/**
* Compute full calls at a given locus. Entry point for engine calls from the UnifiedGenotyper.
*
* <p>If allSamples != null, then the output variantCallContext is guarenteed to contain a
* genotype for every sample in allSamples. If it's null there's no such guarentee. Providing this
* argument is critical when the resulting calls will be written to a VCF file.
*
* @param tracker the meta data tracker
* @param refContext the reference base
* @param rawContext contextual information around the locus
* @param allSamples set of all sample names that we might call (i.e., those in the VCF header)
* @return the VariantCallContext object
*/
public List<VariantCallContext> calculateLikelihoodsAndGenotypes(
final RefMetaDataTracker tracker,
final ReferenceContext refContext,
final AlignmentContext rawContext,
final Set<String> allSamples) {
final List<VariantCallContext> results = new ArrayList<VariantCallContext>(2);
final List<GenotypeLikelihoodsCalculationModel.Model> models =
getGLModelsToUse(tracker, refContext, rawContext);
final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap>
perReadAlleleLikelihoodMap =
new HashMap<
String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap>();
if (models.isEmpty()) {
results.add(
UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES
&& UAC.GenotypingMode
== GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES
? generateEmptyContext(tracker, refContext, null, rawContext)
: null);
} else {
for (final GenotypeLikelihoodsCalculationModel.Model model : models) {
perReadAlleleLikelihoodMap.clear();
final Map<String, AlignmentContext> stratifiedContexts =
getFilteredAndStratifiedContexts(UAC, refContext, rawContext, model);
if (stratifiedContexts == null) {
results.add(
UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES
&& UAC.GenotypingMode
== GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE
.GENOTYPE_GIVEN_ALLELES
? generateEmptyContext(tracker, refContext, null, rawContext)
: null);
} else {
final VariantContext vc =
calculateLikelihoods(
tracker,
refContext,
stratifiedContexts,
AlignmentContextUtils.ReadOrientation.COMPLETE,
null,
true,
model,
perReadAlleleLikelihoodMap);
if (vc != null)
results.add(
calculateGenotypes(
tracker,
refContext,
rawContext,
stratifiedContexts,
vc,
model,
true,
perReadAlleleLikelihoodMap));
}
}
}
return results;
}
