diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FisherStrand.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FisherStrand.java index 1d051d5da..c69d9d290 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FisherStrand.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/FisherStrand.java @@ -105,8 +105,8 @@ public class FisherStrand extends StrandBiasTest implements StandardAnnotation, @Override protected Map calculateAnnotationFromStratifiedContexts(final Map stratifiedContexts, final VariantContext vc){ - final int[][] tableNoFiltering = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), -1, MIN_COUNT); - final int[][] tableFiltering = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), MIN_QUAL_FOR_FILTERED_TEST, MIN_COUNT); + final int[][] tableNoFiltering = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAlternateAlleles(), -1, MIN_COUNT); + final int[][] tableFiltering = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAlternateAlleles(), MIN_QUAL_FOR_FILTERED_TEST, MIN_COUNT); printTable("unfiltered", tableNoFiltering); printTable("filtered", tableFiltering); return pValueForBestTable(tableFiltering, tableNoFiltering); diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.java index 4db1fbaa7..05f6c3253 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandBiasTest.java @@ -192,7 +192,7 @@ public abstract class StrandBiasTest extends InfoFieldAnnotation { */ protected static int[][] getSNPContingencyTable(final Map stratifiedContexts, final Allele ref, - final Allele alt, + final List allAlts, final int minQScoreToConsider, final int minCount ) { int[][] table = new int[2][2]; @@ -207,11 +207,13 @@ public abstract class StrandBiasTest extends InfoFieldAnnotation { if ( p.getQual() < minQScoreToConsider || p.getMappingQual() < minQScoreToConsider ) continue; - updateTable(myTable, Allele.create(p.getBase(), false), p.getRead(), ref, alt); + updateTable(myTable, Allele.create(p.getBase(), false), p.getRead(), ref, allAlts); } - if ( passesMinimumThreshold( myTable, minCount ) ) + if ( passesMinimumThreshold( myTable, minCount ) ) { copyToMainTable(myTable, table); + } + } return table; @@ -232,6 +234,7 @@ public abstract class StrandBiasTest extends InfoFieldAnnotation { final Allele ref = vc.getReference(); final Allele alt = vc.getAltAlleleWithHighestAlleleCount(); + final List allAlts = vc.getAlternateAlleles(); final int[][] table = new int[2][2]; for (final PerReadAlleleLikelihoodMap maps : stratifiedPerReadAlleleLikelihoodMap.values() ) { @@ -239,7 +242,7 @@ public abstract class StrandBiasTest extends InfoFieldAnnotation { for (final Map.Entry> el : maps.getLikelihoodReadMap().entrySet()) { final MostLikelyAllele mostLikelyAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue()); final GATKSAMRecord read = el.getKey(); - updateTable(myTable, mostLikelyAllele.getAlleleIfInformative(), read, ref, alt); + updateTable(myTable, mostLikelyAllele.getAlleleIfInformative(), read, ref, allAlts); } if ( passesMinimumThreshold(myTable, minCount) ) copyToMainTable(myTable, table); @@ -276,12 +279,13 @@ public abstract class StrandBiasTest extends InfoFieldAnnotation { ((int) p.getQual()) < QualityUtils.MIN_USABLE_Q_SCORE); } - private static void updateTable(final int[] table, final Allele allele, final GATKSAMRecord read, final Allele ref, final Allele alt) { + private static void updateTable(final int[] table, final Allele allele, final GATKSAMRecord read, final Allele ref, final List allAlts) { final boolean matchesRef = allele.equals(ref, true); - final boolean matchesAlt = allele.equals(alt, true); + final boolean matchesAlt = allele.equals(allAlts.get(0), true); + final boolean matchesAnyAlt = allAlts.contains(allele); - if ( matchesRef || matchesAlt ) { + if ( matchesRef || matchesAnyAlt ) { final int offset = matchesRef ? 0 : 2; if ( read.isStrandless() ) { diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatio.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatio.java index a8714aca2..fc50fd8dc 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatio.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/StrandOddsRatio.java @@ -114,7 +114,7 @@ public class StrandOddsRatio extends StrandBiasTest implements StandardAnnotatio @Override protected Map calculateAnnotationFromStratifiedContexts(Map stratifiedContexts, final VariantContext vc){ - final int[][] tableNoFiltering = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), -1, MIN_COUNT); + final int[][] tableNoFiltering = getSNPContingencyTable(stratifiedContexts, vc.getReference(), vc.getAlternateAlleles(), -1, MIN_COUNT); final double ratio = calculateSOR(tableNoFiltering); return annotationForOneTable(ratio); } 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 10946a183..eead26186 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 @@ -94,7 +94,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testHasAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("62b6dacf131695f81eccbfe2b1efa128")); + Arrays.asList("4f7ebd519451a776c1aa61493ff33943")); executeTest("test file has annotations, asking for annotations, #1", spec); } @@ -128,7 +128,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testNoAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("6a93ce9ce7bda8de285c9c67d93a0b10")); + Arrays.asList("a4df0258a61170c74c85b3cd516c8153")); executeTest("test file doesn't have annotations, asking for annotations, #1", spec); } @@ -144,7 +144,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { public void testExcludeAnnotations() { WalkerTestSpec spec = new WalkerTestSpec( baseTestString() + " -G Standard -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("9c1aa104de4735be4f7e418014b6536b")); + Arrays.asList("11935c8d5cc5a170d06f0b624b31079f")); executeTest("test exclude annotations", spec); } 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 ff8143a84..a3458305b 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 @@ -74,7 +74,7 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe @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", "71b196793025aa1f99cb8f6f9929d0bf"); + 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", "972c8db4b1cc971bd714fd9c1a72b65a"); } @Test(enabled = true) @@ -84,6 +84,6 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe @Test(enabled = true) public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() { - executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "ea5b4124be3ab15a14b670506a98fd9b"); + executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "6007e0735aa5a680da92396345824077"); } } 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 005387bc9..a2f2262fa 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 @@ -63,7 +63,7 @@ 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","e0060cbb6d5e1af3b274a1e577ba47a9"); + executor.PC_LSV_Test_NoRef("-A AlleleCountBySample -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","fdcdfbed14fb7d703cd991ee7d2821a6"); } @Test(enabled = true) 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 a63af7f44..8475cbd18 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 @@ -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("053913cb29fee481158e1f497a4fffdc")); + Arrays.asList("781d305993aedcc1a4c199a5c63ac54c")); executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2); } 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 b9a2f4fad..b97d108c7 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 @@ -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("37594ce48695bf443c9251f70006f2f0")); + Arrays.asList("837847b512c8f60d7c572dd6a80239d8")); executeTest("test Multiple SNP alleles", 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("ad2be9f69ae8c6776b3bfba069735f50")); + Arrays.asList("0fc44ff26d3f913e7012b000a4de9682")); 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("1cc9c3e45e0296bb33042b409db18ca4")); + Arrays.asList("0dba3bc42c0eb43fea205d528739e9da")); 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 21d1b53fb..9baa01e9b 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 @@ -69,7 +69,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa @Test public void testHaplotypeCallerMultiSampleComplex1() { - HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "f4018f734d64f1f88b3ac4b712311567"); + HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "438933e7d6345b80ff09d9be40bdb42e"); } private void HCTestSymbolicVariants(String bam, String args, String md5) { @@ -93,7 +93,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa @Test public void testHaplotypeCallerMultiSampleGGAComplex() { HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538", - "9de64c4405e0dab99c70c2fae54d4841"); + "a571eb20a5bd17a41b2bd29d00adacc1"); } @Test @@ -111,7 +111,7 @@ 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", - "272e096b7dc2839d11343f35e5d5442d"); + "4c8352d71877a585b8a9b74567be72e6"); } } 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 d00444202..454f3e005 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 @@ -72,8 +72,8 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { // 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, "646ec07bd026da1e72b5e789f5aa3a3d"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "9acbee336e91cbfc1abeebd41bbcc9dd"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "e696ffc927af7f7a36dc7d49dad2c4f8"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "cb598bee733db0461f6a24d265daed45"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "d875592d1fd8057250dafad793768535"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "c223d6fe112d2bb698811600c3b7f6af"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "dacb94af2632e4dc4a1948306dd1661c"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "ef9093880efedac09b78c8fb26420e84"}); @@ -90,9 +90,9 @@ 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, "0a982ba98be666d56452791df32109d7"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "5edcfa5ab96bc327783484c2bbe1c06f"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "b60c70fac56f129af78eaff9ad769557"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "83b96e3e364821c51e6a2c2a64616b24"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "f38178834961798d79e7190dbca004bf"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "762dde6b938dd7bb988f132dd9e4b76f"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "1c3570461e96ad6d66c6abb0fd6ee865"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "66019a0914f905522da6bd3b557a57d1"}); @@ -113,9 +113,9 @@ 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, "7db552463cf779644335bfa09fcddf82"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "90600d209cf778fdfca6a844b8ee4acb"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "db3c99786c5726b20dbfe47e31e50d60"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.NONE, PCRFreeIntervals, "254b4bed7fc8ef5d3c4cb4ebf4ea73c2"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "3f9e2b721c3bc8a6d76aa75bb7544f28"}); + tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "dac179dc0c314e2ac7e39ecb9d334493"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "eac793500fbc7de46259000dbbcdd27d"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "4a431e0e387de3f791318f67d8855b0b"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.GVCF, WExIntervals, "1058d3fe6553e07f002f994759c9647d"}); 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 9d00c1d0c..73e1eda36 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 @@ -90,7 +90,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSample() { - HCTest(CEUTRIO_BAM, "", "5468f50b4ed198e6e9b05a67c3103f72"); + HCTest(CEUTRIO_BAM, "", "bd0c2401f0c0a1f35ca0563a74672116"); } @Test @@ -101,7 +101,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSampleHaploid() { HCTest(CEUTRIO_BAM, - "-ploidy 1", "5046d3f77a56fcc4ccc8a216670effac"); + "-ploidy 1", "1adc1d54b9d0cd493d85c6406ae4d4a7"); } @Test @@ -136,12 +136,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerGraphBasedMultiSampleHaploid() { - HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "1425b46f3cd50040a1272c8775672fc0"); + HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "1cf7e07f659c0aa462e17d2fe2981613"); } @Test public void testHaplotypeCallerGraphBasedMultiSample() { - HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "987c0bb684fc03bcc46cb619e8269fe4"); + HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "f9388b9a6c8bd76862dc716adfb9fd5d"); } @Test @@ -153,19 +153,19 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void testHaplotypeCallerMultiSampleGGA() { 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, - "86a060e9514eaf90c14ddaa7e6d07259"); + "48b11c06729a99d4d54c5aa99663343c"); } @Test public void testHaplotypeCallerMultiSampleGGAHaploid() { 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", - "2d32509234571132ec1fc84ebbc0c48b"); + "5c619c63de7ecf35b29562cf155ff5a0"); } @Test public void testHaplotypeCallerMultiSampleGGATetraploid() { 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", - "b47d6e7b99a8e3413fa94d83a9e760fa"); + "506f0b55414dbdb900c8705609f69d57"); } @Test