @@ -72,7 +72,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa @Test public void testHaplotypeCallerMultiSampleComplex1() { - HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "39a1dfa5143e04f75ecd2b24f9c69578"); + HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "32ce23b3830f5f2c693161b40de8b15e"); } private void HCTestSymbolicVariants(String bam, String args, String md5) { @@ -84,7 +84,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa // TODO -- need a better symbolic allele test @Test public void testHaplotypeCallerSingleSampleSymbolic() { - HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "8a83ab27177f0b7adf50031f061f9cd7"); + HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "e158212aba1d7d229563db11b08b7974"); } private void HCTestComplexGGA(String bam, String args, String md5) { @@ -96,13 +96,13 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa @Test public void testHaplotypeCallerMultiSampleGGAComplex() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538", - "af3a490e5f41e890c59927426ac0fe9a"); + "8f8680bd8e1549ad88691c9c8af9977c"); } @Test public void testHaplotypeCallerMultiSampleGGAMultiAllelic() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337", - "12b1826ee23243c64a002c3cbdfa569a"); + "82b53501bc3254def885e09866377e7c"); } private void HCTestComplexConsensusMode(String bam, String args, String md5) { @@ -114,7 +114,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa @Test public void testHaplotypeCallerMultiSampleConsensusModeComplex() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538 -L 20:133041-133161 -L 20:300207-300337", - "9765065daf3a008bd92c755d882c5f07"); + "353f1895047b15b1fec22b559c9da0c1"); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java index 02699eb6a..4ff188851 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java @@ -84,12 +84,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { //TODO this might need to be addressed at some point. //TODO the following test is commented out for the record //tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "7f09c261950bf86e435edfa69ed2ec71"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "1c1ca2d76bc5d7dd45a5e7aef756ad8f"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "7ddfd33f2efcd2617d896826434fb43c"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "30accd7a171e9a13969fa543fde3fed1"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "20d896bbf750739f937ccd2fb152d902"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "99dd66a5b36ba9e2d1b0f408ecfbb50b"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "72d90fe0f5641b373744f75a21d4d14c"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "8d30370465d74fd549d76dd31adc4c0c"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "b7a5f4e40d5ebaf5f6c46a3d4355c817"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "0f5e6f2584649a1b7386d94e3dc60f91"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "2e81881e92061ad4eb29025ffdc129c7"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "2c67bdc08c8784f2114c2039270b9766"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "63fa5841a21e2c13f1e1a8e2d4ea3380"}); return tests.toArray(new Object[][]{}); } @@ -103,13 +103,13 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals; // this functionality can be adapted to provide input data for whatever you might want in your data - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "9b2914cf121c411aad3a65cfdc98c1d4"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "259110565155a3a27ab3e98113bedef8"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "8058ce63339701d33425769217bffed1"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "3abdde9d9ddbe9ec7cef28c65844a409"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "f5f0cef38a529e1542a8fd8bcce7ab1e"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "3ae2c7e570855f6d6ca58ddd1089a970"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "22e03f01e91177011ac028d2347751ba"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "cb3f16bc10e1cc75f2093bec92145d18"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "63ff771eed3e62340c8938b4963d0add"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "1122a0b3849f42d1c4a654f93b660e1b"}); - final String NA12878bandedResolutionMD5 = "0f848ee7240ca48827bdfb85b455c1ad"; + final String NA12878bandedResolutionMD5 = "8d4a51af32cd13ba4b3e33dd00c58398"; tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5}); tests.add(new Object[]{NA12878_WEx + " -I " + privateTestDir + "NA20313.highCoverageRegion.bam -sn NA12878", ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5}); @@ -126,12 +126,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals; // this functionality can be adapted to provide input data for whatever you might want in your data - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "1f99396292974df55ef6497be79b1917"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "eabb44785fd4a84ade3c674a0bda16d9"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "904feadac0e4a2a0c6b2cc7e55718f3b"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "b430a401310b3812346d7496f9c62011"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "6e481747c50734b7fb0c4de39405044f"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "cff5e49456d5ecc0dafd31cd014def4f"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "0c87e26fdd7ab5629eb33f36833e3607"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "90b25f3050435c9e67aa0ee325c24167"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "5f329540dc5c4556ab029d0e2cfcabcb"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "6ad7855dbf6dda2060aa93a3ee010b3e"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "a0be095ed902a8acdb80fb56ca4e8fb4"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "8123d8b68b6fa77ef084f292e191622a"}); return tests.toArray(new Object[][]{}); } @@ -144,12 +144,12 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals; // this functionality can be adapted to provide input data for whatever you might want in your data - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "50156c819a0096fa22ed1b9749affecc"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "d91aace2100dc040659d77f366053a2e"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "d86dc51757e69aa3f2608fbbfaa90069"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "27c73b8b1ec384a880bf60daf0b0f80e"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "a6c70203e43d62b42c4b751fe9018410"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "7ebbbcab78d090d70a24819093812748"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "0820ae1d19ba0a2da25737ded8e2c96f"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "70ee4e60d9f86b63aaab09075a71ddd3"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "700d79df3b0b481444e81471204e242e"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "09d1ae38586465b98dea0a0e432a7146"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "228e1d2ec2e729a5f79c37f3f2557708"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "2fc7020457dde4439b4133c098d9ab9b"}); return tests.toArray(new Object[][]{}); } @@ -275,7 +275,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { public void testWrongGVCFNonVariantRecordOrderBugFix() { final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, WRONG_GVCF_RECORD_ORDER_BUGFIX_BAM, WRONG_GVCF_RECORD_ORDER_BUGFIX_INTERVALS, GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("1c3d390b467a9b0e1e307419796142fd")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("6facd3d2cf9f52877182d627cef1c872")); spec.disableShadowBCF(); executeTest("testMissingGVCFIndexingStrategyException", spec); } @@ -292,7 +292,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { public void testNoCallGVCFMissingPLsBugFix() { final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, NOCALL_GVCF_BUGFIX_BAM, NOCALL_GVCF_BUGFIX_INTERVALS, GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("c5a017f1cbd60219506be76f30fc4468")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("d55ccf214fd5095e6d586c1547cb1a7a")); spec.disableShadowBCF(); executeTest("testNoCallGVCFMissingPLsBugFix", spec); } @@ -325,7 +325,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { public void testAlleleSpecificAnnotations() { final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -G Standard -G AS_Standard --disableDithering", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "20:10433000-10437000", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("169c2145c9981b8a1bb1d64a6d776d66")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("6f6b2fa85cd1bae7f8f72e144fe56c96")); spec.disableShadowBCF(); executeTest(" testAlleleSpecificAnnotations", spec); } @@ -334,7 +334,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { public void testASMQMateRankSumAnnotation() { final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -A AS_MQMateRankSumTest --disableDithering", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "20:10433000-10437000", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("75b78770469c5aaa73f1c95db8fda574")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9613ec1ec93547cfb0651673e914bee4")); spec.disableShadowBCF(); executeTest(" testASMQMateRankSumAnnotation", spec); } @@ -343,7 +343,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { public void testASInsertSizeRankSum() { final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -G Standard -G AS_Standard --disableDithering -A AS_InsertSizeRankSum", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "20:10433000-10437000", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("4fd0fcf44b1121c15e9d38de4171002c")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("a8765c11b9130c815aae4e06c1f90e45")); spec.disableShadowBCF(); executeTest(" testASInsertSizeRankSum", spec); } @@ -352,7 +352,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { public void testHaplotypeCallerMultiAllelicNonRef() { final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -A StrandAlleleCountsBySample", b37KGReference, privateTestDir + "multiallelic-nonref.bam", "2:47641259-47641859", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("2bd863f0b54b9c9a5014097cd3d3f61a")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("87f9203f5ac637080469052b702c61c7")); spec.disableShadowBCF(); executeTest(" testHaplotypeCallerMultiAllelicNonRef", spec); } @@ -361,7 +361,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { public void testHaplotypeCallerMaxNumPLValues() { final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 70", b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("7ea93210277fa4b590790a81c4b3994b")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("a4b5c40b1993573c5efd992f3f0db8a9")); spec.disableShadowBCF(); executeTest("testHaplotypeCallerMaxNumPLValues", spec); } @@ -378,7 +378,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 30 -log %s", b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER, logFileName); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9d69cb9dc67e0d0ee9863767428e6841")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("19f5398e4013c06b52c0085fe0b3469e")); spec.disableShadowBCF(); executeTest("testHaplotypeCallerMaxNumPLValuesExceededWithWarnLogLevel", spec); // Make sure the "Maximum allowed number of PLs exceeded" messages are in the log @@ -403,7 +403,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -ploidy 4 -maxNumPLValues 30 -log %s", b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER, logFileName); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9d69cb9dc67e0d0ee9863767428e6841")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("19f5398e4013c06b52c0085fe0b3469e")); spec.disableShadowBCF(); executeTest("testHaplotypeCallerMaxNumPLValuesExceededWithDebugLogLevel", spec); // Make sure the "Maximum allowed number of PLs exceeded" messages are in the log diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java index e02ea56b6..19d4a675b 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java @@ -106,92 +106,92 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeBAMOutFlags() throws IOException { - HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "1ad8934dc0ea624ffeb89d3e877176b2", "6a81bbefa6c4ed7a6b8d2c3e0e5a4756"); + HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "08943fb76d1cd5b5b8815e3991754911", "6a81bbefa6c4ed7a6b8d2c3e0e5a4756"); } @Test public void testHaplotypeCallerMultiSample() throws IOException { - HCTest(CEUTRIO_BAM, "", "5d9b06d7bf88bb18aa3e8fa6322dff89"); + HCTest(CEUTRIO_BAM, "", "ad472fbd63864caacf5bc018dcae9df9"); } @Test public void testHaplotypeCallerSingleSample() throws IOException { - HCTest(NA12878_BAM, "", "b35ba8b7ec8ddfe8268b82e77709c9ca"); + HCTest(NA12878_BAM, "", "c04293cb8466a1a217bce4ef419bdabe"); } @Test public void testHaplotypeCallerMultiSampleHaploid() throws IOException { - HCTest(CEUTRIO_BAM, "-ploidy 1", "84bd5a2ac22aa47b4436ecaf656b73b1"); + HCTest(CEUTRIO_BAM, "-ploidy 1", "7ee30877f0153257afdc691c638e7684"); } @Test public void testHaplotypeCallerSingleSampleHaploid() throws IOException { - HCTest(NA12878_BAM, "-ploidy 1", "6e9855e22ed78a60eaaf0a06ed967b77"); + HCTest(NA12878_BAM, "-ploidy 1", "9ca97bb743a369a1abb1e61168d63d69"); } @Test public void testHaplotypeCallerSingleSampleTetraploid() throws IOException { - HCTest(NA12878_BAM, "-ploidy 4", "894b56fa3afd35e240a7db394da7b4ef"); + HCTest(NA12878_BAM, "-ploidy 4", "5098645e8b570bc4521570654fa91806"); } @Test public void testHaplotypeCallerMinBaseQuality() throws IOException { - HCTest(NA12878_BAM, "-mbq 15", "b35ba8b7ec8ddfe8268b82e77709c9ca"); + HCTest(NA12878_BAM, "-mbq 15", "c04293cb8466a1a217bce4ef419bdabe"); } @Test public void testHaplotypeCallerMinBaseQualityHaploid() throws IOException { - HCTest(NA12878_BAM, "-mbq 15 -ploidy 1", "6e9855e22ed78a60eaaf0a06ed967b77"); + HCTest(NA12878_BAM, "-mbq 15 -ploidy 1", "9ca97bb743a369a1abb1e61168d63d69"); } @Test public void testHaplotypeCallerMinBaseQualityTetraploid() throws IOException { - HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "894b56fa3afd35e240a7db394da7b4ef"); + HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "5098645e8b570bc4521570654fa91806"); } @Test public void testHaplotypeCallerGraphBasedSingleSample() throws IOException { - HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "94dc1ca52ebe24ab118b13558e667253"); + HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "ba0dc5f416d69558cb5dd3e0a0a5a084"); } @Test public void testHaplotypeCallerGraphBasedMultiSampleHaploid() throws IOException { - HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "8aae4fe36d14158ea2cbf5db151f39a1"); + HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "129bca18bb9eec23004b2d28aa541de2"); } @Test public void testHaplotypeCallerGraphBasedMultiSample() throws IOException { - HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "ea4365e2dd6ae627d6347f2a53ceeaef"); + HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "2b89c9e102a049e223bc0d91156a08a3"); } @Test public void testHaplotypeCallerSingleSampleWithDbsnp() throws IOException { - HCTest(NA12878_BAM, "-D " + b37dbSNP132, "626abc84e03d4488b781cfc5a5f50290"); + HCTest(NA12878_BAM, "-D " + b37dbSNP132, "ff8e142f491b06e17e64e3a5d59737a7"); } @Test public void testHaplotypeCallerMultiSampleGGA() throws IOException { HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf" + " -isr INTERSECTION -L " + GGA_INTERVALS_FILE, - "03a9fa3a1c7163c68807d8c713d8040c"); + "6d3cea3ee76b6eba14c1dfe230cff96b"); } @Test public void testHaplotypeCallerMultiSampleGGAHaploid() throws IOException { HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -ploidy 1 -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf -isr INTERSECTION -L 20:10080000-10100000", - "6120365c05e74a8e1e1c44d739cbf8cd"); + "e60065998227f4ba8002165fb1729a71"); } @Test public void testHaplotypeCallerMultiSampleGGATetraploid() throws IOException { HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -ploidy 4 -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf -isr INTERSECTION -L 20:10080000-10100000", - "a3a547a7bf7e488651733da08fd22049"); + "9315d146a66c7baf3b615eb480c54dc1"); } @Test public void testHaplotypeCallerInsertionOnEdgeOfContig() throws IOException { - HCTest(CEUTRIO_MT_TEST_BAM, "-L MT:1-10", "da1f6b9a7e5913910531b00f3b35ce06"); + HCTest(CEUTRIO_MT_TEST_BAM, "-L MT:1-10", "60e98012fbad5f429b3b2abc3a7aa454"); } private void HCTestIndelQualityScores(String bam, String args, String md5) { @@ -202,7 +202,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerSingleSampleIndelQualityScores() { - HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "a048ea02eeb9610660e31f36e6114bf4"); + HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "3625167f0e788d409c7eab1898d5eafe"); } private void HCTestNearbySmallIntervals(String bam, String args, String md5) { @@ -239,7 +239,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerNearbySmallIntervals() { - HCTestNearbySmallIntervals(NA12878_BAM, "", "796f4a44a29fc3c1a1461f90aef45846"); + HCTestNearbySmallIntervals(NA12878_BAM, "", "591a58f16104fbb83ccf81c97cef931a"); } // This problem bam came from a user on the forum and it spotted a problem where the ReadClipper @@ -249,14 +249,14 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void HCTestProblematicReadsModifiedInActiveRegions() { final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965"; - final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("188ce2d74ee42f4187c7b41a01a193bb")); + final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("eb79b4c0bf9142c955f0a4501e9e6d8f")); executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec); } @Test public void HCTestStructuralIndels() { final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730"; - final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("034c6b151dfde537d5843f70880bf8a4")); + final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("8bddb7f343302ed20bc549df4b82825a")); executeTest("HCTestStructuralIndels: ", spec); } @@ -311,7 +311,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestDBSNPAnnotationWGS() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1, - Arrays.asList("5430b91902813cf64f5bb781b25d76c6")); + Arrays.asList("b56895e6d28ea0b9dadeecd0ff61687e")); executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec); } @@ -320,7 +320,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,100,000-11,000,000 -D " + b37dbSNP132 + " -L " + hg19Intervals + " -isr INTERSECTION", 1, - Arrays.asList("8b775d84ea981f1e8207fa69a92b5e1f")); + Arrays.asList("7b52164df8bf76d789836f990bd6066a")); executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec); } @@ -328,7 +328,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestDBSNPAnnotationWGSGraphBased() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,090,000-10,100,000 -D " + b37dbSNP132, 1, - Arrays.asList("f6f5b7e9348fc6dccd63110de0371d78")); + Arrays.asList("096826325215f79fe70661d984ae45a4")); executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec); } @@ -337,7 +337,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-11,000,000 -D " + b37dbSNP132 + " -L " + hg19Intervals + " -isr INTERSECTION", 1, - Arrays.asList("82cd0142146521fd659905737dc6192c")); + Arrays.asList("ff3b24412090ce7693d66d750ae84ac9")); executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec); } @@ -360,7 +360,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestAggressivePcrIndelModelWGS() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1, - Arrays.asList("c43caebd09b69dbc9d1e4b5f5f449712")); + Arrays.asList("c2dab66ad3740320004874c83051bbfc")); executeTest("HC calling with aggressive indel error modeling on WGS intervals", spec); } @@ -368,7 +368,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestConservativePcrIndelModelWGS() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -pairHMMSub " + HMM_SUB_IMPLEMENTATION + " " + ALWAYS_LOAD_VECTOR_HMM + " -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,270,000-10,300,000", 1, - Arrays.asList("54e7595f6d82a69566f4c0163045688d")); + Arrays.asList("a8ea15ac136042891434ccb0b3c3b686")); executeTest("HC calling with conservative indel error modeling on WGS intervals", spec); } @@ -397,7 +397,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void testLackSensitivityDueToBadHaplotypeSelectionFix() { final String commandLine = String.format("-T HaplotypeCaller -pairHMMSub %s %s -R %s -I %s -L %s --no_cmdline_in_header --maxNumHaplotypesInPopulation 16", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReferenceWithDecoy, privateTestDir + "hc-lack-sensitivity.bam", privateTestDir + "hc-lack-sensitivity.interval_list"); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("8d44a2e1967e6e844f221960d6ea42bb")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("5514cfbcf12954bb12c725b77eaac248")); spec.disableShadowBCF(); executeTest("testLackSensitivityDueToBadHaplotypeSelectionFix", spec); } @@ -406,7 +406,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void testMissingKeyAlternativeHaplotypesBugFix() { final String commandLine = String.format("-T HaplotypeCaller -pairHMMSub %s %s -R %s -I %s -L %s --no_cmdline_in_header ", HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReferenceWithDecoy, privateTestDir + "lost-alt-key-hap.bam", privateTestDir + "lost-alt-key-hap.interval_list"); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("cf8912f84153b2357a4d1ddb361f786f")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("e6d8c32585906122a6407cb40261d00d")); spec.disableShadowBCF(); executeTest("testMissingKeyAlternativeHaplotypesBugFix", spec); } @@ -429,7 +429,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { // but please make sure that both outputs get the same variant, // alleles all with DBSNP ids // We test here that change in active region size does not have an effect in placement of indels. - final String md5 = "6121d05f96eca3b1dbe3a881d968b6c5"; + final String md5 = "87b687b5476eb38b11db6a156b4066c8"; final WalkerTestSpec shortSpec = new WalkerTestSpec(commandLineShortInterval + " -o %s",Arrays.asList(md5)); executeTest("testDifferentIndelLocationsDueToSWExactDoubleComparisonsFix::shortInterval",shortSpec); final WalkerTestSpec longSpec = new WalkerTestSpec(commandLineLongInterval + " -o %s",Arrays.asList(md5)); @@ -483,12 +483,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerTandemRepeatAnnotator() throws IOException{ - HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "57eed4eec7b49efa1269fd8d58bde718"); + HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "34328c475325b7dfaa57ab5920478e0c"); } @Test public void testHBaseCountsBySample() throws IOException{ - HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A BaseCountsBySample", "5e5d064f2bb90e05e1ab28a087d8469d"); + HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A BaseCountsBySample", "f5ad4e03c0faaa806ee6ae536af8a479"); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmissionIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmissionIntegrationTest.java index 1a66f0467..6a1aea7ba 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmissionIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhaseByTransmissionIntegrationTest.java @@ -88,7 +88,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest { "-o %s" ), 2, - Arrays.asList("af979bcb353edda8dee2127605c71daf","3934b5de598024496a5de0ec35bde5b0") + Arrays.asList("af979bcb353edda8dee2127605c71daf","7ed46f6aa4565b5012acde17119a1a31") ); executeTest("testTrueNegativeMV", spec); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java index 7539b23e2..0638804d6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/ReadBackedPhasingIntegrationTest.java @@ -151,7 +151,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest { " -o %s" + " --no_cmdline_in_header", 1, - Arrays.asList("b251b4378fda9784f2175c7e3d80f032")); + Arrays.asList("0b47205ebdf2cf752ad91ff49e82c401")); executeTest("Do not merge unphased SNPs", spec); } @@ -166,7 +166,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest { " -o %s" + " --no_cmdline_in_header", 1, - Arrays.asList("630816da701b9ea8674c23c91fa61bec")); + Arrays.asList("1419d9292d6e5db6282204826cb53bf7")); executeTest("Merge SNPs if on the same read", spec); } @@ -184,7 +184,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest { " -o %s" + " --no_cmdline_in_header", 1, - Arrays.asList("b334de5ad35665f0d65034197ac05b32")); + Arrays.asList("8a3cd58dd6b1d04ab8c699f4e328dff4")); executeTest("Don't merge symbolic SPAN_DEL (*) alleles (into the nonexistent ** MNP).", spec); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java index f94dbca8e..1e4d0681a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java @@ -197,7 +197,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { VRTest bcfTest = new VRTest(privateTestDir + "vqsr.bcf_test.snps.unfiltered.bcf", "3ad7f55fb3b072f373cbce0b32b66df4", // tranches "48c21792897bdbb9adcc64886d03c5d1", // recal file - "0bd2067f831e5388b790e7bb7f45d98f"); // cut VCF + "93a6e7ab6cbd6ae24a5b2a6f0fd29d92"); // cut VCF @DataProvider(name = "VRBCFTest") public Object[][] createVRBCFTest() { @@ -359,7 +359,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { " -tranchesFile " + privateTestDir + "VQSR.AStest.snps.tranches" + " -recalFile " + privateTestDir + "VQSR.AStest.snps.recal"; - final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("cd087f2824fac5fe04c6c50cbdab1fab")); + final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("dbcf0cb5c2a0eb2312e6ca7d4e3aeeda")); final List outputFiles = executeTest("testApplyRecalibrationAlleleSpecificSNPmode", spec).getFirst(); setPDFsForDeletion(outputFiles); } @@ -377,7 +377,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { " -tranchesFile " + privateTestDir + "VQSR.AStest.indels.tranches" + " -recalFile " + privateTestDir + "VQSR.AStest.indels.recal"; - final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("b0d14f1c0647f46819018cd378036024")); + final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList("38d4b8e89dbf8acb6a36dfa1bb55c54c")); final List outputFiles = executeTest("testApplyRecalibrationAlleleSpecificINDELmode", spec).getFirst(); setPDFsForDeletion(outputFiles); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java index 525320be4..9c2594ed0 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java @@ -74,7 +74,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest { " -L 20:10,000,000-10,001,432" + " -V " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf", 1, - Arrays.asList("3e60ca3e04fecf5d6004c08d6f7503ca")); + Arrays.asList("43fa27382e654081af69ea05bd26e281")); executeTest("testUsingDiscoveredAF", spec); } @@ -89,7 +89,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest { " -L 20:10,000,000-10,001,432" + " -V " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf", 1, - Arrays.asList("1cca249ebc2599c7f24210d4f3204049")); + Arrays.asList("d63893f530fb749505ec685a5c57ff69")); executeTest("testMissingPriors", spec); } @@ -103,7 +103,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest { " -V " + validationDataLocation + "NA12878.Jan2013.haplotypeCaller.subset.indels.vcf" + " -supporting " + validationDataLocation + "1000G.phase3.broad.withGenotypes.chr20.1MB.vcf", 1, - Arrays.asList("cc59ceb6dab620a353edf03ef14090f1")); + Arrays.asList("a5d7bcad5a2a194441d00eb6574b8300")); executeTest("testInputINDELs", spec); } @@ -117,7 +117,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest { " -V " + CEUtrioTest + " -supporting " + CEUtrioPopPriorsTest, 1, - Arrays.asList("c7d35ce5f3675528fc484baa1c5df7b4")); + Arrays.asList("98bf63fd2ae3fa1cc42e66fa6b4f50f5")); executeTest("testFamilyPriors", spec); } @@ -131,7 +131,7 @@ public class CalculateGenotypePosteriorsIntegrationTest extends WalkerTest { " -V " + getThreeMemberNonTrioTest + " -skipPop", 1, - Arrays.asList("c523b99da1f7e0c0ea4090b916ae7379")); + Arrays.asList("e71420099fcfc824f1cf92ff2010b69e")); executeTest("testFamilyPriors", spec); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java index dcd6357d5..97ba4fc07 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java @@ -100,7 +100,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "tetraploid-gvcf-3.vcf" + " -L " + privateTestDir + "tetraploid-gvcfs.intervals", 1, - Arrays.asList("f3538bcaf27f5e8b036d4c1f8734e4c2")); + Arrays.asList("787aca81ad51cd40267f92f3309fa47e")); executeTest("combineSingleSamplePipelineGVCF", spec); } @@ -112,7 +112,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" + " -L " + privateTestDir + "tetraploid-gvcfs.intervals", 1, - Arrays.asList("32cd060d6662bdc835f70a848d48fb0e")); + Arrays.asList("d52f018643ffed072f43dfd4d33ca082")); executeTest("combineSingleSamplePipelineGVCF", spec); } @@ -190,7 +190,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { @Test public void testMD5s() throws Exception { final String cmd = baseTestString(" -L 1:69485-69791"); - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("82fa951ce741451267dbf30335e0f71d")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("021ec495e70044039d092ebd5ef4b82a")); spec.disableShadowBCF(); executeTest("testMD5s", spec); } @@ -198,7 +198,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { @Test public void testBasepairResolutionOutput() throws Exception { final String cmd = baseTestString(" -L 1:69485-69791 --convertToBasePairResolution"); - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("8e1bfa842d53f86d46b2166574c0c66c")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("d5bc938a26cd197d9b1c80cb8dfefbba")); spec.disableShadowBCF(); executeTest("testBasepairResolutionOutput", spec); } @@ -206,7 +206,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { @Test public void testBreakBlocks() throws Exception { final String cmd = baseTestString(" -L 1:69485-69791 --breakBandsAtMultiplesOf 5"); - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("76d78f83c7db247ce12087d6118dc5df")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("31c2f26e6b172a957a3f504734df5eff")); spec.disableShadowBCF(); executeTest("testBreakBlocks", spec); } @@ -217,7 +217,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.1.g.vcf -V " + privateTestDir + "spanningDel.2.g.vcf", 1, - Arrays.asList("cb46cb8fd6506ab3e80bd50f9231643c")); + Arrays.asList("097160606e65547722a1726e031529ec")); spec.disableShadowBCF(); executeTest("testSpanningDeletions", spec); } @@ -228,7 +228,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.many.g.vcf", 1, - Arrays.asList("5aeb14d64b9103b62d053aeb6158e5de")); + Arrays.asList("f517c2d361defeaac245916c835811d5")); spec.disableShadowBCF(); executeTest("testMultipleSpanningDeletionsForOneSample", spec); } @@ -239,7 +239,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.many.haploid.g.vcf", 1, - Arrays.asList("3fca32a67922bf30f72fe066fe7159fe")); + Arrays.asList("0a8d217b2833070dcaa3bbc1e7602b1c")); spec.disableShadowBCF(); executeTest("testMultipleSpanningDeletionsForOneSampleHaploid", spec); } @@ -250,7 +250,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { "-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.many.tetraploid.g.vcf", 1, - Arrays.asList("6891eaaef2991d7f967c7876fd2e4f5c")); + Arrays.asList("3fd437ad1f9e18303fec517653a30b6d")); spec.disableShadowBCF(); executeTest("testMultipleSpanningDeletionsForOneSampleTetraploid", spec); } @@ -259,7 +259,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { public void testWrongReferenceBaseBugFix() throws Exception { final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -V " + (privateTestDir + "combine-gvcf-wrong-ref-input1.vcf" + " -V " + (privateTestDir + "combine-gvcf-wrong-ref-input2.vcf") + " -o %s --no_cmdline_in_header"); - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("224c3d6e06f7ce4bdb55411b2e376577")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("129879954e5b453d30326f100cbc2e83")); spec.disableShadowBCF(); executeTest("testWrongReferenceBaseBugFix",spec); @@ -268,7 +268,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { @Test public void testBasepairResolutionInput() throws Exception { final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -V " + privateTestDir + "gvcf.basepairResolution.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("d3244d99e9423b45099a220f19fac516")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("d5b4abe639081e6bf9c8970ca8405dbe")); spec.disableShadowBCF(); executeTest("testBasepairResolutionInput", spec); } @@ -277,7 +277,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { public void testAlleleSpecificAnnotations() throws Exception { final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -V " + privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("cbb2571eeb95e661acee8f9e1d1cbfbd")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("f6a7fa62c33de963c55262820effe44a")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations", spec); } @@ -286,7 +286,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { public void testASMateRankSumAnnotation() throws Exception { final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -A AS_MQMateRankSumTest -V " + privateTestDir + "NA12878.AS.MateRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.MateRankSum.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("005bf0087480cce364c20d67aab5ad59")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("2c264ed0057c93276c647f55998c4f25")); spec.disableShadowBCF(); executeTest("testASMateRankSumAnnotation", spec); } @@ -295,7 +295,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { public void testASInsertSizeRankSumAnnotation() throws Exception { final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -V " + privateTestDir + "NA12878.AS.InsertSizeRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.InsertSizeRankSum.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("309ddf2a8b0c431cdabec8dafa4ab3a0")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("ff5ca958e81e406cfe010d5649b5c0d1")); spec.disableShadowBCF(); executeTest("testASInsertSizeRankSumAnnotation", spec); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java index 7f0888c53..eddf113ac 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariantsIntegrationTest.java @@ -207,7 +207,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest { + " -R " + b37KGReference + " -V " + privateTestDir + "combineVariantsLeavesRecordsUnfiltered.vcf", 1, - Arrays.asList("11aab642395645589e48edee1fb179e2")); + Arrays.asList("0f221847e76521250de1abcba535e49c")); cvExecuteTest("combineLeavesUnfilteredRecordsUnfiltered: ", spec, false); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java index e0de90a10..59d146167 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java @@ -84,7 +84,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf", b37KGReference), 1, - Arrays.asList("beebc536d20d69a45c6f56fbb041c9bc")); + Arrays.asList("8d9788afd0de26bd9d9e55dd0e9fc3ed")); executeTest("testUpdatePGT", spec); } @@ -94,7 +94,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf -A StrandAlleleCountsBySample -log " + logFileName, b37KGReference), 1, - Arrays.asList("527d513874a787821daf54b8fc8a33e3")); + Arrays.asList("5dd4698da963a423446bb1e183eb75aa")); executeTest("testUpdatePGTStrandAlleleCountsBySample", spec); File file = new File(logFileName); @@ -109,7 +109,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + " -L 20:10,000,000-11,000,000", b37KGReference), 1, - Arrays.asList("24ea3dd1f13b6636cf51aea7d5a4ce06")); + Arrays.asList("d3fab0d45f0054b71aa1d031876a4bbb")); executeTest("combineSingleSamplePipelineGVCF", spec); } @@ -121,7 +121,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "tetraploid-gvcf-3.vcf" + " -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference), 1, - Arrays.asList("3708b0d993a683e8c7421f60d7123cf4")); + Arrays.asList("64fa89f20ee25df21ad20ce4ada7e7ad")); executeTest("combineSingleSamplePipelineGVCF", spec); } @@ -133,7 +133,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" + " -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference), 1, - Arrays.asList("7d7a65ea549fcd30553766ad4333f9e2")); + Arrays.asList("b1d93f4cd93093c208be2c9842f38d12")); executeTest("combineSingleSamplePipelineGVCF", spec); } @@ -145,7 +145,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + " --includeNonVariantSites -L 20:10,030,000-10,033,000 -L 20:10,386,000-10,386,500", b37KGReference), 1, - Arrays.asList("65497a0711a33d131a165c9cfc8bc3cf")); + Arrays.asList("c2f30f25ba4a84e38c04aa49b95694e8")); executeTest("combineSingleSamplePipelineGVCF_includeNonVariants", spec); } @@ -158,7 +158,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + " -L 20:10,000,000-20,000,000", b37KGReference), 1, - Arrays.asList("70dcdc1a111ebd048d32e7e61a9b7052")); + Arrays.asList("54a86ade63b84c87ff4e537e276987fc")); executeTest("combineSingleSamplePipelineGVCFHierarchical", spec); } @@ -170,7 +170,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + " -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference), 1, - Arrays.asList("f911428f0f3bfba9b1d96a6b5ace3dee")); + Arrays.asList("1a2728e7295a6ffca6c2ba5a01af3593")); executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec); } @@ -180,7 +180,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -L 1:69485-69791 -o %s -R " + b37KGReference + " -V " + privateTestDir + "gvcfExample1.vcf", 1, - Arrays.asList("84ad9c6e7582dbcc693deacdeff5984a")); + Arrays.asList("9ff344a5ab87a2c3b128e435e2e86db0")); executeTest("testJustOneSample", spec); } @@ -191,14 +191,14 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V " + privateTestDir + "gvcfExample1.vcf" + " -V " + privateTestDir + "gvcfExample2.vcf", 1, - Arrays.asList("54b76f721811c9c7958e849c40b8d4e2")); + Arrays.asList("0c07ed795562ea96eab427e63a970384")); executeTest("testSamplesWithDifferentLs", spec); } @Test(enabled = true) public void testNoPLsException() { // Test with input files with (1) 0/0 and (2) ./. - final String md5 = "276159213ddaaf82cd0e640cc7a77fc4"; + final String md5 = "2f3d71272fdac19ac861cc7159edfb08"; WalkerTestSpec spec1 = new WalkerTestSpec( "-T GenotypeGVCFs --no_cmdline_in_header -L 1:1115550-1115551 -o %s -R " + hg19Reference + " --variant " + privateTestDir + "combined_genotype_gvcf_exception.vcf", @@ -218,7 +218,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseBPResolutionString("-nda"), 1, - Arrays.asList("3c9c84b78e7d3b358c8cb7e29a2d302b")); + Arrays.asList("ce064429e6cbcaa956d52ef22e102f2f")); executeTest("testNDA", spec); } @@ -227,7 +227,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseBPResolutionString("-maxAltAlleles 1"), 1, - Arrays.asList("87ed70b8f910b662aa67e8ed1b2ed174")); + Arrays.asList("1f1c0605fc8a500c9646132e0d7420a0")); executeTest("testMaxAltAlleles", spec); } @@ -236,7 +236,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseBPResolutionString("-stand_call_conf 300 -stand_emit_conf 100"), 1, - Arrays.asList("1d98fb542a39090db3a8f89ae232e1e5")); + Arrays.asList("0283e784ed49bc2dce32a26137c43409")); executeTest("testStandardConf", spec); } @@ -259,7 +259,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { final WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V " + gVCF.getAbsolutePath(), b37KGReference), 1, - Arrays.asList("d8eb4a64a2ae7e7dad1efc4fe8b4b3ed")); + Arrays.asList("34d76dc8dabc6a97e6d8f5365d7531e5")); spec.disableShadowBCF(); //TODO: Remove when BaseTest.assertAttributesEquals() works with SAC executeTest("testStrandAlleleCountsBySample", spec); } @@ -276,7 +276,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:combined2 " + privateTestDir + "combine.single.sample.pipeline.combined.vcf" + " --uniquifySamples", b37KGReference), 1, - Arrays.asList("1c552a9d76a1bbba4b92a94532f54a1a")); + Arrays.asList("16d7374502fa3cf99863d15d31b5ef86")); executeTest("testUniquifiedSamples", spec); } @@ -448,7 +448,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { } - private static final String simpleSpanningDeletionsMD5 = "85c14341171548997e4503f7b5a9253f"; + private static final String simpleSpanningDeletionsMD5 = "4629c2f02ff58c111828269091cded82"; @Test(enabled = true) public void testSpanningDeletionsMD5() { @@ -478,7 +478,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.1.g.vcf -V " + privateTestDir + "spanningDel.2.g.vcf -V " + privateTestDir + "spanningDel.3.g.vcf", 1, - Arrays.asList("6c5761ffb7a0c5252f3f5048d52f500e")); + Arrays.asList("7fe5364565585d31a0bb6a9dfa4a01d4")); spec.disableShadowBCF(); executeTest("testMultipleSpanningDeletionsMD5", spec); } @@ -489,7 +489,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.delOnly.g.vcf", 1, - Arrays.asList("c8414446dbac9a3639bfc2f347cc2c1d")); + Arrays.asList("057f9368f380bf3c12b539a749deac61")); spec.disableShadowBCF(); executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec); } @@ -500,7 +500,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "spanningDel.depr.delOnly.g.vcf", 1, - Arrays.asList("d1d8c3db65905b4ef79f960f9565ca94")); + Arrays.asList("e8f5186718050fe0784416e41425563f")); spec.disableShadowBCF(); executeTest("testSpanningDeletionDoesNotGetGenotypedWithNoOtherAlleles", spec); } @@ -523,7 +523,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "ad-bug-input.vcf", 1, - Arrays.asList("a8dcb9024e3701449ec2a1fe75e0d057")); + Arrays.asList("5ed5cb6aac68aa8943dc45b8b90eb508")); spec.disableShadowBCF(); executeTest("testBadADPropagationHaploidBugTest", spec); } @@ -534,7 +534,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "261_S01_raw_variants_gvcf.vcf", 1, - Arrays.asList("01a9eee63801d46de8fcf1d6f80f8359")); + Arrays.asList("37eec6aedd26aa3430a15d90d7f8a011")); spec.disableShadowBCF(); executeTest("testSAC", spec); } @@ -545,7 +545,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { "-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference + " -V " + privateTestDir + "tetraploid-multisample-sac.g.vcf", 1, - Arrays.asList("8c79a16f6a524d49ff402b8c0b39b396")); + Arrays.asList("76532a74d4ba49f23362c149ad31a229")); spec.disableShadowBCF(); executeTest("testSACMultisampleTetraploid", spec); } @@ -556,8 +556,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { baseTestString(" -V " + privateTestDir + "set.zero.RGQs.no.call.sample1.g.vcf" + " -V " + privateTestDir + "set.zero.RGQs.no.call.sample2.g.vcf" + " -L chr16:1279274-1279874 -allSites", hg19ReferenceWithChrPrefixInChromosomeNames), - 1, - Arrays.asList("6505d305441b4e6ff975a40ef5d352b5")); + Arrays.asList("b7106be316e43ca04204b78038f65c9f")); executeTest("testSetZeroRGQsToNoCall", spec); } @@ -565,7 +564,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testAlleleSpecificAnnotations() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V " + privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("d4dd179d8a53c4a550d4a22cc9ef1aa8")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("89712a9fe5b6db16be2257be2b0b4759")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations", spec); } @@ -574,7 +573,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testASMateRankSumAnnotation() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -A AS_MQMateRankSumTest --disableDithering -V " + privateTestDir + "NA12878.AS.MateRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.MateRankSum.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("515771fa88b0c4bc2a40e9c233806fb1")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("8e41a139600ab58a67910cdc60053726")); spec.disableShadowBCF(); executeTest("testASMateRankSumAnnotation", spec); } @@ -583,7 +582,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testASInsertSizeRankSumAnnotation() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V " + privateTestDir + "NA12878.AS.InsertSizeRankSum.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.InsertSizeRankSum.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("c8a096f2533d06c28ec115a24ffb7ca0")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("b1334fbfbf21934aac1c1eda0b5062d5")); spec.disableShadowBCF(); executeTest("testASInsertSizeRankSumAnnotation", spec); } @@ -596,7 +595,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testAlleleSpecificAnnotations_oneSample() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V " + privateTestDir + "NA12878.AS.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("558486182a84d0a274534fc00fee326e")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("7d86260e91fe74588e01339a2064b59c")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations_oneSample", spec); } @@ -606,7 +605,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testAlleleSpecificAnnotations_elevenSamples() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V " + privateTestDir + "multiSamples.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("84b5723c9c8eeb5549aaceb4fd4053b5")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("a889fe6775575513e84905b4fa98f8b3")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations_elevenSamples", spec); } @@ -615,7 +614,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testMonomorphicVCwithAlt() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -G AS_Standard -o %s --no_cmdline_in_header --disableDithering -V " + privateTestDir + "monomorphicGVCwithAlt.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("ddf0a386c007b797fce3eb4ddc204216")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("8bf329a40637623515972dcc0e09a49e")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations", spec); } @@ -624,7 +623,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { public void testFractionInformativeReads() { final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -G AS_Standard -o %s --no_cmdline_in_header -A FractionInformativeReads --disableDithering -V " + privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.chr20snippet.g.vcf"; - final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("70fda103f68709e32d691393e9228a9b")); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Collections.singletonList("b338bf1807791b23255b8cb1947c01b2")); spec.disableShadowBCF(); executeTest("testAlleleSpecificAnnotations", spec); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java index 368f97751..1bcbc50e3 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java @@ -136,7 +136,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forHardLeftAlignVariantsTest.vcf --no_cmdline_in_header -split", 1, - Arrays.asList("1158324223c312e4767fcefe9dde2fe1")); + Arrays.asList("58c09033814d41fab5da4c152eab7fa2")); executeTest("test left alignment with hard multiple alleles", spec); } @@ -145,7 +145,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forHardLeftAlignVariantsTest.vcf --dontTrimAlleles --no_cmdline_in_header -split", 1, - Arrays.asList("923cb1d06e2d0d9a98cda8f8f637d108")); + Arrays.asList("6d22a6b78d24ee2329b91f27a91751cf")); executeTest("test left alignment with hard multiple alleles, don't trim", spec); } @@ -154,7 +154,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "multiallele-gt.vcf --no_cmdline_in_header -split", 1, - Arrays.asList("f7be485b0cc7b8db75b7139f31c0708d")); + Arrays.asList("0acb354a2c28e250ef2853c1e0a0fafb")); executeTest("test left alignment of multiple alleles with genoptypes", spec); } @@ -163,7 +163,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "multiallele-gt-het-noref.vcf --no_cmdline_in_header -split", 1, - Arrays.asList("cd686641ab7fe491a0acc7ff07535192")); + Arrays.asList("a335913de938082061d6bbb863626ee2")); executeTest("test left alignment of multiple alleles with genoptypes, including het-noref", spec); } @@ -172,7 +172,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "multiallele-gt.vcf --no_cmdline_in_header -split -keepOriginalAC", 1, - Arrays.asList("5da4ca9705fbb63446c1d317f7b6cae0")); + Arrays.asList("67657ee509665fd0d7a2c9024981ba92")); executeTest("test left alignment of multiple alleles with genoptypes, keep original AC", spec); } } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java index 59f1ea955..b434d97d3 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java @@ -369,7 +369,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants --keepOriginalDP -R " + b37KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header", 1, - Arrays.asList("ce5168e2eadee2550188892b1ea444be") + Arrays.asList("9ad02f0df308eecb0634b3cd386956e9") ); executeTest("testKeepOriginalDP--" + testFile, spec); @@ -395,7 +395,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants -R " + b37KGReference + " --variant " + testFile + " -o %s --no_cmdline_in_header", 1, - Arrays.asList("cc33eb41a821d9aebdfb99d309854db0") + Arrays.asList("c78a65b41edbdd386211042e8f65220b") ); executeTest("testNoGTs--" + testFile, spec); @@ -408,7 +408,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header -sf " + samplesFile + " --excludeNonVariants -trimAlternates --variant " + testfile, 1, - Arrays.asList("b86340de516d6c37cc3a2eeb3bfb4821") + Arrays.asList("c963ca96d543ecccab8055295d2a4dab") ); executeTest("test select from multi allelic with excludeNonVariants --" + testfile, spec); } @@ -420,7 +420,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header " + "-sn SAMPLE-CC -sn SAMPLE-CT -sn SAMPLE-CA --excludeNonVariants --variant " + testfile, 1, - Arrays.asList("7807bb2bf8c70963f65a97f30c8deb39") + Arrays.asList("7f5484a74ab648608228eafea96f8ad3") ); executeTest("test multi allelic annotation ordering --" + testfile, spec); } @@ -471,19 +471,19 @@ public class SelectVariantsIntegrationTest extends WalkerTest { final String testFile = privateTestDir + "forHardLeftAlignVariantsTest.vcf"; final String cmd = "-T SelectVariants -R " + b37KGReference + " -sn NA12878 -env -trimAlternates " + "-V " + testFile + " -o %s --no_cmdline_in_header"; - WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("354cd7aa25791465d0f4c7d53b81a3a3")); + WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("21d83006b012eeea84c6612976348d3c")); executeTest("testAlleleTrimming", spec); } @DataProvider(name="unusedAlleleTrimmingProvider") public Object[][] unusedAlleleTrimmingProvider() { return new Object[][] { - { privateTestDir+"forHardLeftAlignVariantsTest.vcf", "-trimAlternates", "354cd7aa25791465d0f4c7d53b81a3a3"}, - { privateTestDir+"forHardLeftAlignVariantsTest.vcf", "", "5e81af1825aa207b0a352f5eeb5db700"}, - { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT", "339cca608ff18a355abc629bca448043"}, - { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env", "3e8e2ebbc576ceee717a7ce80e23dd35"}, - { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -trimAlternates", "2cbf4c8c991777254145aacf19cba508"}, - { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env -trimAlternates", "14538e17d5aca22c655c42e130f8cebc"} + { privateTestDir+"forHardLeftAlignVariantsTest.vcf", "-trimAlternates", "21d83006b012eeea84c6612976348d3c"}, + { privateTestDir+"forHardLeftAlignVariantsTest.vcf", "", "8fc0c8a7de6bb579e1534b936f844090"}, + { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT", "595392b623b0869f1d87e46edf3de122"}, + { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env", "bba873b8eeeb4c01199140c37deb6f6b"}, + { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -trimAlternates", "93858f706dac876a8581f6b89bb85cc5"}, + { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env -trimAlternates", "5d831401367eb8b0ab49ffa34e0dd278"} }; } @@ -655,7 +655,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants -R "+b37KGReference + " -mv -mvq 0 --variant " + testFile + " -ped " + pedFile + " -o %s --no_cmdline_in_header", 1, - Arrays.asList("f7fe7cbc84b3f2dfadcc40e19eeeb1f9")); + Arrays.asList("c68779547b28dfef39792598df8a93e9")); executeTest("testMendelianViolationSelection--" + testFile, spec); } @@ -668,7 +668,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants -R "+b37KGReference + " -mv -mvq 0 -invMv --variant " + testFile + " -ped " + pedFile + " -o %s --no_cmdline_in_header", 1, - Arrays.asList("865418a69ee57be4432f248c027e6aff")); + Arrays.asList("0ac6fda76228080bdb39c0e698440718")); executeTest("testInvertMendelianViolationSelection--" + testFile, spec); } @@ -758,7 +758,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header -trimAlternates", 1, - Arrays.asList("c9d297e7758bf5681270029401cc97c2")); + Arrays.asList("d3bb7ea37a7c9dce8b34bf2020961619")); spec.disableShadowBCF(); executeTest("testSACSimpleDiploid", spec); } @@ -770,7 +770,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T SelectVariants -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header -sn NA12891 -trimAlternates", 1, - Arrays.asList("a8c23f4d6f93806a34d432dd2c7a0449")); + Arrays.asList("67a92b4d4174ff41f6f88ddf5ab6e422")); spec.disableShadowBCF(); executeTest("testSACDiploid", spec); } diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java index 396805970..45677ffee 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java @@ -95,12 +95,12 @@ public class SelectVariantsParallelIntegrationTest extends WalkerTest { { // new tests on b37 using testdir VCF final String testfile = privateTestDir + "NA12878.hg19.example1.vcf"; final String args = "-select 'DP > 30' -V " + testfile; - new ParallelSelectTestProvider(b37KGReference, args, "b899cebdd30e6641437489b746301797", nt); + new ParallelSelectTestProvider(b37KGReference, args, "64f9258e9e3024b6361abbeeeefafee9", nt); } { // AD and PL decoding race condition final String testfile = privateTestDir + "race_condition.vcf"; final String args = "-env -trimAlternates -sn SAMPLE -L 1:1-10,000,000 -V " + testfile; - new ParallelSelectTestProvider(b37KGReference, args, "ace613ed2e4929f448d30d85110d6ced", nt); + new ParallelSelectTestProvider(b37KGReference, args, "f289f22aacf1a5638a9fb6b32c5cf6fb", nt); } } diff --git a/public/external-example/pom.xml b/public/external-example/pom.xml index 17919f365..9aa973f0a 100644 --- a/public/external-example/pom.xml +++ b/public/external-example/pom.xml @@ -136,7 +136,7 @@ org.apache.maven.plugins maven-shade-plugin - 2.1 + 2.4.3 ${gatk.shade.phase} diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java index df03b0b33..aa04e905f 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java @@ -758,8 +758,8 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { @DataProvider(name = "vcfFeaturesData") public Object[][] getVCFFeaturesData() { return new Object[][]{ - {"--sites_only", "6ef742ee6d9bcbc7b23f928c0e8a1d0e"}, - {"--bcf", "cdea454ac0af9e9228147f9c2ed1e0a6"} + {"--sites_only", "99c07e55fc44694087af6a7d4795e1be"}, + {"--bcf", "b300dd7a1300c55640d9f2e42520d086"} }; } @@ -775,8 +775,8 @@ public class EngineFeaturesIntegrationTest extends WalkerTest { @DataProvider(name = "vcfFormatHandlingData") public Object[][] getVCFFormatHandlingData() { return new Object[][]{ - {true, "870f39e19ec89c8a09f7eca0f5c4bcb9"}, - {false, "baf9a1755d3b4e0ed25b03233e99ca91"} + {true, "7517264dd6eb0c1ac5ca8dfd103c94fb"}, + {false, "4c69e6ae1d506ba3c029de3229de407b"} }; } diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java index 62d358f1e..244f67daf 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java @@ -41,16 +41,16 @@ public class CramIntegrationTest extends WalkerTest { return new Object[][] { {"PrintReads", "exampleBAM.bam", "", "cram", ""}, // Bypass MD5 check since the CRAM header stores the file name {"PrintReads", "exampleCRAM.cram", "", "cram", ""}, - {"PrintReads", "exampleCRAM.cram", "", "bam", "247805098718dd74b8a871796424d359"}, - {"PrintReads", "exampleCRAM.cram", " -L chr1:200", "bam", "a5b26631cd89f86f6184bcac7bc9c9ca"}, + {"PrintReads", "exampleCRAM.cram", "", "bam", "e7834d5992a69143d7c463275213bbf8"}, + {"PrintReads", "exampleCRAM.cram", " -L chr1:200", "bam", "d362fbf30a2c77a2653f1c8eb2dd8fc1"}, {"CountLoci", "exampleCRAM.cram", "", "txt", "ade93df31a6150321c1067e749cae9be"}, {"CountLoci", "exampleCRAM.cram", " -L chr1:200", "txt", "b026324c6904b2a9cb4b88d6d61c81d1"}, {"CountReads", "exampleCRAM.cram", "", "txt", "4fbafd6948b6529caa2b78e476359875"}, {"CountReads", "exampleCRAM.cram", " -L chr1:200", "txt", "b026324c6904b2a9cb4b88d6d61c81d1"}, - {"PrintReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "bam", "24dbd14b60220461f47ec5517962cb7f"}, + {"PrintReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "bam", "a11bd125b69f651aaa2ae68c8ccab22f"}, {"CountLoci", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "txt", "26ab0db90d72e28ad0ba1e22ee510510"}, {"CountReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "txt", "6d7fce9fee471194aa8b5b6e47267f03"}, - {"PrintReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "bam", "84bee5063d8fa0d07e7c3ff7e825ae3a"}, + {"PrintReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "bam", "9e3e8b5a58dfcb50f5b270547c01d56a"}, {"CountLoci", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "txt", "26ab0db90d72e28ad0ba1e22ee510510"}, {"CountReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "txt", "6d7fce9fee471194aa8b5b6e47267f03"}, }; diff --git a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java index 0f4789cfe..6ba25ec8e 100644 --- a/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java +++ b/public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java @@ -89,7 +89,7 @@ public class IntervalIntegrationTest extends WalkerTest { File baseOutputFile = createTempFile("testMultipleIntervalInclusionOnCRAM", ".cram"); spec.setOutputFileLocation(baseOutputFile); spec.addAuxFile("", createTempFileFromBase(baseOutputFile.getAbsolutePath())); // Bypass MD5 check since the CRAM header stores the file name - spec.addAuxFile("ebbe6e311b6bb240554ec96ed9809216", createTempFileFromBase(baseOutputFile.getAbsolutePath() + ".bai")); + spec.addAuxFile("4bd9185ce1c7d2e97e8c131b77f76aef", createTempFileFromBase(baseOutputFile.getAbsolutePath() + ".bai")); executeTest("testMultipleIntervalInclusionOnCRAM", spec); } diff --git a/public/gatk-root/pom.xml b/public/gatk-root/pom.xml index e94b307be..c10fa86ec 100644 --- a/public/gatk-root/pom.xml +++ b/public/gatk-root/pom.xml @@ -24,8 +24,8 @@ UTF-8 ${sourceEncoding} ${sourceEncoding} - 1.7 - 1.7 + 1.8 + 1.8 yyyy/MM/dd HH:mm:ss ${project.basedir}/../.. true @@ -44,8 +44,8 @@ org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.gatk.utils.TestNGTestTransformer,org.broadinstitute.gatk.utils.GATKTextReporter,org.uncommons.reportng.HTMLReporter - 2.0.0 - 2.0.0 + 2.3.0 + 2.3.0 @@ -373,7 +373,7 @@ org.apache.maven.plugins maven-shade-plugin - 2.1 + 2.4.3 org.apache.maven.plugins diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java index fe5f47a58..8f848aa01 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java @@ -66,7 +66,7 @@ public class PrintReadsIntegrationTest extends WalkerTest { // See: GATKBAMIndex.getStartOfLastLinearBin(), BAMScheduler.advance(), IntervalOverlapFilteringIterator.advance() {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, "", "0b58c903f54e8543a8b2ce1439aa769b")}, {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1", "5b1154cc81dba6bcfe76188e4df8d79c")}, - {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.cram"}, " -L 1:10001 -L GL000192.1:500204", "e9caf8a0e6ec947cdcbdfc48a4292eb5")}, + {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.cram"}, " -L 1:10001 -L GL000192.1:500204", "a84efdc3d4a8d6329b5f0b494dd280d2")}, {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L unmapped", "cbd3d1d50c8674f79033aa8c36aa3cd1")}, {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1 -L unmapped", "5b1154cc81dba6bcfe76188e4df8d79c")}, {new PRTest(b37KGReference, new String[]{"oneReadAllInsertion.bam"}, "", "e212d1799ae797e781b17e630656a9a1")}, diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java index 397626023..d7ba67fd0 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VCFIntegrationTest.java @@ -55,7 +55,7 @@ public class VCFIntegrationTest extends WalkerTest { @Test(enabled = true) public void testReadingAndWritingWitHNoChanges() { - String md5ofInputVCF = "3dc9ac85f2c0541df9bc57b4d81f480b"; + String md5ofInputVCF = "a492a97a8d18ace8eeef02a6fe5f179b"; String testVCF = privateTestDir + "vcf4.1.example.vcf"; String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s "; diff --git a/public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.pom b/public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.pom index 92fbea553..fb3102be3 100644 --- a/public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.pom +++ b/public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.pom @@ -80,9 +80,9 @@ com.sun tools - 1.5.0 + 1.8.0 system - ${toolsjar} + ${java.home}/lib/tools.jar