/** * Returns a context identical to this with the REF and ALT alleles reverse complemented. * * @param vc variant context * @return new vc */ public static VariantContext reverseComplement(VariantContext vc) { // create a mapping from original allele to reverse complemented allele HashMap<Allele, Allele> alleleMap = new HashMap<Allele, Allele>(vc.getAlleles().size()); for (Allele originalAllele : vc.getAlleles()) { Allele newAllele; if (originalAllele.isNoCall() || originalAllele.isNull()) newAllele = originalAllele; else newAllele = Allele.create( BaseUtils.simpleReverseComplement(originalAllele.getBases()), originalAllele.isReference()); alleleMap.put(originalAllele, newAllele); } // create new Genotype objects GenotypesContext newGenotypes = GenotypesContext.create(vc.getNSamples()); for (final Genotype genotype : vc.getGenotypes()) { List<Allele> newAlleles = new ArrayList<Allele>(); for (Allele allele : genotype.getAlleles()) { Allele newAllele = alleleMap.get(allele); if (newAllele == null) newAllele = Allele.NO_CALL; newAlleles.add(newAllele); } newGenotypes.add(Genotype.modifyAlleles(genotype, newAlleles)); } return new VariantContextBuilder(vc).alleles(alleleMap.values()).genotypes(newGenotypes).make(); }
public static VariantContext createVariantContextWithTrimmedAlleles(VariantContext inputVC) { // see if we need to trim common reference base from all alleles boolean trimVC; // We need to trim common reference base from all alleles in all genotypes if a ref base is // common to all alleles Allele refAllele = inputVC.getReference(); if (!inputVC.isVariant()) trimVC = false; else if (refAllele.isNull()) trimVC = false; else { trimVC = (AbstractVCFCodec.computeForwardClipping( new ArrayList<Allele>(inputVC.getAlternateAlleles()), inputVC.getReference().getDisplayString()) > 0); } // nothing to do if we don't need to trim bases if (trimVC) { List<Allele> alleles = new ArrayList<Allele>(); GenotypesContext genotypes = GenotypesContext.create(); // set the reference base for indels in the attributes Map<String, Object> attributes = new TreeMap<String, Object>(inputVC.getAttributes()); Map<Allele, Allele> originalToTrimmedAlleleMap = new HashMap<Allele, Allele>(); for (Allele a : inputVC.getAlleles()) { if (a.isSymbolic()) { alleles.add(a); originalToTrimmedAlleleMap.put(a, a); } else { // get bases for current allele and create a new one with trimmed bases byte[] newBases = Arrays.copyOfRange(a.getBases(), 1, a.length()); Allele trimmedAllele = Allele.create(newBases, a.isReference()); alleles.add(trimmedAllele); originalToTrimmedAlleleMap.put(a, trimmedAllele); } } // detect case where we're trimming bases but resulting vc doesn't have any null allele. In // that case, we keep original representation // example: mixed records such as {TA*,TGA,TG} boolean hasNullAlleles = false; for (Allele a : originalToTrimmedAlleleMap.values()) { if (a.isNull()) hasNullAlleles = true; if (a.isReference()) refAllele = a; } if (!hasNullAlleles) return inputVC; // now we can recreate new genotypes with trimmed alleles for (final Genotype genotype : inputVC.getGenotypes()) { List<Allele> originalAlleles = genotype.getAlleles(); List<Allele> trimmedAlleles = new ArrayList<Allele>(); for (Allele a : originalAlleles) { if (a.isCalled()) trimmedAlleles.add(originalToTrimmedAlleleMap.get(a)); else trimmedAlleles.add(Allele.NO_CALL); } genotypes.add(Genotype.modifyAlleles(genotype, trimmedAlleles)); } final VariantContextBuilder builder = new VariantContextBuilder(inputVC); return builder .alleles(alleles) .genotypes(genotypes) .attributes(attributes) .referenceBaseForIndel(new Byte(inputVC.getReference().getBases()[0])) .make(); } return inputVC; }