From 22d94a70962ea5c4fe87a4579ced9501c77807bb Mon Sep 17 00:00:00 2001 From: Ron Levine Date: Mon, 14 Nov 2016 12:03:54 -0500 Subject: [PATCH] Fix adapter bounday for positive strand --- .../walkers/bqsr/BQSRIntegrationTest.java | 14 ++-- .../ErrorRatePerCycleIntegrationTest.java | 2 +- ...perGeneralPloidySuite1IntegrationTest.java | 6 +- .../UnifiedGenotyperIntegrationTest.java | 26 +++--- ...GenotyperNormalCallingIntegrationTest.java | 6 +- ...lexAndSymbolicVariantsIntegrationTest.java | 2 +- .../HaplotypeCallerGVCFIntegrationTest.java | 44 +++++----- .../HaplotypeCallerIntegrationTest.java | 26 +++--- ...aplotypeCallerParallelIntegrationTest.java | 2 +- .../coverage/CallableLociIntegrationTest.java | 8 +- .../DepthOfCoverageIntegrationTest.java | 26 +++--- .../qc/PileupWalkerIntegrationTest.java | 6 +- .../gatk/utils/sam/ReadUtils.java | 2 +- .../fragments/FragmentUtilsUnitTest.java | 83 ++++++++++--------- .../LocusIteratorByStateUnitTest.java | 4 +- .../gatk/utils/sam/ReadUtilsUnitTest.java | 4 +- 16 files changed, 131 insertions(+), 130 deletions(-) diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java index 4a148698b..8d35c0135 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java @@ -109,13 +109,13 @@ public class BQSRIntegrationTest extends WalkerTest { @DataProvider(name = "BQSRTest") public Object[][] createBQSRTestData() { return new Object[][]{ - {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, "", "fc9df1faf67bab70d32f89bcf4fa39db")}, - {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov ContextCovariate", "73ec38eb23b1739ecef8194cbb1132a3")}, - {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov CycleCovariate", "2d5721193ed4410d1a7d8db467a1fa05")}, - {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --indels_context_size 4", "16df7f1745f17f190c9fc33c475b91d8")}, - {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --low_quality_tail 5", "01811003ae811ee74c4b8d3eb5e992fe")}, - {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --quantizing_levels 6", "5e0eea6b0b300fbd2edabc3506ad3a60")}, - {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --mismatches_context_size 4", "8500b9747c16cb8eb17082163bdb8069")}, + {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, "", "dde4269a873c6f7a751e775cbc79fdb9")}, + {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov ContextCovariate", "fae427cb969638060e2294540e120dfc")}, + {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --no_standard_covs -cov CycleCovariate", "651be7dcd798c71ceaefb773ed792193")}, + {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --indels_context_size 4", "f5fd024e900d0d77c681483da1e5dfd5")}, + {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --low_quality_tail 5", "751189ec8cd406628cf4e698c69e8d11")}, + {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --quantizing_levels 6", "b921c36eb7f5be8f8b91b651247a83d7")}, + {new BQSRTest(hg18Reference, HiSeqBam, HiSeqInterval, " --mismatches_context_size 4", "6c3c6176eb6214dc7ef121fa11916e5d")}, {new BQSRTest(b36KGReference, SimpleCigarMatchMismatchBam, SimpleCigarMatchMismatchInterval, "", "56dfb2918a4cdae3ef9d705a43e85194")}, {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", "", "0b5a8e259e997e4c7b5836d4c28e6f4d")}, {new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-10,200,000", "", "281682124584ab384f23359934df0c3b")}, diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java index 82b842604..f619036e6 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java @@ -62,7 +62,7 @@ public class ErrorRatePerCycleIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-T ErrorRatePerCycle -R " + b37KGReference + " -I " + b37GoodBAM + " -L 20:10,000,000-10,100,000 -o %s", 1, - Arrays.asList("6191340f0b56ee81fb248c8f5c913a8e")); + Arrays.asList("a83453820b7afb5ee79856093d62901f")); executeTest("ErrorRatePerCycle:", spec); } } \ No newline at end of file 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 8e9027de7..9382cbe2a 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", "853b47780322b8133577aea528b9fd77"); + executor.PC_LSV_Test_short("-A AlleleCountBySample -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES", "LSV_SNP_ACS", "SNP", "90ed6f1c268b9c57ecb52b35a88b9368"); } @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", "ee5a2f8954f38d6e5d44fe50b22e43a1"); + 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", "5ad4dd6b0c3c170ba44fdad6d4fa58cf"); } @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", "5cb3fe396302f3d4a4a9b7b3cc1877cc"); + 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", "d26b0ba07e056b73fe4cfe873636d0d6"); } @Test(enabled = true) 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 18f091d4c..6c7c633b3 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("52a3064863b97e43d8df878edc29275c")); + Arrays.asList("d0499af17dc66e77849e547bc5a182ff")); executeTest("test min_base_quality_score 26", 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("2f2d7dd623446fc3cae62a44a016c16d")); + Arrays.asList("5f69de274c0705cf1cb9387651df98bf")); executeTest("test NDA", spec); } @@ -124,17 +124,17 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testOutputParameterSitesOnly() { - testOutputParameters("-sites_only", "3c0e109190cfbe41d24e7726cc8fe6e3"); + testOutputParameters("-sites_only", "4355f5b6fd8cd769a479677f1255bee5"); } @Test public void testOutputParameterAllConfident() { - testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "06386b0a4495583aa924e5addd56c5dc"); + testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "182af9490667cb6ce1415305de4f3fdd"); } @Test public void testOutputParameterAllSites() { - testOutputParameters("--output_mode EMIT_ALL_SITES", "b8b21ad6a2ff1f908e8e0073b57ba0e0"); + testOutputParameters("--output_mode EMIT_ALL_SITES", "524e85c225ce330fd094de93f078fa56"); } 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("5c7d237e666439edb0ef8c697e37933c")); + Arrays.asList("c794c7681856c1ec3c3429dbd9e5dc75")); 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("24b550bbc3c9f0577e069b3fd3122d52")); + Arrays.asList("39d15f041a0c86058f46f23960bb129b")); 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("f60b6705daec1059ce3e533bf8e44c89")); + Arrays.asList("00bff7a5dc584b5b6931a826eae6b013")); 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("ae778a64323abe0da5194f0b936f48aa")); + Arrays.asList("afcb9c4fd4a0e9ba4694d911bc75a7b2")); // 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, "7bbba110f720fc8c115fe2d53b34d693" ); + testHeterozosity( 0.01, "8abbec54f4bf82d7c48bf40b43fdaa91" ); } @Test public void testHeterozyosity2() { - testHeterozosity( 1.0 / 1850, "767e8eacd216ac7437456e690287cecf" ); + testHeterozosity( 1.0 / 1850, "4221b00b0d10c005fb69fd2a298e384c" ); } 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("6464138c0bd2ab2cac06773f19e37a4c")); + Arrays.asList("482f6b310e59d05508811932ec21c801")); 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("8885492069487efcf67e13608e762acd")); + Arrays.asList("c99b7dbe881aa3274cb9876e495cf8f3")); executeTest(String.format("test calling with BAQ"), 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 0ec669c01..11e910752 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 @@ -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("e5c34be242c9b6bec687c7384ef83cb2")); + Arrays.asList("5919639094d775cdd6b6965e1210753a")); 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("fca6cacfb523114a3fb93772569deb08")); + Arrays.asList("3304a20af6745beeec07ef2c47d617d3")); executeTest("test Multiple SNP alleles", 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("c41ff9e1e3cfb6bd45d772787dd8e2d3")); + Arrays.asList("5dc0ccd66105e0f12c72987d56c85235")); 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 39d2cf8c8..755e4af49 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", "", "79567a4e4307495e880e9782b3a88f7d"); + HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "4f30d9c9f1eb4529071b7060e497235d"); } private void HCTestSymbolicVariants(String bam, String args, String md5) { 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 1b9f72c7a..334e38907 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 @@ -87,11 +87,11 @@ 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, "a4286ada7f9efaa83f7a8f0e72c3cb45"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "cf5545094ebb264fa8eb879fd848d9ef"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "0086cc735cf792a9f236ec057c73b750"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "c87ff5438d4a6559b33970f1294f77c6"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "2cc9f789100e138ffc0c383b12a1322a"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "44cc8f78e28d905efc30c218d821cc7c"}); 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.BP_RESOLUTION, WExIntervals, "39b2ad53ffdfcbaa4af3454c321daaa7"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "861fa31b135d200f765914126b422cf4"}); return tests.toArray(new Object[][]{}); @@ -106,11 +106,11 @@ 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, "3ae2c7e570855f6d6ca58ddd1089a970"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "1961007bd98a174a4a1b3e76a9c2f156"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "b34b0b61583628fbd51221627adcdb81"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "cbf988eca3f368ef5b17108595cd8c5e"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "d146c8dc4fc0605b3776ab5fec837d53"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "c317193f0d1c9a8168f2625c8bf1dd2b"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "63ff771eed3e62340c8938b4963d0add"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "1122a0b3849f42d1c4a654f93b660e1b"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "c6c19ff9dc229f6af6080a175267344c"}); final String NA12878bandedResolutionMD5 = "7240907ec3dc2ed49b55c9956546ba13"; tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, NA12878bandedResolutionMD5}); @@ -129,11 +129,11 @@ 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, "8bf132d73cf6b0851ae73c6799f19ba9"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "654c8264cfcbcb71da479761912fbd71"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "4959f20a8bd3327760d94ccc40157f81"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "85749762dac9684f4c8f9da18a210109"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "6c727b804084a2324ecd1c98b72734b9"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "190cef14684c95ba290d7a5fa13fdc07"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "6ad7855dbf6dda2060aa93a3ee010b3e"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "50e628de2a79cd6887af020b713ca3b8"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "21c87a3edafee3cb080169963e1e2623"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "e48bbcf453e63a6ea5eeda05f6865f94"}); return tests.toArray(new Object[][]{}); @@ -147,11 +147,11 @@ 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, "6662cfc41393257dfd6c39f1af1e3843"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "dd9fdcae44ab316c04650bf50c38e4b2"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "cb318100ae15cb3dcc342b6142ac6361"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "532188686870c7edd2ea3352ea93f66a"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "48521b89cecceb9846e4dfc0dd415874"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "eaacbeaff99a37ffa07e1f11e7f1deb2"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "af0fe243e3b96e59097187cd16ba1597"}); - tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "8a094080fb25bbcd39325dcdd62bcf65"}); + tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "868a097a8a108f5159dbbabbfdb2e38b"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "685025831ac783784d7838e568e35f46"}); return tests.toArray(new Object[][]{}); @@ -294,7 +294,7 @@ 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("66f242cf3f1f1776c743505b84505f94")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("883fdc6c10fd7cbc1de375ed26ce5734")); spec.disableShadowBCF(); executeTest("testNoCallGVCFMissingPLsBugFix", spec); } @@ -363,7 +363,7 @@ 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", Collections.singletonList("19fc2c5218d907fcdcd36de2afbef19c")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("7c707c66f77482e3f6b2b014b152bbf4")); spec.disableShadowBCF(); executeTest(" testHaplotypeCallerMultiAllelicNonRef", spec); } @@ -372,7 +372,7 @@ 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", Collections.singletonList("b2adc744d9dff2f488149bcc96d6bb6d")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Collections.singletonList("dd0bfade4f0a9f23a500fd23c3a24a29")); spec.disableShadowBCF(); executeTest("testHaplotypeCallerMaxNumPLValues", spec); } @@ -389,7 +389,7 @@ 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("cbd37b492f77c50d2da744d5e00c6f90")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("5ea45f32c09e9f7a4132f98d642f260b")); spec.disableShadowBCF(); executeTest("testHaplotypeCallerMaxNumPLValuesExceededWithWarnLogLevel", spec); // Make sure the "Maximum allowed number of PLs exceeded" messages are in the log @@ -414,7 +414,7 @@ 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("cbd37b492f77c50d2da744d5e00c6f90")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("5ea45f32c09e9f7a4132f98d642f260b")); spec.disableShadowBCF(); executeTest("testHaplotypeCallerMaxNumPLValuesExceededWithDebugLogLevel", spec); // Make sure the "Maximum allowed number of PLs exceeded" messages are in the log @@ -458,7 +458,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { public void testHaplotypeCallerGVCSpanDel() { final String commandLine = String.format("-T HaplotypeCaller -R %s -I %s -L 1:26357667 -ERC GVCF --no_cmdline_in_header -A AS_ReadPosRankSumTest -A ReadPosRankSumTest -variant_index_type %s -variant_index_parameter %d", b37KGReference, privateTestDir + "NexPond-377866-1:26357600-26357700.bam", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("b8f0bb74bc099a8f78d600d88861e1b6")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("bb12cf2dfa6f1fa0692395e295792584")); spec.disableShadowBCF(); executeTest("testHaplotypeCallerGVCSpanDel", spec); } 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 aadd03a32..3f80b779b 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 @@ -107,7 +107,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeBAMOutFlags() throws IOException { - HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "700c5d20e9d9d9a431fcda9bff91f72e", "a0daf5a80158d4a462248415c1e17565"); + HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "2e4cd93b4cad12259728d19a41d2a6ff", "9d6bd79cdae3e3222fa93f542fbca153"); } @Test @@ -118,7 +118,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerSingleSample() throws IOException { - HCTest(NA12878_BAM, "", "c04293cb8466a1a217bce4ef419bdabe"); + HCTest(NA12878_BAM, "", "9f17ce83e639a1bd9b3f2d9fa33b15b2"); } @Test @@ -133,12 +133,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerSingleSampleTetraploid() throws IOException { - HCTest(NA12878_BAM, "-ploidy 4", "5098645e8b570bc4521570654fa91806"); + HCTest(NA12878_BAM, "-ploidy 4", "f993db900080aeb48c43982745e1084d"); } @Test public void testHaplotypeCallerMinBaseQuality() throws IOException { - HCTest(NA12878_BAM, "-mbq 15", "c04293cb8466a1a217bce4ef419bdabe"); + HCTest(NA12878_BAM, "-mbq 15", "9f17ce83e639a1bd9b3f2d9fa33b15b2"); } @Test @@ -148,12 +148,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMinBaseQualityTetraploid() throws IOException { - HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "5098645e8b570bc4521570654fa91806"); + HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "f993db900080aeb48c43982745e1084d"); } @Test public void testHaplotypeCallerGraphBasedSingleSample() throws IOException { - HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "8ab21bd6fb7ef37480f556fd5fa5375c"); + HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "420954190aef671edd02bd3c73e22642"); } @Test @@ -168,7 +168,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerSingleSampleWithDbsnp() throws IOException { - HCTest(NA12878_BAM, "-D " + b37dbSNP132, "ff8e142f491b06e17e64e3a5d59737a7"); + HCTest(NA12878_BAM, "-D " + b37dbSNP132, "9e8513ed4065138bee8dd9363a9fd355"); } @Test @@ -312,7 +312,7 @@ 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("b56895e6d28ea0b9dadeecd0ff61687e")); + Arrays.asList("fc71471b01f93bc531e3cf19cdf78b1f")); executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec); } @@ -321,7 +321,7 @@ 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("7b52164df8bf76d789836f990bd6066a")); + Arrays.asList("bf8bb5d13b01facdf90ec24bfbf82faa")); executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec); } @@ -329,7 +329,7 @@ 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("096826325215f79fe70661d984ae45a4")); + Arrays.asList("ec9a1fb56882c21f3e4793e5f71f4e9e")); executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec); } @@ -338,7 +338,7 @@ 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("ff3b24412090ce7693d66d750ae84ac9")); + Arrays.asList("2ffaf2e9ef293a6d5ce7c00be40edba7")); executeTest("HC calling with dbSNP ID annotation on WEx intervals", spec); } @@ -430,7 +430,7 @@ 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 = "87b687b5476eb38b11db6a156b4066c8"; + final String md5 = "66caceac0a54cdfd847bfdf4226bb36a"; 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)); @@ -484,7 +484,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerTandemRepeatAnnotator() throws IOException{ - HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "2cf4cab0035d09aa0aec6f3faa2c9df6"); + HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "408c6940a090d31c11c171ed5e0e033c"); } @Test diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java index fdc51094c..6cc7f63a8 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java @@ -69,7 +69,7 @@ public class HaplotypeCallerParallelIntegrationTest extends WalkerTest { List tests = new ArrayList<>(); for ( final int nct : Arrays.asList(1, 2, 4) ) { - tests.add(new Object[]{nct, "07f969acede5e0ad7e1e94f4383af2a9"}); + tests.add(new Object[]{nct, "da195c6c4c8e765acb35f08e37132108"}); } return tests.toArray(new Object[][]{}); diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLociIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLociIntegrationTest.java index 1889f6f4d..06d74a636 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLociIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/CallableLociIntegrationTest.java @@ -33,13 +33,13 @@ import java.util.Arrays; public class CallableLociIntegrationTest extends WalkerTest { final static String commonArgs = "-R " + b36KGReference + " -T CallableLoci -I " + validationDataLocation + "/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s"; - final static String SUMMARY_MD5 = "a6f5963669f19d9d137ced87d65834b0"; + final static String SUMMARY_MD5 = "27aea9e76af554db5e886dacb0d3edd0"; @Test public void testCallableLociWalkerBed() { String gatk_args = commonArgs + " -format BED -L 1:10,000,000-11,000,000 -summary %s"; WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2, - Arrays.asList("9b4ffea1dbcfefadeb1c9fa74b0e0e59", SUMMARY_MD5)); + Arrays.asList("908a22c0bfe81e6f4c571de290e48d03", SUMMARY_MD5)); executeTest("formatBed", spec); } @@ -47,7 +47,7 @@ public class CallableLociIntegrationTest extends WalkerTest { public void testCallableLociWalkerPerBase() { String gatk_args = commonArgs + " -format STATE_PER_BASE -L 1:10,000,000-11,000,000 -summary %s"; WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2, - Arrays.asList("d6505e489899e80c08a7168777f6e07b", SUMMARY_MD5)); + Arrays.asList("11e7fdd39bb83eec44ca452faf0dc825", SUMMARY_MD5)); executeTest("format_state_per_base", spec); } @@ -63,7 +63,7 @@ public class CallableLociIntegrationTest extends WalkerTest { public void testCallableLociWalker3() { String gatk_args = commonArgs + " -format BED -L 1:10,000,000-11,000,000 -minDepth 10 -maxDepth 100 --minBaseQuality 10 --minMappingQuality 20 -summary %s"; WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2, - Arrays.asList("7f79ad8195c4161060463eeb21d2bb11", "7ee269e5f4581a924529a356cc806e55")); + Arrays.asList("5e5ee8850815810680f205a520d05a0f", "441b7c31bed5c30705f9565b708ecace")); executeTest("formatBed lots of arguments", spec); } } diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java index d064328c0..9515978cf 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java @@ -84,25 +84,25 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest { spec.setOutputFileLocation(baseOutputFile); // now add the expected files that get generated - spec.addAuxFile("0f9603eb1ca4a26828e82d8c8f4991f6", baseOutputFile); - spec.addAuxFile("51e6c09a307654f43811af35238fb179", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts")); + spec.addAuxFile("423571e4c05e7934322172654ac6dbb7", baseOutputFile); + spec.addAuxFile("9df5e7e07efeb34926c94a724714c219", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts")); spec.addAuxFile("3bf1d7247ea68d1afb35c2032c68dbdf", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions")); spec.addAuxFile("9cd395f47b329b9dd00ad024fcac9929", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics")); - spec.addAuxFile("681dcbedcf7ca14bb44134abd1d8da3f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary")); - spec.addAuxFile("0f58e7f0909b84897fea5daebd9d2948", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics")); - spec.addAuxFile("2832e48c12b1d8811ccd319a8ffb8dc1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary")); - spec.addAuxFile("a836b92ac17b8ff9788e2aaa9116b5d4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts")); + spec.addAuxFile("31f9aa7ddad7809bc2f6675014dd4eaf", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary")); + spec.addAuxFile("958667ce6f92106a32a77098c1533d4f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics")); + spec.addAuxFile("5e87db30702e44031920f7417cfac844", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary")); + spec.addAuxFile("b82846df660f0aac8429aec57c2a62d6", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts")); spec.addAuxFile("22fee04ffca7fa489ae2e66309de12e4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions")); spec.addAuxFile("7b9d0e93bf5b5313995be7010ef1f528", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics")); - spec.addAuxFile("2de22ad840bf40621e51316728a32fe9", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary")); - spec.addAuxFile("6c84a067016c63e8c2face2de800acc7", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics")); - spec.addAuxFile("2629883b99428f51e2d90d820b45504a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary")); - spec.addAuxFile("6909d50a7da337cd294828b32b945eb8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts")); + spec.addAuxFile("e0f0d44cb4bc0557ee55b8b2aaa0cb9f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary")); + spec.addAuxFile("d69d08fd37f63941eea52d7b66a625df", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics")); + spec.addAuxFile("de1795f42397d1282c012a3b9c396b5c", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary")); + spec.addAuxFile("d53431022f7387fe9ac47814ab1fcd88", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts")); spec.addAuxFile("f6e52c5659f53afdcfc69c25272b9e99", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions")); spec.addAuxFile("df0ba76e0e6082c0d29fcfd68efc6b77", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics")); - spec.addAuxFile("c2fb3a31d02df03c35afbe7f2284ad66", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary")); - spec.addAuxFile("d1b3d08c6e9565a1dab727d089085761", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics")); - spec.addAuxFile("c0fadfcfd88cec81ba0d57b33bdec277", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary")); + spec.addAuxFile("a72253b8e06dc6c653355b20e56e2f6e", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary")); + spec.addAuxFile("23ca7c647e3e53eb9b713d46b92bf6a2", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics")); + spec.addAuxFile("cd4ef2d43dc98f1bd7e6db532c60b3d1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary")); execute("testBaseOutputNoFiltering",spec); } diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java index a52059bb5..db75bf6f6 100644 --- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java +++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/qc/PileupWalkerIntegrationTest.java @@ -77,10 +77,10 @@ public class PileupWalkerIntegrationTest extends WalkerTest { @DataProvider(name="GATKBAMIndexTest") public Object[][] makeMyDataProvider() { List tests = new ArrayList(); - tests.add(new Object[]{"-L 20:1-76,050","8702701350de11a6d28204acefdc4775"}); + tests.add(new Object[]{"-L 20:1-76,050","f275a2de053f44db19bc6591fe1c8dae"}); tests.add(new Object[]{"-L 20:10,000,000-10,001,100","818cf5a8229efe6f89fc1cd8145ccbe3"}); - tests.add(new Object[]{"-L 20:62,954,114-63,025,520","22471ea4a12e5139aef62bf8ff2a5b63"}); - tests.add(new Object[]{"-L 20:1-76,050 -L 20:20,000,000-20,000,100 -L 20:40,000,000-40,000,100 -L 20:30,000,000-30,000,100 -L 20:50,000,000-50,000,100 -L 20:62,954,114-63,025,520 ","08d899ed7c5a76ef3947bf67338acda1"}); + tests.add(new Object[]{"-L 20:62,954,114-63,025,520","7e3462745d298de3b7493b42d3603392"}); + tests.add(new Object[]{"-L 20:1-76,050 -L 20:20,000,000-20,000,100 -L 20:40,000,000-40,000,100 -L 20:30,000,000-30,000,100 -L 20:50,000,000-50,000,100 -L 20:62,954,114-63,025,520 ","977298255b04d66c17bb5466da8251f7"}); return tests.toArray(new Object[][]{}); } diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java index afa486cac..72254c884 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/sam/ReadUtils.java @@ -215,7 +215,7 @@ public class ReadUtils { return read.getMateAlignmentStart() - 1; // case 1 (see header) } else { final int insertSize = Math.abs(read.getInferredInsertSize()); // the inferred insert size can be negative if the mate is mapped before the read (so we take the absolute value) - return read.getAlignmentStart() + insertSize + 1; // case 2 (see header) + return read.getAlignmentStart() + insertSize; // case 2 (see header) } } diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java index 1791f2274..d6bbb927e 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/fragments/FragmentUtilsUnitTest.java @@ -54,8 +54,8 @@ public class FragmentUtilsUnitTest extends BaseTest { private final static boolean DEBUG = false; private class FragmentUtilsTest extends TestDataProvider { - List statesForPileup = new ArrayList(); - List statesForReads = new ArrayList(); + List statesForPileup = new ArrayList<>(); + List statesForReads = new ArrayList<>(); private FragmentUtilsTest(String name, int readLen, int leftStart, int rightStart, boolean leftIsFirst, boolean leftIsNegative) { @@ -70,8 +70,8 @@ public class FragmentUtilsUnitTest extends BaseTest { boolean posCoveredByRight = pos >= right.getAlignmentStart() && pos <= right.getAlignmentEnd(); if ( posCoveredByLeft || posCoveredByRight ) { - List reads = new ArrayList(); - List offsets = new ArrayList(); + List reads = new ArrayList<>(); + List offsets = new ArrayList<>(); if ( posCoveredByLeft ) { reads.add(left); @@ -174,7 +174,7 @@ public class FragmentUtilsUnitTest extends BaseTest { @DataProvider(name = "MergeFragmentsTest") public Object[][] createMergeFragmentsTest() throws Exception { - List tests = new ArrayList(); + List tests = new ArrayList<>(); final String leftFlank = "CCC"; final String rightFlank = "AAA"; @@ -248,29 +248,29 @@ public class FragmentUtilsUnitTest extends BaseTest { final byte[] commonQuals = Utils.dupBytes((byte)30, common.length()); final String adapter = "NNNN"; - final GATKSAMRecord read1 = makeOverlappingRead(adapter, 30, common, commonQuals, "", 30, 10); - final GATKSAMRecord read2 = makeOverlappingRead("", 30, common, commonQuals, adapter, 30, 10); + final GATKSAMRecord readLeftAdapter = makeOverlappingRead(adapter, 30, common, commonQuals, "", 30, 10); + final GATKSAMRecord readRightAdapter = makeOverlappingRead("", 30, common, commonQuals, adapter, 30, 10); final GATKSAMRecord expectedMerged = makeOverlappingRead("", 30, common, commonQuals, "", 30, 10); - read1.setCigarString("4S" + common.length() + "M"); - read1.setProperPairFlag(true); - read1.setReadPairedFlag(true); - read1.setFirstOfPairFlag(true); - read1.setReadNegativeStrandFlag(true); - read1.setMateNegativeStrandFlag(false); - read1.setMateAlignmentStart(read2.getAlignmentStart()); - read2.setCigarString(common.length() + "M4S"); - read2.setProperPairFlag(true); - read2.setReadPairedFlag(true); - read2.setFirstOfPairFlag(false); - read2.setReadNegativeStrandFlag(false); - read2.setMateNegativeStrandFlag(true); - read2.setMateAlignmentStart(read1.getAlignmentStart()); + readLeftAdapter.setCigarString(adapter.length() + "S" + common.length() + "M"); + readLeftAdapter.setProperPairFlag(true); + readLeftAdapter.setReadPairedFlag(true); + readLeftAdapter.setFirstOfPairFlag(true); + readLeftAdapter.setReadNegativeStrandFlag(true); + readLeftAdapter.setMateNegativeStrandFlag(false); + readLeftAdapter.setMateAlignmentStart(readRightAdapter.getAlignmentStart()); + readRightAdapter.setCigarString(common.length() + "M4S"); + readRightAdapter.setProperPairFlag(true); + readRightAdapter.setReadPairedFlag(true); + readRightAdapter.setFirstOfPairFlag(false); + readRightAdapter.setReadNegativeStrandFlag(false); + readRightAdapter.setMateNegativeStrandFlag(true); + readRightAdapter.setMateAlignmentStart(readLeftAdapter.getAlignmentStart()); - final int insertSize = common.length() - 1; - read1.setInferredInsertSize(-insertSize); - read2.setInferredInsertSize(insertSize); + final int insertSize = common.length(); + readLeftAdapter.setInferredInsertSize(-insertSize); + readRightAdapter.setInferredInsertSize(insertSize); - final GATKSAMRecord actual = FragmentUtils.mergeOverlappingPairedFragments(read1, read2); + final GATKSAMRecord actual = FragmentUtils.mergeOverlappingPairedFragments(readLeftAdapter, readRightAdapter); Assert.assertEquals(actual.getCigarString(), expectedMerged.getCigarString()); Assert.assertEquals(actual.getReadBases(), expectedMerged.getReadBases()); Assert.assertEquals(actual.getReadGroup(), expectedMerged.getReadGroup()); @@ -282,24 +282,25 @@ public class FragmentUtilsUnitTest extends BaseTest { @Test(enabled = true) public void testHardClippingBeforeMergeResultingInCompletelyContainedSecondRead() { final String adapter = "NNNN"; + final int minReadSize = 7; - final GATKSAMRecord read1 = makeOverlappingRead(adapter, 30, Utils.dupString("A", 10), Utils.dupBytes((byte)30, 10), "", 30, 10); - final GATKSAMRecord read2 = makeOverlappingRead("", 30, Utils.dupString("A", 7), Utils.dupBytes((byte)30, 7), adapter, 30, 10); - read1.setCigarString("4S10M"); - read1.setProperPairFlag(true); - read1.setFirstOfPairFlag(true); - read1.setReadNegativeStrandFlag(true); - read1.setMateAlignmentStart(10); - read2.setCigarString("7M4S"); - read2.setProperPairFlag(true); - read2.setFirstOfPairFlag(false); - read2.setReadNegativeStrandFlag(false); + final GATKSAMRecord readLeftAdapter = makeOverlappingRead(adapter, 30, Utils.dupString("A", 10), Utils.dupBytes((byte)30, 10), "", 30, 10); + final GATKSAMRecord readRightAdapter = makeOverlappingRead("", 30, Utils.dupString("A", minReadSize), Utils.dupBytes((byte)30, minReadSize), adapter, 30, 10); + readLeftAdapter.setCigarString(adapter.length() + "S10M"); + readLeftAdapter.setProperPairFlag(true); + readLeftAdapter.setFirstOfPairFlag(true); + readLeftAdapter.setReadNegativeStrandFlag(true); + readLeftAdapter.setMateAlignmentStart(10); + readRightAdapter.setCigarString(minReadSize + "M4S"); + readRightAdapter.setProperPairFlag(true); + readRightAdapter.setFirstOfPairFlag(false); + readRightAdapter.setReadNegativeStrandFlag(false); - final int insertSize = 7 - 1; - read1.setInferredInsertSize(insertSize); - read2.setInferredInsertSize(-insertSize); + final int insertSize = minReadSize; + readLeftAdapter.setInferredInsertSize(insertSize); + readRightAdapter.setInferredInsertSize(-insertSize); - final GATKSAMRecord actual = FragmentUtils.mergeOverlappingPairedFragments(read1, read2); + final GATKSAMRecord actual = FragmentUtils.mergeOverlappingPairedFragments(readLeftAdapter, readRightAdapter); Assert.assertNull(actual); } @@ -356,7 +357,7 @@ public class FragmentUtilsUnitTest extends BaseTest { @DataProvider(name = "AdjustFragmentsTest") public Object[][] createAdjustFragmentsTest() throws Exception { - List tests = new ArrayList(); + List tests = new ArrayList<>(); final String leftFlank = "CCC"; final String rightFlank = "AAA"; diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java index 3fecd369c..70d1308aa 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateUnitTest.java @@ -710,7 +710,7 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { read.setReadNegativeStrandFlag(false); read.setMateNegativeStrandFlag(true); read.setMateAlignmentStart(start - 1); - read.setInferredInsertSize(goodBases - 1); + read.setInferredInsertSize(goodBases); tests.add(new Object[]{0, goodBases, nClips, read}); } } @@ -738,6 +738,6 @@ public class LocusIteratorByStateUnitTest extends LocusIteratorByStateBaseTest { } final int nExpectedPileups = nReadContainingPileups; - Assert.assertEquals(nPileups, nExpectedPileups, "Wrong number of pileups seen"); + Assert.assertEquals(nPileups, nExpectedPileups, "Wrong number of pileups seen for " + read + " with " + nClipsOnLeft + " clipped bases."); } } diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java index 6df455d18..b0677cd8f 100644 --- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java +++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/sam/ReadUtilsUnitTest.java @@ -90,7 +90,7 @@ public class ReadUtilsUnitTest extends BaseTest { read.setReadNegativeStrandFlag(false); read.setMateNegativeStrandFlag(true); boundary = get.getAdaptor(read); - Assert.assertEquals(boundary, myStart + fragmentSize + 1); + Assert.assertEquals(boundary, myStart + fragmentSize); // Test case 2: positive strand, second read read = makeRead(fragmentSize, mateStart); @@ -99,7 +99,7 @@ public class ReadUtilsUnitTest extends BaseTest { read.setReadNegativeStrandFlag(false); read.setMateNegativeStrandFlag(true); boundary = get.getAdaptor(read); - Assert.assertEquals(boundary, myStart + fragmentSize + 1); + Assert.assertEquals(boundary, myStart + fragmentSize); // Test case 3: negative strand, second read read = makeRead(fragmentSize, mateStart);