private String getAlleleRepresentation(Allele allele) {
if (allele.isNull()) { // deletion wrt the ref
return DEL;
} else { // insertion, pass actual bases
return allele.getBaseString();
}
}
public Allele getLikelihoods(
RefMetaDataTracker tracker,
ReferenceContext ref,
Map<String, AlignmentContext> contexts,
AlignmentContextUtils.ReadOrientation contextType,
GenotypePriors priors,
Map<String, MultiallelicGenotypeLikelihoods> GLs,
Allele alternateAlleleToUse,
boolean useBAQedPileup) {
if (tracker == null) return null;
GenomeLoc loc = ref.getLocus();
Allele refAllele, altAllele;
VariantContext vc = null;
if (!ref.getLocus().equals(lastSiteVisited)) {
// starting a new site: clear allele list
alleleList.clear();
lastSiteVisited = ref.getLocus();
indelLikelihoodMap.set(new HashMap<PileupElement, LinkedHashMap<Allele, Double>>());
haplotypeMap.clear();
if (getAlleleListFromVCF) {
for (final VariantContext vc_input : tracker.getValues(UAC.alleles, loc)) {
if (vc_input != null
&& allowableTypes.contains(vc_input.getType())
&& ref.getLocus().getStart() == vc_input.getStart()) {
vc = vc_input;
break;
}
}
// ignore places where we don't have a variant
if (vc == null) return null;
alleleList.clear();
if (ignoreSNPAllelesWhenGenotypingIndels) {
// if there's an allele that has same length as the reference (i.e. a SNP or MNP), ignore
// it and don't genotype it
for (Allele a : vc.getAlleles())
if (a.isNonReference() && a.getBases().length == vc.getReference().getBases().length)
continue;
else alleleList.add(a);
} else {
for (Allele a : vc.getAlleles()) alleleList.add(a);
}
} else {
alleleList = computeConsensusAlleles(ref, contexts, contextType);
if (alleleList.isEmpty()) return null;
}
}
// protect against having an indel too close to the edge of a contig
if (loc.getStart() <= HAPLOTYPE_SIZE) return null;
// check if there is enough reference window to create haplotypes (can be an issue at end of
// contigs)
if (ref.getWindow().getStop() < loc.getStop() + HAPLOTYPE_SIZE) return null;
if (!(priors instanceof DiploidIndelGenotypePriors))
throw new StingException(
"Only diploid-based Indel priors are supported in the DINDEL GL model");
if (alleleList.isEmpty()) return null;
refAllele = alleleList.get(0);
altAllele = alleleList.get(1);
// look for alt allele that has biggest length distance to ref allele
int maxLenDiff = 0;
for (Allele a : alleleList) {
if (a.isNonReference()) {
int lenDiff = Math.abs(a.getBaseString().length() - refAllele.getBaseString().length());
if (lenDiff > maxLenDiff) {
maxLenDiff = lenDiff;
altAllele = a;
}
}
}
final int eventLength = altAllele.getBaseString().length() - refAllele.getBaseString().length();
final int hsize = (int) ref.getWindow().size() - Math.abs(eventLength) - 1;
final int numPrefBases = ref.getLocus().getStart() - ref.getWindow().getStart() + 1;
haplotypeMap =
Haplotype.makeHaplotypeListFromAlleles(
alleleList, loc.getStart(), ref, hsize, numPrefBases);
// For each sample, get genotype likelihoods based on pileup
// compute prior likelihoods on haplotypes, and initialize haplotype likelihood matrix with
// them.
// initialize the GenotypeLikelihoods
GLs.clear();
for (Map.Entry<String, AlignmentContext> sample : contexts.entrySet()) {
AlignmentContext context = AlignmentContextUtils.stratify(sample.getValue(), contextType);
ReadBackedPileup pileup = null;
if (context.hasExtendedEventPileup()) pileup = context.getExtendedEventPileup();
else if (context.hasBasePileup()) pileup = context.getBasePileup();
if (pileup != null) {
final double[] genotypeLikelihoods =
pairModel.computeReadHaplotypeLikelihoods(
pileup, haplotypeMap, ref, eventLength, getIndelLikelihoodMap());
GLs.put(
sample.getKey(),
new MultiallelicGenotypeLikelihoods(
sample.getKey(), alleleList, genotypeLikelihoods, getFilteredDepth(pileup)));
if (DEBUG) {
System.out.format("Sample:%s Alleles:%s GL:", sample.getKey(), alleleList.toString());
for (int k = 0; k < genotypeLikelihoods.length; k++)
System.out.format("%1.4f ", genotypeLikelihoods[k]);
System.out.println();
}
}
}
return refAllele;
}
public void writeBeagleOutput(
VariantContext preferredVC, VariantContext otherVC, boolean isValidationSite, double prior) {
GenomeLoc currentLoc =
VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), preferredVC);
StringBuffer beagleOut = new StringBuffer();
String marker = String.format("%s:%d ", currentLoc.getContig(), currentLoc.getStart());
beagleOut.append(marker);
if (markers != null)
markers.append(marker).append("\t").append(Integer.toString(markerCounter++)).append("\t");
for (Allele allele : preferredVC.getAlleles()) {
String bglPrintString;
if (allele.isNoCall() || allele.isNull()) bglPrintString = "-";
else bglPrintString = allele.getBaseString(); // get rid of * in case of reference allele
beagleOut.append(String.format("%s ", bglPrintString));
if (markers != null) markers.append(bglPrintString).append("\t");
}
if (markers != null) markers.append("\n");
GenotypesContext preferredGenotypes = preferredVC.getGenotypes();
GenotypesContext otherGenotypes = goodSite(otherVC) ? otherVC.getGenotypes() : null;
for (String sample : samples) {
boolean isMaleOnChrX = CHECK_IS_MALE_ON_CHR_X && getSample(sample).getGender() == Gender.MALE;
Genotype genotype;
boolean isValidation;
// use sample as key into genotypes structure
if (preferredGenotypes.containsSample(sample)) {
genotype = preferredGenotypes.get(sample);
isValidation = isValidationSite;
} else if (otherGenotypes != null && otherGenotypes.containsSample(sample)) {
genotype = otherGenotypes.get(sample);
isValidation = !isValidationSite;
} else {
// there is magically no genotype for this sample.
throw new StingException(
"Sample "
+ sample
+ " arose with no genotype in variant or validation VCF. This should never happen.");
}
/*
* Use likelihoods if: is validation, prior is negative; or: is not validation, has genotype key
*/
double[] log10Likelihoods = null;
if ((isValidation && prior < 0.0) || genotype.hasLikelihoods()) {
log10Likelihoods = genotype.getLikelihoods().getAsVector();
// see if we need to randomly mask out genotype in this position.
if (GenomeAnalysisEngine.getRandomGenerator().nextDouble() <= insertedNoCallRate) {
// we are masking out this genotype
log10Likelihoods =
isMaleOnChrX ? HAPLOID_FLAT_LOG10_LIKELIHOODS : DIPLOID_FLAT_LOG10_LIKELIHOODS;
}
if (isMaleOnChrX) {
log10Likelihoods[1] = -255; // todo -- warning this is dangerous for multi-allele case
}
}
/** otherwise, use the prior uniformly */
else if (!isValidation && genotype.isCalled() && !genotype.hasLikelihoods()) {
// hack to deal with input VCFs with no genotype likelihoods. Just assume the called
// genotype
// is confident. This is useful for Hapmap and 1KG release VCFs.
double AA = (1.0 - prior) / 2.0;
double AB = (1.0 - prior) / 2.0;
double BB = (1.0 - prior) / 2.0;
if (genotype.isHomRef()) {
AA = prior;
} else if (genotype.isHet()) {
AB = prior;
} else if (genotype.isHomVar()) {
BB = prior;
}
log10Likelihoods = MathUtils.toLog10(new double[] {AA, isMaleOnChrX ? 0.0 : AB, BB});
} else {
log10Likelihoods =
isMaleOnChrX ? HAPLOID_FLAT_LOG10_LIKELIHOODS : DIPLOID_FLAT_LOG10_LIKELIHOODS;
}
writeSampleLikelihoods(beagleOut, preferredVC, log10Likelihoods);
}
beagleWriter.println(beagleOut.toString());
}