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;