public Map<String, Object> annotate(
RefMetaDataTracker tracker,
AnnotatorCompatible walker,
ReferenceContext ref,
Map<String, AlignmentContext> stratifiedContexts,
VariantContext vc) {
if (stratifiedContexts.size()
== 0) // size 0 means that call was made by someone else and we have no data here
return null;
if (!vc.isSNP() && !vc.isIndel() && !vc.isMixed()) return null;
final AlignmentContext context =
AlignmentContextUtils.joinContexts(stratifiedContexts.values());
final int contextWingSize = Math.min((ref.getWindow().size() - 1) / 2, MIN_CONTEXT_WING_SIZE);
final int contextSize = contextWingSize * 2 + 1;
final int locus =
ref.getLocus().getStart() + (ref.getLocus().getStop() - ref.getLocus().getStart()) / 2;
final ReadBackedPileup pileup = context.getBasePileup();
// Compute all haplotypes consistent with the current read pileup
final List<Haplotype> haplotypes = computeHaplotypes(pileup, contextSize, locus, vc);
final MathUtils.RunningAverage scoreRA = new MathUtils.RunningAverage();
if (haplotypes != null) {
for (final Genotype genotype : vc.getGenotypes()) {
final AlignmentContext thisContext = stratifiedContexts.get(genotype.getSampleName());
if (thisContext != null) {
final ReadBackedPileup thisPileup = thisContext.getBasePileup();
if (vc.isSNP())
scoreRA.add(
scoreReadsAgainstHaplotypes(
haplotypes,
thisPileup,
contextSize,
locus)); // Taking the simple average of all sample's score since the score can
// be negative and the RMS doesn't make sense
else if (vc.isIndel() || vc.isMixed()) {
Double d = scoreIndelsAgainstHaplotypes(thisPileup);
if (d == null) return null;
scoreRA.add(
d); // Taking the simple average of all sample's score since the score can be
// negative and the RMS doesn't make sense
}
}
}
}
// annotate the score in the info field
final Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%.4f", scoreRA.mean()));
return map;
}
