@Override
public void update2(
VariantContext eval,
VariantContext comp,
RefMetaDataTracker tracker,
ReferenceContext ref,
AlignmentContext context) {
if (comp != null) { // we only need to consider sites in comp
if (REQUIRE_IDENTICAL_ALLELES && (eval != null && haveDifferentAltAlleles(eval, comp)))
nDifferentAlleleSites++;
else {
SiteStatus evalStatus = calcSiteStatus(eval);
final Set<String> evalSamples = getWalker().getSampleNamesForEvaluation();
if (comp.hasGenotypes() && !evalSamples.isEmpty() && comp.hasGenotypes(evalSamples))
// if we have genotypes in both eval and comp, subset comp down just the samples in eval
comp = comp.subContextFromSamples(evalSamples, false);
SiteStatus compStatus = calcSiteStatus(comp);
counts[compStatus.ordinal()][evalStatus.ordinal()]++;
}
}
}
private int getCounts(SiteStatus comp, SiteStatus eval) {
return counts[comp.ordinal()][eval.ordinal()];
}
