private static void mergeGenotypes( GenotypesContext mergedGenotypes, VariantContext oneVC, AlleleMapper alleleMapping, boolean uniqifySamples) { for (Genotype g : oneVC.getGenotypes()) { String name = mergedSampleName(oneVC.getSource(), g.getSampleName(), uniqifySamples); if (!mergedGenotypes.containsSample(name)) { // only add if the name is new Genotype newG = g; if (uniqifySamples || alleleMapping.needsRemapping()) { final List<Allele> alleles = alleleMapping.needsRemapping() ? alleleMapping.remap(g.getAlleles()) : g.getAlleles(); newG = new Genotype( name, alleles, g.getLog10PError(), g.getFilters(), g.getAttributes(), g.isPhased()); } mergedGenotypes.add(newG); } } }
public static Genotype removePLs(Genotype g) { Map<String, Object> attrs = new HashMap<String, Object>(g.getAttributes()); attrs.remove(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY); attrs.remove(VCFConstants.GENOTYPE_LIKELIHOODS_KEY); return new Genotype( g.getSampleName(), g.getAlleles(), g.getLog10PError(), g.filtersWereApplied() ? g.getFilters() : null, attrs, g.isPhased()); }
public static VariantContext purgeUnallowedGenotypeAttributes( VariantContext vc, Set<String> allowedAttributes) { if (allowedAttributes == null) return vc; GenotypesContext newGenotypes = GenotypesContext.create(vc.getNSamples()); for (final Genotype genotype : vc.getGenotypes()) { Map<String, Object> attrs = new HashMap<String, Object>(); for (Map.Entry<String, Object> attr : genotype.getAttributes().entrySet()) { if (allowedAttributes.contains(attr.getKey())) attrs.put(attr.getKey(), attr.getValue()); } newGenotypes.add(Genotype.modifyAttributes(genotype, attrs)); } return new VariantContextBuilder(vc).genotypes(newGenotypes).make(); }
public static VariantContext createVariantContextWithPaddedAlleles( VariantContext inputVC, boolean refBaseShouldBeAppliedToEndOfAlleles) { // see if we need to pad common reference base from all alleles boolean padVC; // We need to pad a VC with a common base if the length of the reference allele is less than the // length of the VariantContext. // This happens because the position of e.g. an indel is always one before the actual event (as // per VCF convention). long locLength = (inputVC.getEnd() - inputVC.getStart()) + 1; if (inputVC.hasSymbolicAlleles()) padVC = true; else if (inputVC.getReference().length() == locLength) padVC = false; else if (inputVC.getReference().length() == locLength - 1) padVC = true; else throw new IllegalArgumentException( "Badly formed variant context at location " + String.valueOf(inputVC.getStart()) + " in contig " + inputVC.getChr() + ". Reference length must be at most one base shorter than location size"); // nothing to do if we don't need to pad bases if (padVC) { if (!inputVC.hasReferenceBaseForIndel()) throw new ReviewedStingException( "Badly formed variant context at location " + inputVC.getChr() + ":" + inputVC.getStart() + "; no padded reference base is available."); Byte refByte = inputVC.getReferenceBaseForIndel(); List<Allele> alleles = new ArrayList<Allele>(); for (Allele a : inputVC.getAlleles()) { // get bases for current allele and create a new one with trimmed bases if (a.isSymbolic()) { alleles.add(a); } else { String newBases; if (refBaseShouldBeAppliedToEndOfAlleles) newBases = a.getBaseString() + new String(new byte[] {refByte}); else newBases = new String(new byte[] {refByte}) + a.getBaseString(); alleles.add(Allele.create(newBases, a.isReference())); } } // now we can recreate new genotypes with trimmed alleles GenotypesContext genotypes = GenotypesContext.create(inputVC.getNSamples()); for (final Genotype g : inputVC.getGenotypes()) { List<Allele> inAlleles = g.getAlleles(); List<Allele> newGenotypeAlleles = new ArrayList<Allele>(g.getAlleles().size()); for (Allele a : inAlleles) { if (a.isCalled()) { if (a.isSymbolic()) { newGenotypeAlleles.add(a); } else { String newBases; if (refBaseShouldBeAppliedToEndOfAlleles) newBases = a.getBaseString() + new String(new byte[] {refByte}); else newBases = new String(new byte[] {refByte}) + a.getBaseString(); newGenotypeAlleles.add(Allele.create(newBases, a.isReference())); } } else { // add no-call allele newGenotypeAlleles.add(Allele.NO_CALL); } } genotypes.add( new Genotype( g.getSampleName(), newGenotypeAlleles, g.getLog10PError(), g.getFilters(), g.getAttributes(), g.isPhased())); } return new VariantContextBuilder(inputVC).alleles(alleles).genotypes(genotypes).make(); } else return inputVC; }