038cbcf80e69c8a43140c4fc9c16df1a842a4b6e,java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/IVFSecondaryBases.java,IVFSecondaryBases,compute,#char#LocusContext#,38

Before Change


            double offPrior = MathUtils.binomialProbability(offIsGenotypic, offTotal, p2off[genotypeIndex]);
            double onPrior = MathUtils.binomialProbability(onIsGenotypic, onTotal, p2on[genotypeIndex]);

            likelihoods[genotypeIndex] = Math.log10(offPrior) + Math.log10(onPrior);
        }

        return likelihoods;

After Change


            double onPrior = MathUtils.binomialProbability(onIsGenotypic, onTotal, p2on[genotypeIndex]);

            double logOffPrior = MathUtils.compareDoubles(offPrior, 0.0, 1e-10) == 0 ? Math.log10(Double.MIN_VALUE) : Math.log10(offPrior);
            double logOnPrior = MathUtils.compareDoubles(onPrior, 0.0, 1e-10) == 0 ? Math.log10(Double.MIN_VALUE) : Math.log10(onPrior);

            likelihoods[genotypeIndex] += logOffPrior + logOnPrior;
        }

        return likelihoods;