// 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;
}
/**
* 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);
}
