ee8f2871f730b307d377e681ec04863db85693cb,java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java,SampleSummaryStats,generateSampleSummaryStats,#SampleStats#,650

Before Change


            // Summary 3: % homVar called as homVar
            numer = stats[Genotype.Type.HOM_VAR.ordinal()][Genotype.Type.HOM_VAR.ordinal()];
            denom = sumStatsAllPairs(stats, EnumSet.of(Genotype.Type.HOM_VAR), allGenotypes);
            updateSummaries(3, summary,  numer, denom);

            // Summary 4: % homVars called as var
            numer = sumStatsAllPairs(stats, EnumSet.of(Genotype.Type.HOM_VAR), allVariantGenotypes);

After Change


            // MAD: this is known as the non-reference sensitivity (# non-ref according to comp found in eval / # non-ref in comp)
            numer = sumStatsAllPairs(stats, allVariantGenotypes, allVariantGenotypes);
            denom = sumStatsAllPairs(stats, allVariantGenotypes, allGenotypes);
            updateSummaries(3, summary,  numer, denom);

            // Summary 4: overall genotype concordance of sites called in eval track
            // MAD: this is the tradition genotype concordance