@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()]++;
}
}
}
public boolean selectSiteInSamples(VariantContext vc) {
if (samples == null || samples.isEmpty()) return true;
// want to include a site in the given samples if it is *likely* to be variant (via the EXACT
// model)
// first subset to the samples
VariantContext subContext = vc.subContextFromSamples(samples);
if (!subContext.isPolymorphicInSamples()) return false;
// now check to see (using EXACT model) whether this should be variant
// do we want to apply a prior? maybe user-spec?
if (flatPriors == null) {
flatPriors = new double[1 + 2 * samples.size()];
AFCalculator = AFCalcFactory.createAFCalc(samples.size(), 4, 2);
}
final AFCalcResult result = AFCalculator.getLog10PNonRef(subContext, flatPriors);
// do we want to let this qual go up or down?
if (result.getLog10LikelihoodOfAFEq0() < referenceLikelihood) {
return true;
}
return false;
}
