diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java index aa4b4ab78..4760893ca 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java @@ -342,9 +342,10 @@ public class PhaseByTransmission extends RodWalker, HashMa private Genotype getPhasedGenotype(Allele refAllele, Allele altAllele, Genotype genotype, double transmissionProb, Genotype phasedGenotype){ int phredScoreTransmission = -1; - if(transmissionProb != NO_TRANSMISSION_PROB) - phredScoreTransmission = MathUtils.probabilityToPhredScale(1-(transmissionProb)); - + if(transmissionProb != NO_TRANSMISSION_PROB){ + double dphredScoreTransmission = MathUtils.log10ProbabilityToPhredScale(Math.log10(1-(transmissionProb))); + phredScoreTransmission = dphredScoreTransmission < Byte.MAX_VALUE ? (byte)dphredScoreTransmission : Byte.MAX_VALUE; + } //Handle null, missing and unavailable genotypes //Note that only cases where a null/missing/unavailable genotype was passed in the first place can lead to a null/missing/unavailable //genotype so it is safe to return the original genotype in this case. @@ -410,7 +411,7 @@ public class PhaseByTransmission extends RodWalker, HashMa buildMatrices(); if(mvFile != null) - mvFile.println("#CHROM\tPOS\tFILTER\tAC\tFAMILY\tTP\tMOTHER_GT\tMOTHER_DP\tMOTHER_RAD\tMOTHER_AAD\tMOTHER_HRPL\tMOTHER_HETPL\tMOTHER_HAPL\tFATHER_GT\tFATHER_DP\tFATHER_RAD\tFATHER_AAD\tFATHER_HRPL\tFATHER_HETPL\tFATHER_HAPL\tCHILD_GT\tCHILD_DP\tCHILD_RAD\tCHILD_AAD\tCHILD_HRPL\tCHILD_HETPL\tCHILD_HAPL"); + mvFile.println("CHROM\tPOS\tAC\tFAMILY\tTP\tMOTHER_GT\tMOTHER_DP\tMOTHER_AD\tMOTHER_PL\tFATHER_GT\tFATHER_DP\tFATHER_AD\tFATHER_PL\tCHILD_GT\tCHILD_DP\tCHILD_AD\tCHILD_PL"); } @@ -776,7 +777,7 @@ public class PhaseByTransmission extends RodWalker, HashMa return metricsCounters; final VariantContext vc = tracker.getFirstValue(variantCollection.variants, context.getLocation()); - if (vc == null) + if (vc == null || !vc.isBiallelic()) return metricsCounters; final VariantContextBuilder builder = new VariantContextBuilder(vc); @@ -805,8 +806,8 @@ public class PhaseByTransmission extends RodWalker, HashMa if(father != null){ genotypesContext.replace(phasedFather); updateTrioMetricsCounters(phasedMother,phasedFather,phasedChild,mvCount,metricsCounters); - mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s\t%s:%s:%s:%s\t%s:%s:%s:%s\t%s:%s:%s:%s", - vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(), + mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s", + vc.getChr(),vc.getStart(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.getFamilyID(), phasedMother.getExtendedAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getDP(),Arrays.asList(phasedMother.getAD()), phasedMother.getLikelihoodsString(), phasedFather.getGenotypeString(),phasedFather.getDP(),Arrays.asList(phasedFather.getAD()),phasedFather.getLikelihoodsString(), phasedChild.getGenotypeString(),Arrays.asList(phasedChild.getDP()),phasedChild.getAD(),phasedChild.getLikelihoodsString()); @@ -817,8 +818,8 @@ public class PhaseByTransmission extends RodWalker, HashMa updatePairMetricsCounters(phasedMother,phasedChild,mvCount,metricsCounters); if(!(phasedMother.getType()==mother.getType() && phasedChild.getType()==child.getType())) metricsCounters.put(NUM_GENOTYPES_MODIFIED,metricsCounters.get(NUM_GENOTYPES_MODIFIED)+1); - mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s\t%s:%s:%s:%s\t.:.:.:.\t%s:%s:%s:%s", - vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(), + mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s:%s:%s:%s\t.\t.\t.\t.\t%s\t%s\t%s\t%s", + vc.getChr(),vc.getStart(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.getFamilyID(), phasedMother.getExtendedAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getDP(),Arrays.asList(phasedMother.getAD()),phasedMother.getLikelihoodsString(), phasedChild.getGenotypeString(),phasedChild.getDP(),Arrays.asList(phasedChild.getAD()),phasedChild.getLikelihoodsString()); } @@ -828,15 +829,15 @@ public class PhaseByTransmission extends RodWalker, HashMa updatePairMetricsCounters(phasedFather,phasedChild,mvCount,metricsCounters); if(!(phasedFather.getType()==father.getType() && phasedChild.getType()==child.getType())) metricsCounters.put(NUM_GENOTYPES_MODIFIED,metricsCounters.get(NUM_GENOTYPES_MODIFIED)+1); - mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s\t.:.:.:.\t%s:%s:%s:%s\t%s:%s:%s:%s", - vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(), + mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t.\t.\t.\t.\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s", + vc.getChr(),vc.getStart(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.getFamilyID(), phasedFather.getExtendedAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedFather.getGenotypeString(),phasedFather.getDP(),Arrays.asList(phasedFather.getAD()),phasedFather.getLikelihoodsString(), phasedChild.getGenotypeString(),phasedChild.getDP(),Arrays.asList(phasedChild.getAD()),phasedChild.getLikelihoodsString()); } //Report violation if set so //TODO: ADAPT FOR PAIRS TOO!! - if(mvCount>0 && mvFile != null) + if(mvCount>0 && mvFile != null && !vc.isFiltered()) mvFile.println(mvfLine); } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java index 19d1e4cb3..9b0fbf650 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java @@ -29,7 +29,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest { "-o %s" ), 2, - Arrays.asList("cd112ec37a9e28d366aff29a85fdcaa0","f8721f4f5d3bae2848ae15c3f120709b") + Arrays.asList("f4b0b5471e03306ee2fad27d88b217b6","f8721f4f5d3bae2848ae15c3f120709b") ); executeTest("testTrueNegativeMV", spec); } @@ -48,7 +48,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest { "-o %s" ), 2, - Arrays.asList("27ccd6feb51de7e7dcdf35f4697fa4eb","547fdfef393f3045a96d245ef6af8acb") + Arrays.asList("dbc64776dcc9e01a468b61e4e0db8277","547fdfef393f3045a96d245ef6af8acb") ); executeTest("testTruePositiveMV", spec); } @@ -67,7 +67,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest { "-o %s" ), 2, - Arrays.asList("719d681bb0a52a40bc854bba107c5c94","9529e2bf214d72e792d93fbea22a3b91") + Arrays.asList("37793e78861bb0bc070884da67dc10e6","9529e2bf214d72e792d93fbea22a3b91") ); executeTest("testFalsePositiveMV", spec); } @@ -86,7 +86,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest { "-o %s" ), 2, - Arrays.asList("7f4a277aee2c7398fcfa84d6c98d5fb3","8c157d79dd00063d2932f0d2b96f53d8") + Arrays.asList("e4da7639bb542d6440975da12b94973f","8c157d79dd00063d2932f0d2b96f53d8") ); executeTest("testSpecialCases", spec); } @@ -108,7 +108,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest { "-o %s" ), 2, - Arrays.asList("44e09d2f9e4d8a9488226d03a97fe999","343e418850ae4a687ebef2acd55fcb07") + Arrays.asList("ab92b714471a000285577d540e1fdc2e","343e418850ae4a687ebef2acd55fcb07") ); executeTest("testPriorOption", spec); } @@ -149,7 +149,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest { "-fatherAlleleFirst" ), 2, - Arrays.asList("60ced3d078792a150a03640b62926857","52ffa82428e63ade22ea37b72ae58492") + Arrays.asList("4b937c1b4e96602a7479b07b59254d06","52ffa82428e63ade22ea37b72ae58492") ); executeTest("testFatherAlleleFirst", spec); }