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;
}
