diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculator.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculator.java index 882627d36..0357999f1 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculator.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalculator.java @@ -48,8 +48,10 @@ package org.broadinstitute.gatk.tools.walkers.genotyper.afcalc; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; -import org.broadinstitute.gatk.utils.MathUtils; import htsjdk.variant.variantcontext.*; +import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculators; +import org.broadinstitute.gatk.utils.MathUtils; +import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils; import java.util.*; @@ -167,9 +169,54 @@ import java.util.*; // fast path for the very common bi-allelic use case return independentResultTrackers.get(0); } else { + final AFCalculationResult combinedAltAllelesResult = combineAltAlleleIndependentExact(vc,defaultPloidy,log10AlleleFrequencyPriors); // we are a multi-allelic, so we need to actually combine the results final List withMultiAllelicPriors = applyMultiAllelicPriors(independentResultTrackers); - return combineIndependentPNonRefs(vc, withMultiAllelicPriors); + return combineIndependentPNonRefs(vc, withMultiAllelicPriors, combinedAltAllelesResult); + } + } + + private AFCalculationResult combineAltAlleleIndependentExact(final VariantContext vc, int defaultPloidy, double[] log10AlleleFrequencyPriors) { + final VariantContext combinedAltAllelesVariantContext = makeCombinedAltAllelesVariantContext(vc); + final AFCalculationResult resultTracker = biAlleleExactModel.getLog10PNonRef(combinedAltAllelesVariantContext, defaultPloidy, vc.getNAlleles() - 1, log10AlleleFrequencyPriors); + return resultTracker; + } + + private VariantContext makeCombinedAltAllelesVariantContext(final VariantContext vc) { + final int nAltAlleles = vc.getNAlleles() - 1; + + if ( nAltAlleles == 1 ) + return vc; + else { + final VariantContextBuilder vcb = new VariantContextBuilder(vc); + final Allele reference = vcb.getAlleles().get(0); + vcb.alleles(Arrays.asList(reference, GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE)); + final int genotypeCount = GenotypeLikelihoodCalculators.genotypeCount(2, vc.getNAlleles()); + final double[] hetLikelihoods = new double[vc.getNAlleles() - 1]; + final double[] homAltLikelihoods = new double[genotypeCount - hetLikelihoods.length - 1]; + final double[] newLikelihoods = new double[3]; + final List newGenotypes = new ArrayList<>(vc.getNSamples()); + for (final Genotype oldGenotype : vc.getGenotypes()) { + final GenotypeBuilder gb = new GenotypeBuilder(oldGenotype); + final List oldAlleles = oldGenotype.getAlleles(); + if (oldAlleles != null) { + final List newAlleles = new ArrayList<>(oldAlleles.size()); + for (int i = 0; i < oldAlleles.size(); i++) { + final Allele oldAllele = oldAlleles.get(i); + if (oldAllele.isReference()) + newAlleles.add(reference); + else if (oldAllele.isNoCall()) + newAlleles.add(Allele.NO_CALL); + else + newAlleles.add(GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE); + } + gb.alleles(newAlleles); + } + if (combineAltAlleleLikelihoods(oldGenotype, genotypeCount, newLikelihoods, hetLikelihoods, homAltLikelihoods)) + gb.PL(newLikelihoods); + newGenotypes.add(gb.make()); + } + return vcb.genotypes(newGenotypes).make(); } } @@ -427,18 +474,17 @@ import java.util.*; * @param sortedResultsWithThetaNPriors the pNonRef result for each allele independently */ protected AFCalculationResult combineIndependentPNonRefs(final VariantContext vc, - final List sortedResultsWithThetaNPriors) { + final List sortedResultsWithThetaNPriors, + final AFCalculationResult combinedAltAllelesResult) { + + int nEvaluations = 0; final int nAltAlleles = sortedResultsWithThetaNPriors.size(); final int[] alleleCountsOfMLE = new int[nAltAlleles]; - final double[] log10PriorsOfAC = new double[2]; final Map log10pRefByAllele = new HashMap(nAltAlleles); // the sum of the log10 posteriors for AF == 0 and AF > 0 to determine joint probs - double log10PosteriorOfACEq0Sum = 0.0; - double log10PosteriorOfACGt0Sum = 0.0; - boolean anyPoly = false; for ( final AFCalculationResult sortedResultWithThetaNPriors : sortedResultsWithThetaNPriors ) { final Allele altAllele = sortedResultWithThetaNPriors.getAllelesUsedInGenotyping().get(1); final int altI = vc.getAlleles().indexOf(altAllele) - 1; @@ -446,16 +492,6 @@ import java.util.*; // MLE of altI allele is simply the MLE of this allele in altAlleles alleleCountsOfMLE[altI] = sortedResultWithThetaNPriors.getAlleleCountAtMLE(altAllele); - // the AF > 0 case requires us to store the normalized likelihood for later summation - if ( sortedResultWithThetaNPriors.getLog10PosteriorOfAFGT0() > MIN_LOG10_CONFIDENCE_TO_INCLUDE_ALLELE_IN_POSTERIOR ) { - anyPoly = true; - log10PosteriorOfACEq0Sum += sortedResultWithThetaNPriors.getLog10PosteriorOfAFEq0(); - log10PriorsOfAC[0] += sortedResultWithThetaNPriors.getLog10PriorOfAFEq0(); - log10PriorsOfAC[1] += sortedResultWithThetaNPriors.getLog10PriorOfAFGT0(); - } - - log10PosteriorOfACGt0Sum += sortedResultWithThetaNPriors.getLog10PosteriorOfAFGT0(); - // bind pNonRef for allele to the posterior value of the AF > 0 with the new adjusted prior log10pRefByAllele.put(altAllele, sortedResultWithThetaNPriors.getLog10PosteriorOfAFEq0()); @@ -463,36 +499,32 @@ import java.util.*; nEvaluations += sortedResultWithThetaNPriors.nEvaluations; } - // If no alleles were polymorphic, make sure we have the proper priors (the defaults) for likelihood calculation - if ( ! anyPoly ) { - log10PriorsOfAC[0] = sortedResultsWithThetaNPriors.get(0).getLog10PriorOfAFEq0(); - log10PriorsOfAC[1] = sortedResultsWithThetaNPriors.get(0).getLog10PriorOfAFGT0(); - } - - // In principle, if B_p = x and C_p = y are the probabilities of being poly for alleles B and C, - // the probability of being poly is (1 - B_p) * (1 - C_p) = (1 - x) * (1 - y). We want to estimate confidently - // log10((1 - x) * (1 - y)) which is log10(1 - x) + log10(1 - y). This sum is log10PosteriorOfACEq0 - // - // note we need to handle the case where the posterior of AF == 0 is 0.0, in which case we - // use the summed log10PosteriorOfACGt0Sum directly. This happens in cases where - // AF > 0 : 0.0 and AF == 0 : -16, and if you use the inverse calculation you get 0.0 and MathUtils.LOG10_P_OF_ZERO - final double log10PosteriorOfACGt0; - if ( log10PosteriorOfACEq0Sum == 0.0 ) - log10PosteriorOfACGt0 = log10PosteriorOfACGt0Sum; - else - log10PosteriorOfACGt0 = Math.max(Math.log10(1 - Math.pow(10, log10PosteriorOfACEq0Sum)), MathUtils.LOG10_P_OF_ZERO); - - final double[] log10LikelihoodsOfAC = new double[] { - // L + prior = posterior => L = poster - prior - log10PosteriorOfACEq0Sum - log10PriorsOfAC[0], - log10PosteriorOfACGt0 - log10PriorsOfAC[1] - }; - return new MyAFCalculationResult(alleleCountsOfMLE, nEvaluations, vc.getAlleles(), // necessary to ensure all values < 0 - MathUtils.normalizeFromLog10(log10LikelihoodsOfAC, true), + MathUtils.normalizeFromLog10(new double[] { combinedAltAllelesResult.getLog10LikelihoodOfAFEq0(), combinedAltAllelesResult.getLog10LikelihoodOfAFGT0() }, true), // priors incorporate multiple alt alleles, must be normalized - MathUtils.normalizeFromLog10(log10PriorsOfAC, true), + MathUtils.normalizeFromLog10(new double[] { combinedAltAllelesResult.getLog10PriorOfAFEq0(), combinedAltAllelesResult.getLog10PriorOfAFGT0() }, true), log10pRefByAllele, sortedResultsWithThetaNPriors); } + + private boolean combineAltAlleleLikelihoods(final Genotype g, final int plMaxIndex, final double[] dest, + final double[] hetLikelihoods, final double[] homAltLikelihoods) { + + final int[] pls = g.getPL(); + if (pls == null) + return false; + int hetNextIndex = 0; + int homAltNextIndex = 0; + for (int plIndex = 1; plIndex < plMaxIndex; plIndex++) { + final GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(plIndex); + if (alleles.alleleIndex1 == 0 || alleles.alleleIndex2 == 0) + hetLikelihoods[hetNextIndex++] = pls[plIndex] * PHRED_2_LOG10_COEFF; + else + homAltLikelihoods[homAltNextIndex++] = pls[plIndex] * PHRED_2_LOG10_COEFF; + } + dest[0] = pls[0] * PHRED_2_LOG10_COEFF; + dest[1] = MathUtils.approximateLog10SumLog10(hetLikelihoods); + dest[2] = MathUtils.approximateLog10SumLog10(homAltLikelihoods); + return 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 c1d43f328..15ef5a392 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 @@ -135,7 +135,7 @@ 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("34a92dd832bbb8ed53abf21ba88c6faa")); + Arrays.asList("053913cb29fee481158e1f497a4fffdc")); 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 ae34ca172..8046906b5 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 @@ -65,7 +65,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testMultiSamplePilot1() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1, - Arrays.asList("a15a28d854789c71ef2879dd4c606b1a")); + Arrays.asList("b43bf9147e30cc68068a91a5e8405767")); executeTest("test MultiSample Pilot1", spec); } @@ -97,7 +97,7 @@ 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("1a36b5c036e0452f526dc1a5fdd60929")); + Arrays.asList("37594ce48695bf443c9251f70006f2f0")); executeTest("test Multiple SNP alleles", spec); } @@ -113,7 +113,7 @@ 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("451a6a39d74bd3cc367da80f76b2f98d")); + Arrays.asList("ad2be9f69ae8c6776b3bfba069735f50")); executeTest("test reverse trim", spec); } @@ -121,7 +121,7 @@ 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("a3b299d1dd256fec5425e4175f747bfe")); + Arrays.asList("1cc9c3e45e0296bb33042b409db18ca4")); 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 a76d0876c..9b0bf3536 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 @@ -64,7 +64,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa @Test public void testHaplotypeCallerMultiSampleComplex1() { - HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "29f216779f0db9a08f4907ea82f0c7fb"); + HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "f4018f734d64f1f88b3ac4b712311567"); } 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 060ff9cca..3fce3c7d4 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 @@ -85,9 +85,9 @@ 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, "f8bc02b296d89369fe7ddf3923743c26"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "ad0b6274991d451a6491f3118f0e7b2b"}); - tests.add(new Object[]{NA12878_PCRFREE, ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "956938fd1b5c7bf1b717326a7dd46d91"}); + 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_WEx, ReferenceConfidenceMode.NONE, WExIntervals, "1c3570461e96ad6d66c6abb0fd6ee865"}); tests.add(new Object[]{NA12878_WEx, ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "66019a0914f905522da6bd3b557a57d1"}); @@ -218,7 +218,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { public void testNoCallGVCFMissingPLsBugFix() { final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d", b37KGReference, NOCALL_GVCF_BUGFIX_BAM, NOCALL_GVCF_BUGFIX_INTERVALS, HaplotypeCaller.OPTIMAL_GVCF_INDEX_TYPE, HaplotypeCaller.OPTIMAL_GVCF_INDEX_PARAMETER); - final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("187e43b1034478edced1eb5c664bac34")); + final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("7ef1f30d92178f75e5220b16508b47cd")); spec.disableShadowBCF(); executeTest("testNoCallGVCFMissingPLsBugFix", 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 c0b7ff730..0389afeba 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 @@ -85,12 +85,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSample() { - HCTest(CEUTRIO_BAM, "", "7bc718c6a604405e6d33c3073630cc66"); + HCTest(CEUTRIO_BAM, "", "5468f50b4ed198e6e9b05a67c3103f72"); } @Test public void testHaplotypeCallerSingleSample() { - HCTest(NA12878_BAM, "", "07125724eb465a739df9c6ab191216b0"); + HCTest(NA12878_BAM, "", "e85ada8486a4ed7231918187a100e1c3"); } @Test @@ -111,7 +111,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMinBaseQuality() { - HCTest(NA12878_BAM, "-mbq 15", "07125724eb465a739df9c6ab191216b0"); + HCTest(NA12878_BAM, "-mbq 15", "e85ada8486a4ed7231918187a100e1c3"); } @Test @@ -126,7 +126,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerGraphBasedSingleSample() { - HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "79b0f8fa5e42ef23f3d166d84d92fa23"); + HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "129965453a3ad9a22aa241f8c4afcbbf"); } @Test @@ -136,19 +136,19 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerGraphBasedMultiSample() { - HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "10119fbb494e966a6f1b54307cfbeb8b"); + HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "987c0bb684fc03bcc46cb619e8269fe4"); } @Test public void testHaplotypeCallerSingleSampleWithDbsnp() { - HCTest(NA12878_BAM, "-D " + b37dbSNP132, "fded195a0436242673718e6dc083c172"); + HCTest(NA12878_BAM, "-D " + b37dbSNP132, "0f9f45384669cde243731ca803fa3a0b"); } @Test 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, - "5bc8892b68e281a3ceb4f2d141f8c723"); + "86a060e9514eaf90c14ddaa7e6d07259"); } @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 cd203cf38..0de169c5f 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 @@ -60,7 +60,7 @@ public class HaplotypeCallerParallelIntegrationTest extends WalkerTest { List tests = new ArrayList<>(); for ( final int nct : Arrays.asList(1, 2, 4) ) { - tests.add(new Object[]{nct, "faaf2217a920225b6937d87e949d1a68"}); + tests.add(new Object[]{nct, "8bcf149228e8845915733d6fd889a141"}); } return tests.toArray(new Object[][]{}); diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java index f0a0f669e..810d4d96a 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java @@ -66,7 +66,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf", b37KGReference), 1, - Arrays.asList("bc3d3eff337836af245b81f52b94d70c")); + Arrays.asList("27bc40f7cc46bdc347284d7522b2aa6c")); executeTest("testUpdatePGT", spec); } @@ -78,7 +78,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + " -L 20:10,000,000-20,000,000", b37KGReference), 1, - Arrays.asList("9d9ddeb831e5512c5b1084ee22e65459")); + Arrays.asList("bb7775a555ee9859e18a28cbc044a160")); executeTest("combineSingleSamplePipelineGVCF", spec); } @@ -127,7 +127,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + " -L 20:10,000,000-20,000,000", b37KGReference), 1, - Arrays.asList("aa0f9604bb496be143a6dde775e157fe")); + Arrays.asList("9b7f2ba1bde2e0a0eb3ebc0afb6bc513")); executeTest("combineSingleSamplePipelineGVCFHierarchical", spec); } @@ -139,7 +139,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" + " -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference), 1, - Arrays.asList("49f8ff728246d08cd20cd1c1521651f9")); + Arrays.asList("8201cee7120dfdb3fdeace0ec511c7b1")); executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec); } @@ -186,7 +186,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseBPResolutionString("-nda"), 1, - Arrays.asList("27cddeb2287827a58d79fc7d3ddad080")); + Arrays.asList("d50e5035488f63c574dcb8485ff61fcb")); executeTest("testNDA", spec); } @@ -204,7 +204,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseBPResolutionString("-stand_call_conf 300 -stand_emit_conf 100"), 1, - Arrays.asList("c841b408e41596529009bf7f07de9b3f")); + Arrays.asList("bd58c026e9c8df4d4166f22cd0f0ce65")); executeTest("testStandardConf", spec); } } \ No newline at end of file diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerIntegrationTest.java index 2fc925e11..7a5bca563 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerIntegrationTest.java @@ -65,9 +65,7 @@ public class NanoSchedulerIntegrationTest extends WalkerTest { for ( final int nt : Arrays.asList(1, 2) ) for ( final int nct : Arrays.asList(1, 2) ) { -// tests.add(new Object[]{ "SNP", "a1c7546f32a8919a3f3a70a04b2e8322", nt, nct }); -//// tests.add(new Object[]{ "INDEL", "0a6d2be79f4f8a4b0eb788cc4751b31b", nt, nct }); - tests.add(new Object[]{ "BOTH", "392dc99dc279082fc6e729b249adfa2b", nt, nct }); + tests.add(new Object[]{ "BOTH", "18418ddc2bdbe20c38ece6dd18535be7", nt, nct }); } return tests.toArray(new Object[][]{}); @@ -79,7 +77,6 @@ public class NanoSchedulerIntegrationTest extends WalkerTest { buildCommandLine( "-T UnifiedGenotyper -R " + b37KGReference, "--no_cmdline_in_header -G none", - //"--dbsnp " + b37dbSNP132, "-I " + privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "-L 20:10,000,000-10,100,000", "-glm " + glm,