private boolean isConcordant(VariantContext vc, Collection<VariantContext> compVCs) {
if (vc == null || compVCs == null || compVCs.isEmpty()) return false;
// if we're not looking for specific samples then the fact that we have both VCs is enough to
// call it concordant.
if (NO_SAMPLES_SPECIFIED) return true;
// make a list of all samples contained in this variant VC that are being tracked by the user
// command line arguments.
Set<String> variantSamples = vc.getSampleNames();
variantSamples.retainAll(samples);
// check if we can find all samples from the variant rod in the comp rod.
for (String sample : variantSamples) {
boolean foundSample = false;
for (VariantContext compVC : compVCs) {
Genotype varG = vc.getGenotype(sample);
Genotype compG = compVC.getGenotype(sample);
if (haveSameGenotypes(varG, compG)) {
foundSample = true;
break;
}
}
// if at least one sample doesn't have the same genotype, we don't have concordance
if (!foundSample) {
return false;
}
}
return true;
}
