a8faacda4e57d4cfea2b6f6539a7f924c5d3fab1,java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java,SNPGenotypeLikelihoodsCalculationModel,getLikelihoods,#RefMetaDataTracker#ReferenceContext#Map#AlignmentContextUtils.ReadOrientation#GenotypePriors#Map#Allele#boolean#,84

Before Change


            DiploidGenotype refGenotype = DiploidGenotype.createHomGenotype(refBase);
            DiploidGenotype hetGenotype = DiploidGenotype.createDiploidGenotype(refBase, bestAlternateAllele);
            DiploidGenotype homGenotype = DiploidGenotype.createHomGenotype(bestAlternateAllele);
            GLs.put(sample.getKey(), new BiallelicGenotypeLikelihoods(sample.getKey(),
                    refAllele,
                    altAllele,
                    likelihoods[refGenotype.ordinal()],
                    likelihoods[hetGenotype.ordinal()],
                    likelihoods[homGenotype.ordinal()],
                    getFilteredDepth(pileup)));
        }

        return refAllele;

After Change


            ArrayList<Allele> aList = new ArrayList<Allele>();
            aList.add(refAllele);
            aList.add(altAllele);
            double[] dlike = new double[]{likelihoods[refGenotype.ordinal()],likelihoods[hetGenotype.ordinal()],likelihoods[homGenotype.ordinal()]} ;
            GLs.put(sample.getKey(), new MultiallelicGenotypeLikelihoods(sample.getKey(),
                    aList,  dlike, getFilteredDepth(pileup)));
        }

        return refAllele;