050d2aa6fd2c0a400743958b06be47594df6db62,public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java,UnifiedGenotyperEngine,calculateGenotypes,#RefMetaDataTracker#ReferenceContext#AlignmentContext#Map#VariantContext#GenotypeLikelihoodsCalculationModel.Model#boolean#Map#,351

Before Change


            
            // the forward lod
            VariantContext vcForward = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.FORWARD, allAllelesToUse, false, model, perReadAlleleLikelihoodMap);
            afcm.get().getLog10PNonRef(vcForward, getAlleleFrequencyPriors(model), AFresult);
            //double[] normalizedLog10Posteriors = MathUtils.normalizeFromLog10(AFresult.log10AlleleFrequencyPosteriors, true);
            double forwardLog10PofNull = AFresult.getLog10PosteriorOfAFzero();
            double forwardLog10PofF = AFresult.getLog10PosteriorsMatrixSumWithoutAFzero();

After Change


            
            // the forward lod
            VariantContext vcForward = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.FORWARD, allAllelesToUse, false, model, perReadAlleleLikelihoodMap);
            AFresult = afcm.get().getLog10PNonRef(vcForward, getAlleleFrequencyPriors(model));
            //double[] normalizedLog10Posteriors = MathUtils.normalizeFromLog10(AFresult.log10AlleleFrequencyPosteriors, true);
            double forwardLog10PofNull = AFresult.getLog10PosteriorOfAFzero();
            double forwardLog10PofF = AFresult.getLog10PosteriorsMatrixSumWithoutAFzero();