// decide whether we are currently processing SNPs, indels, neither, or both
private List<GenotypeLikelihoodsCalculationModel.Model> getGLModelsToUse(
final RefMetaDataTracker tracker,
final ReferenceContext refContext,
final AlignmentContext rawContext) {
final List<GenotypeLikelihoodsCalculationModel.Model> models =
new ArrayList<GenotypeLikelihoodsCalculationModel.Model>(2);
String modelPrefix = "";
if (UAC.GLmodel.name().toUpperCase().contains("BOTH"))
modelPrefix = UAC.GLmodel.name().toUpperCase().replaceAll("BOTH", "");
if (!UAC.GLmodel.name().contains(GPSTRING)
&& UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY)
modelPrefix = GPSTRING + modelPrefix;
// if we're genotyping given alleles and we have a requested SNP at this position, do SNP
if (UAC.GenotypingMode
== GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) {
final VariantContext vcInput =
getVCFromAllelesRod(
tracker, refContext, rawContext.getLocation(), false, logger, UAC.alleles);
if (vcInput == null) return models;
if (vcInput.isSNP()) {
// ignore SNPs if the user chose INDEL mode only
if (UAC.GLmodel.name().toUpperCase().contains("BOTH")
|| UAC.GLmodel.name().toUpperCase().contains("SNP"))
models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix + "SNP"));
} else if (vcInput.isIndel() || vcInput.isMixed()) {
// ignore INDELs if the user chose SNP mode only
if (UAC.GLmodel.name().toUpperCase().contains("BOTH")
|| UAC.GLmodel.name().toUpperCase().contains("INDEL"))
models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix + "INDEL"));
}
// No support for other types yet
} else {
if (UAC.GLmodel.name().toUpperCase().contains("BOTH")) {
models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix + "SNP"));
models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix + "INDEL"));
} else {
models.add(
GenotypeLikelihoodsCalculationModel.Model.valueOf(
modelPrefix + UAC.GLmodel.name().toUpperCase()));
}
}
return models;
}
// private method called by both UnifiedGenotyper and UGCalcLikelihoods entry points into the
// engine
private VariantContext calculateLikelihoods(
final RefMetaDataTracker tracker,
final ReferenceContext refContext,
final Map<String, AlignmentContext> stratifiedContexts,
final AlignmentContextUtils.ReadOrientation type,
final List<Allele> alternateAllelesToUse,
final boolean useBAQedPileup,
final GenotypeLikelihoodsCalculationModel.Model model,
final Map<String, org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap>
perReadAlleleLikelihoodMap) {
// initialize the data for this thread if that hasn't been done yet
if (glcm.get() == null) {
glcm.set(getGenotypeLikelihoodsCalculationObject(logger, UAC));
}
return glcm.get()
.get(model.name().toUpperCase())
.getLikelihoods(
tracker,
refContext,
stratifiedContexts,
type,
alternateAllelesToUse,
useBAQedPileup && BAQEnabledOnCMDLine,
genomeLocParser,
perReadAlleleLikelihoodMap);
}
private Map<String, AlignmentContext> getFilteredAndStratifiedContexts(
UnifiedArgumentCollection UAC,
ReferenceContext refContext,
AlignmentContext rawContext,
final GenotypeLikelihoodsCalculationModel.Model model) {
if (!BaseUtils.isRegularBase(refContext.getBase())) return null;
Map<String, AlignmentContext> stratifiedContexts = null;
if (model.name().contains("INDEL")) {
final ReadBackedPileup pileup =
rawContext.getBasePileup().getMappingFilteredPileup(UAC.MIN_BASE_QUALTY_SCORE);
// don't call when there is no coverage
if (pileup.getNumberOfElements() == 0 && UAC.OutputMode != OUTPUT_MODE.EMIT_ALL_SITES)
return null;
// stratify the AlignmentContext and cut by sample
stratifiedContexts = AlignmentContextUtils.splitContextBySampleName(pileup);
} else if (model.name().contains("SNP")) {
// stratify the AlignmentContext and cut by sample
stratifiedContexts =
AlignmentContextUtils.splitContextBySampleName(rawContext.getBasePileup());
if (!(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES
&& UAC.GenotypingMode
!= GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES)) {
int numDeletions = 0;
for (final PileupElement p : rawContext.getBasePileup()) {
if (p.isDeletion()) numDeletions++;
}
if (((double) numDeletions) / ((double) rawContext.getBasePileup().getNumberOfElements())
> UAC.MAX_DELETION_FRACTION) {
return null;
}
}
}
return stratifiedContexts;
}
protected double getTheta(final GenotypeLikelihoodsCalculationModel.Model model) {
if (model.name().contains("SNP")) return HUMAN_SNP_HETEROZYGOSITY;
if (model.name().contains("INDEL")) return HUMAN_INDEL_HETEROZYGOSITY;
else throw new IllegalArgumentException("Unexpected GenotypeCalculationModel " + model);
}
protected double[] getAlleleFrequencyPriors(
final GenotypeLikelihoodsCalculationModel.Model model) {
if (model.name().toUpperCase().contains("SNP")) return log10AlleleFrequencyPriorsSNPs;
else if (model.name().toUpperCase().contains("INDEL")) return log10AlleleFrequencyPriorsIndels;
else throw new IllegalArgumentException("Unexpected GenotypeCalculationModel " + model);
}
/**
* Compute genotypes at a given locus.
*
* @param vc the GL-annotated variant context
* @return the VariantCallContext object
*/
public VariantCallContext calculateGenotypes(VariantContext vc) {
return calculateGenotypes(
null, null, null, null, vc, GenotypeLikelihoodsCalculationModel.Model.valueOf("SNP"), null);
}