From 9c842df3a3fac3a9175c6874a7869b6c4a9535d8 Mon Sep 17 00:00:00 2001 From: Laura Gauthier Date: Wed, 1 Apr 2015 20:17:03 -0400 Subject: [PATCH] Initialize annotations so that --disableDithering actually works --- .../haplotypecaller/HaplotypeCaller.java | 3 ++ ...lexAndSymbolicVariantsIntegrationTest.java | 8 +-- .../HaplotypeCallerGVCFIntegrationTest.java | 48 +++++++++--------- .../HaplotypeCallerIntegrationTest.java | 50 +++++++++---------- 4 files changed, 56 insertions(+), 53 deletions(-) diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java index fe7d7f4b3..9fd6f19de 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java @@ -828,6 +828,9 @@ public class HaplotypeCaller extends ActiveRegionWalker, In vcfWriter.writeHeader(new VCFHeader(headerInfo, sampleSet)); + //now that we have all the VCF headers, initialize the annotations (this is particularly important to turn off RankSumTest dithering in integration tests) + annotationEngine.invokeAnnotationInitializationMethods(headerInfo); + try { // fasta reference reader to supplement the edges of the reference sequence referenceReader = new CachingIndexedFastaSequenceFile(getToolkit().getArguments().referenceFile); 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 d850191f0..136b656f2 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", "", "329e57675a6bab117597f02e3f109095"); + HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "070729585401dda47838911928ffbd2f"); } private void HCTestSymbolicVariants(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", - "4c12c04c34c782b25df78d37868e742d"); + "64421f715e0258defc9efcfef56bdaab"); } @Test public void testHaplotypeCallerMultiSampleGGAMultiAllelic() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337", - "c3fc8876b9b7247f68d758b8a9d60fe5"); + "d2306f6ecfcee9340423ba251e0736a3"); } 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", - "b6576ef09027cb22fa02efda67f7139d"); + "22c4135a87be18940ff622ea7ff9cabc"); } } 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 783c173aa..d18f24d20 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 @@ -75,12 +75,12 @@ 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, "6bfe8418aefa0d5d04bdc8f5f31bbb97"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "8daf142d0f42967b9c59aae4580a18c5"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "1ad6d0d5764e2bc0839af4b79f1bd351"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "00aa548e22334fc121f0c8bee2b05d7a"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "2e64530bfc8cb0a3ad72cc5d11d4694b"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "c236b1f6bfbbbc258d3077d75bb9e552"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "3e440b1b755a21d7bd3ecb093af8f43e"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "ebe078a1e209a5b231aeeba6deebcb8a"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "b6d3cbc4eecb8d295898d94335be54c2"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "6ca1e6cb78157273a4a96ba00e6d4713"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "8645c191ca5dbbae8dcb1389717f985a"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "82f2efd1e9ec6197344d9001b653c7fb"}); return tests.toArray(new Object[][]{}); } @@ -94,13 +94,13 @@ 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, "58abeeaebe89fa5e65bae305f5325a13"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "ba349abd7370252215ebf9e2f246283c"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "c91ff30df7644c3fd5be1355533d9fef"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "04d025e1102bede70d0aa9dc25a89e01"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "a1fcce758ed1bd8ead5030b598fd66eb"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "92c7415dd1a5793161032d839b88fc28"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "b90d7c900ff4a8b5e58d6bd4ad64d750"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "7abdd32f0d11cbf43f5bceeca946a428"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "7e84e4562d8df6e593e58f017f697355"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "307ce5ada7c68e2f08664937bafa6281"}); - final String NA12878bandedResolutionMD5 = "12ce2c83d71ad3db7269c22e65a47ffb"; + final String NA12878bandedResolutionMD5 = "74f728f1c42e3014776197606ddf5116"; 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}); @@ -117,12 +117,12 @@ 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, "e85d74be34c91ab84ea1e6ab6276fbab"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "10dd974f0fd83b8f187e1e9f39ba9237"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "fc7ae67b25ff3e82062b80827bd30f6d"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "87a745384652813976ee37091be45a14"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "a36a9f819e82f7ba6d77ab0b65475fbc"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "bbd62dbeddfdc7353264870e4379cc04"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "f441aab92b07591281fa44748b7bd71e"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "d54d7988552a13de90977ba06b094b74"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "a1e2f104c50c89b9c562045daebf07ca"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "91164cf1247f5b187ad133b280aa1fd2"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "b5c1b79550a8d8bb479895e2be38d945"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "48b737b4f1739edd275eb347c6ca5997"}); return tests.toArray(new Object[][]{}); } @@ -135,12 +135,12 @@ 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, "7f1b295150967269545096564d5ebcca"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "97c5a77752305990420d5d725c70c2cd"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "04b5f3f7a6d1c53beef14c8b295883b1"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "f0b3e472e175ffa4fdf4e04f88e0ade1"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "747204e4bad4620c5298b683813c65ee"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "5a2d32868f007d9d3537ee9d66bd6f38"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "081d943a092b7ad71d1f1fa6ec191ace"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "93f95c7a51741f8e527f1308ffd91052"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "a6e858123e40efece5a9a43a0c05bdb2"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "3d8f4f849df0b9cddb1ec61279e91a83"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "1fbe1435b860400ecae3115141453c9a"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "af7f383fd675d2edfaba7f67a96e67c7"}); return tests.toArray(new Object[][]{}); } 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 799266e9e..2a3d72839 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 @@ -96,82 +96,82 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSample() throws IOException { - HCTest(CEUTRIO_BAM, "", "6d8a38310a086f4d80f25d2b80a309b2"); + HCTest(CEUTRIO_BAM, "", "e8a73b950d027239b780757d898c7334"); } @Test public void testHaplotypeCallerSingleSample() throws IOException { - HCTest(NA12878_BAM, "", "93990d0fed73087294548e71c4e661e9"); + HCTest(NA12878_BAM, "", "c741efeb6f3e412c4e707da3cabee621"); } @Test public void testHaplotypeCallerMultiSampleHaploid() throws IOException { - HCTest(CEUTRIO_BAM, "-ploidy 1", "deac83402aa9ef26fcc42e5ab08140d3"); + HCTest(CEUTRIO_BAM, "-ploidy 1", "5bfcfdea258a3dafa04a99dd2b000c87"); } @Test public void testHaplotypeCallerSingleSampleHaploid() throws IOException { - HCTest(NA12878_BAM, "-ploidy 1", "633d7bd09d202b062854a647ec0f3ce0"); + HCTest(NA12878_BAM, "-ploidy 1", "304d2ade384406342655fdfd445576a3"); } @Test public void testHaplotypeCallerSingleSampleTetraploid() throws IOException { - HCTest(NA12878_BAM, "-ploidy 4", "605498f14cb0b01695109035068a147e"); + HCTest(NA12878_BAM, "-ploidy 4", "1d7aee93f3f2e331fcfa8f765467c66c"); } @Test public void testHaplotypeCallerMinBaseQuality() throws IOException { - HCTest(NA12878_BAM, "-mbq 15", "93990d0fed73087294548e71c4e661e9"); + HCTest(NA12878_BAM, "-mbq 15", "c741efeb6f3e412c4e707da3cabee621"); } @Test public void testHaplotypeCallerMinBaseQualityHaploid() throws IOException { - HCTest(NA12878_BAM, "-mbq 15 -ploidy 1", "633d7bd09d202b062854a647ec0f3ce0"); + HCTest(NA12878_BAM, "-mbq 15 -ploidy 1", "304d2ade384406342655fdfd445576a3"); } @Test public void testHaplotypeCallerMinBaseQualityTetraploid() throws IOException { - HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "605498f14cb0b01695109035068a147e"); + HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "1d7aee93f3f2e331fcfa8f765467c66c"); } @Test public void testHaplotypeCallerGraphBasedSingleSample() throws IOException { - HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "1bd3336031e18c5f06abe760c33dd6be"); + HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "ffd2363d2f7afd694b8e9b23c51b0cea"); } @Test public void testHaplotypeCallerGraphBasedMultiSampleHaploid() throws IOException { - HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "e4a2b4c7adc7d45e2ad2bb61d263b9ac"); + HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "ab1630552bcc0a46431b3f6b7bd50bb5"); } @Test public void testHaplotypeCallerGraphBasedMultiSample() throws IOException { - HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "dc757f57a6ddac88ddceab5be1533f89"); + HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "31a21023efaf6f030478e5542ec652fe"); } @Test public void testHaplotypeCallerSingleSampleWithDbsnp() throws IOException { - HCTest(NA12878_BAM, "-D " + b37dbSNP132, "c68a0659d6de9fb1c2f8e2db4da2f8a2"); + HCTest(NA12878_BAM, "-D " + b37dbSNP132, "1c91ca0c8c04cbce1ace3e9884efd458"); } @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, - "469228219a10f003e558aae66a838e73"); + "2944a830504b4e0b87bb8babc8ea39ae"); } @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", - "535cde1cbefd5b90cae793cbbdce5893"); + "b4da788ff173453d915a807149d9ab5d"); } @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", - "d8705ab5f7d4532c2ff8063244a72788"); + "7a3a8a81c3f984d74e6e3e35f5e62aa3"); } @Test @@ -187,7 +187,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerSingleSampleIndelQualityScores() { - HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "a139a6d01101064a4a093b24449d8b52"); + HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "60df4797f86c1454c0eb76c5eaf2ad38"); } private void HCTestNearbySmallIntervals(String bam, String args, String md5) { @@ -224,7 +224,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerNearbySmallIntervals() { - HCTestNearbySmallIntervals(NA12878_BAM, "", "f6fe463f338f6c5133ba08f1d667c23e"); + HCTestNearbySmallIntervals(NA12878_BAM, "", "7af25494bf2b05cc838ebf7055407c30"); } // This problem bam came from a user on the forum and it spotted a problem where the ReadClipper @@ -234,7 +234,7 @@ 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("869e786baa1a72a08f0a3781804abb3e")); + final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("3f01b3be2004f784a0fddc9e63aeba2a")); executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec); } @@ -296,7 +296,7 @@ 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("2dc24f409ec1aa402ad892dffe317618")); + Arrays.asList("e894e9f50112edad270f36f78e76a8e3")); executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec); } @@ -305,7 +305,7 @@ 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("a2f40779558c1157353c6fcfd3783a76")); + Arrays.asList("9e384f2bd2eb7a6d5ee1685ab5e75501")); executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec); } @@ -313,7 +313,7 @@ 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("9d7ab1c89cce238cff055dc5e9091fb1")); + Arrays.asList("801a3af44153deee939370dcaaa110ab")); executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec); } @@ -322,7 +322,7 @@ 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("b2240a53e441064a1a60e60de4ca49ad")); + Arrays.asList("efac9fd7e7a92e3f130e7db9cbff4a45")); executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec); } @@ -345,7 +345,7 @@ 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("591f8f31524510ace882a860d6850871")); + Arrays.asList("c851be534595a2547a8ebf81f1b923d1")); executeTest("HC calling with aggressive indel error modeling on WGS intervals", spec); } @@ -353,7 +353,7 @@ 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("038db1cf0dadfe746a14e05f5cf3bb8e")); + Arrays.asList("95a3f339a15b1398cfc9f9e933999ea9")); executeTest("HC calling with conservative indel error modeling on WGS intervals", spec); } @@ -446,6 +446,6 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerTandemRepeatAnnotator() throws IOException{ - HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "ab9907559e5b20dadbb6f24d02b8070c"); + HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "481787c9275ab9f2e2b53025805472b7"); } }