/**
* Checks if vc has a variant call for (at least one of) the samples.
*
* @param vc the variant rod VariantContext. Here, the variant is the dataset you're looking for
* discordances to (e.g. HapMap)
* @param compVCs the comparison VariantContext (discordance
* @return
*/
private boolean isDiscordant(VariantContext vc, Collection<VariantContext> compVCs) {
if (vc == null) return false;
// if we're not looking at specific samples then the absence of a compVC means discordance
if (NO_SAMPLES_SPECIFIED) return (compVCs == null || compVCs.isEmpty());
// check if we find it in the variant rod
Map<String, Genotype> genotypes = vc.getGenotypes(samples);
for (Genotype g : genotypes.values()) {
if (sampleHasVariant(g)) {
// There is a variant called (or filtered with not exclude filtered option set) that is not
// HomRef for at least one of the samples.
if (compVCs == null) return true;
// Look for this sample in the all vcs of the comp ROD track.
boolean foundVariant = false;
for (VariantContext compVC : compVCs) {
if (sampleHasVariant(compVC.getGenotype(g.getSampleName()))) {
foundVariant = true;
break;
}
}
// if (at least one sample) was not found in all VCs of the comp ROD, we have discordance
if (!foundVariant) return true;
}
}
return false; // we only get here if all samples have a variant in the comp rod.
}
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;
}
private VariantContext findMatchingComp(
final VariantContext eval, final Collection<VariantContext> comps) {
// if no comps, return null
if (comps == null || comps.isEmpty()) return null;
// if no eval, return any comp
if (eval == null) return comps.iterator().next();
// find all of the matching comps
VariantContext lenientMatch = null;
for (final VariantContext comp : comps) {
switch (doEvalAndCompMatch(comp, eval, requireStrictAlleleMatch)) {
case STRICT:
return comp;
case LENIENT:
if (lenientMatch == null) lenientMatch = comp;
break;
case NO_MATCH:
// do nothing
}
}
// nothing matched, just return lenientMatch, which might be null
return lenientMatch;
}