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