if ( MQ0freeContext.getPileup().size() == 0 ||
(UAC.MAX_READS_IN_PILEUP > 0 && MQ0freeContext.getPileup().size() > UAC.MAX_READS_IN_PILEUP) )
return null;
DiploidGenotypePriors priors = new DiploidGenotypePriors(ref, UAC.heterozygosity, DiploidGenotypePriors.PROB_OF_TRISTATE_GENOTYPE);
Pair<List<Genotype>, GenotypeLocusData> call = gcm.calculateGenotype(tracker, ref, MQ0freeContext, priors);
<BUG>if ( call != null && call.second != null && call.second instanceof ArbitraryFieldsBacked ) {
Map<String, String> annotations = VariantAnnotator.getAnnotations(refContext, fullContext, call.second, call.first);
((ArbitraryFieldsBacked)call.second).setFields(annotations);</BUG>
}
return call;

if ( MQ0freeContext.getPileup().size() == 0 ||
(UAC.MAX_READS_IN_PILEUP > 0 && MQ0freeContext.getPileup().size() > UAC.MAX_READS_IN_PILEUP) )
return null;
DiploidGenotypePriors priors = new DiploidGenotypePriors(ref, UAC.heterozygosity, DiploidGenotypePriors.PROB_OF_TRISTATE_GENOTYPE);
Pair<List<Genotype>, GenotypeLocusData> call = gcm.calculateGenotype(tracker, ref, MQ0freeContext, priors);
if ( call != null && call.second != null && call.second instanceof ArbitraryFieldsBacked ) {
Map<String, String> annotations;
if ( UAC.ALL_ANNOTATIONS )
annotations = VariantAnnotator.getAllAnnotations(refContext, fullContext, call.second, call.first);
else
annotations = VariantAnnotator.getAnnotations(refContext, fullContext, call.second, call.first);
((ArbitraryFieldsBacked)call.second).setFields(annotations);
}
return call;
