@Override
public Map<String, Object> annotate(
final RefMetaDataTracker tracker,
final AnnotatorCompatible walker,
final ReferenceContext ref,
final Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc,
final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
final GenotypesContext genotypes = vc.getGenotypes();
if (genotypes == null || genotypes.size() < MIN_SAMPLES) {
if (!warningLogged) {
logger.warn("Too few genotypes");
warningLogged = true;
}
return null;
}
int refCount = 0;
int hetCount = 0;
int homCount = 0;
for (final Genotype g : genotypes) {
if (g.isNoCall()) continue;
// TODO - fix me:
// Right now we just ignore genotypes that are not confident, but this throws off
// our HW ratios. More analysis is needed to determine the right thing to do when
// the genotyper cannot decide whether a given sample is het or hom var.
if (g.getLog10PError() > MIN_LOG10_PERROR) continue;
if (g.isHomRef()) refCount++;
else if (g.isHet()) hetCount++;
else homCount++;
}
if (refCount + hetCount + homCount == 0) return null;
double pvalue = HardyWeinbergCalculation.hwCalculate(refCount, hetCount, homCount);
// System.out.println(refCount + " " + hetCount + " " + homCount + " " + pvalue);
Map<String, Object> map = new HashMap<>();
map.put(getKeyNames().get(0), String.format("%.1f", QualityUtils.phredScaleErrorRate(pvalue)));
return map;
}
