From 9604fb2ba34d619d96459938e32d757758216c91 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Wed, 7 Sep 2011 16:49:16 -0400 Subject: [PATCH] Necessary but not sufficient step to fix GenotypeGivenAlleles mode in UG which is now busted --- .../gatk/walkers/genotyper/UnifiedGenotyperEngine.java | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index 06455df6d..b1332bdf9 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -39,10 +39,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.Genotype; -import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; +import org.broadinstitute.sting.utils.variantcontext.*; import java.io.PrintStream; import java.util.*; @@ -239,7 +236,8 @@ public class UnifiedGenotyperEngine { VariantContext vcInput = SNPGenotypeLikelihoodsCalculationModel.getSNPVCFromAllelesRod(tracker, ref, false, logger, UAC.alleles); if ( vcInput == null ) return null; - vc = new VariantContext("UG_call", vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles()); + vc = new VariantContext("UG_call", vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles(), InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, ref.getBase()); + } else { // deal with bad/non-standard reference bases if ( !Allele.acceptableAlleleBases(new byte[]{ref.getBase()}) )