e6d23a5129d57ddbf57fa685fda1591ea389c8d9,public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidExactAFCalculation.java,DiploidExactAFCalculation,computeLog10PNonRef,#VariantContext#number[]#AlleleFrequencyCalculationResult#,59

Before Change


    public void computeLog10PNonRef(final VariantContext vc,
                                    final double[] log10AlleleFrequencyPriors,
                                    final AlleleFrequencyCalculationResult result) {
        linearExactMultiAllelic(vc.getGenotypes(), vc.getNAlleles() - 1, log10AlleleFrequencyPriors, result);
    }

    @Override

After Change


                                    final double[] log10AlleleFrequencyPriors,
                                    final AlleleFrequencyCalculationResult result) {
        final int numAlternateAlleles = vc.getNAlleles() - 1;
        final ArrayList<double[]> genotypeLikelihoods = getGLs(vc.getGenotypes());
        final int numSamples = genotypeLikelihoods.size()-1;
        final int numChr = 2*numSamples;