private Collection<VariantContext> getVariantContexts(
RefMetaDataTracker tracker, ReferenceContext ref) {
List<Feature> features = tracker.getValues(variants, ref.getLocus());
List<VariantContext> VCs = new ArrayList<VariantContext>(features.size());
for (Feature record : features) {
if (VariantContextAdaptors.canBeConvertedToVariantContext(record)) {
// we need to special case the HapMap format because indels aren't handled correctly
if (record instanceof RawHapMapFeature) {
// is it an indel?
RawHapMapFeature hapmap = (RawHapMapFeature) record;
if (hapmap.getAlleles()[0].equals(RawHapMapFeature.NULL_ALLELE_STRING)
|| hapmap.getAlleles()[1].equals(RawHapMapFeature.NULL_ALLELE_STRING)) {
// get the dbsnp object corresponding to this record (needed to help us distinguish
// between insertions and deletions)
VariantContext dbsnpVC = getDbsnp(hapmap.getName());
if (dbsnpVC == null || dbsnpVC.isMixed()) continue;
Map<String, Allele> alleleMap = new HashMap<String, Allele>(2);
alleleMap.put(
RawHapMapFeature.DELETION,
Allele.create(ref.getBase(), dbsnpVC.isSimpleInsertion()));
alleleMap.put(
RawHapMapFeature.INSERTION,
Allele.create(
(char) ref.getBase() + ((RawHapMapFeature) record).getAlleles()[1],
!dbsnpVC.isSimpleInsertion()));
hapmap.setActualAlleles(alleleMap);
// also, use the correct positioning for insertions
hapmap.updatePosition(dbsnpVC.getStart());
if (hapmap.getStart() < ref.getWindow().getStart()) {
logger.warn(
"Hapmap record at "
+ ref.getLocus()
+ " represents an indel too large to be converted; skipping...");
continue;
}
}
}
// ok, we might actually be able to turn this record in a variant context
VariantContext vc =
VariantContextAdaptors.toVariantContext(variants.getName(), record, ref);
if (vc != null) // sometimes the track has odd stuff in it that can't be converted
VCs.add(vc);
}
}
return VCs;
}
// 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;
}
