public Map<String, Object> annotate(
RefMetaDataTracker tracker,
AnnotatorCompatible walker,
ReferenceContext ref,
Map<String, AlignmentContext> stratifiedContexts,
VariantContext vc) {
if (mendelianViolation == null) {
if (checkAndSetSamples(((Walker) walker).getSampleDB())) {
mendelianViolation =
new MendelianViolation(((VariantAnnotator) walker).minGenotypeQualityP);
} else {
throw new UserException(
"Mendelian violation annotation can only be used from the Variant Annotator, and must be provided a valid PED file (-ped) from the command line containing only 1 trio.");
}
}
Map<String, Object> toRet = new HashMap<String, Object>(1);
boolean hasAppropriateGenotypes =
vc.hasGenotype(motherId)
&& vc.getGenotype(motherId).hasLikelihoods()
&& vc.hasGenotype(fatherId)
&& vc.getGenotype(fatherId).hasLikelihoods()
&& vc.hasGenotype(childId)
&& vc.getGenotype(childId).hasLikelihoods();
if (hasAppropriateGenotypes)
toRet.put(
"MVLR", mendelianViolation.violationLikelihoodRatio(vc, motherId, fatherId, childId));
return toRet;
}
