/** * @see #computeEndFromAlleles(java.util.List, int, int) with endForSymbolicAlleles == -1 */ public VariantContextBuilder computeEndFromAlleles(final List<Allele> alleles, final int start) { return computeEndFromAlleles(alleles, start, -1); }
/** * @see #computeEndFromAlleles(java.util.List, int, int) with endForSymbolicAlleles == -1 */ public VariantContextBuilder computeEndFromAlleles(final List<Allele> alleles, final int start) { return computeEndFromAlleles(alleles, start, -1); }
/** * @see #computeEndFromAlleles(java.util.List, int, int) with endForSymbolicAlleles == -1 */ public VariantContextBuilder computeEndFromAlleles(final List<Allele> alleles, final int start) { return computeEndFromAlleles(alleles, start, -1); }
private void writeVariant(VariantContextWriter writer, GenomeVariant genomeVar) { String nameInFasta = mapContigToFasta(genomeVar.getChrName()); List<Allele> alleles = new ArrayList<Allele>(); int shift = 0; if (genomeVar.getRef().isEmpty() || genomeVar.getAlt().isEmpty()) { shift = -1; String left = fasta.getSubsequenceAt(nameInFasta, genomeVar.getPos(), genomeVar.getPos()) .getBaseString(); alleles.add(Allele.create(left + genomeVar.getRef(), true)); alleles.add(Allele.create(left + genomeVar.getAlt(), false)); } else { alleles.add(Allele.create(genomeVar.getRef(), true)); alleles.add(Allele.create(genomeVar.getAlt(), false)); } VariantContextBuilder builder = new VariantContextBuilder(); builder.chr(genomeVar.getChrName()).start(genomeVar.getPos() + shift + 1) .computeEndFromAlleles(alleles, genomeVar.getPos() + shift + 1).alleles(alleles); writer.add(builder.make()); }
builder.computeEndFromAlleles(allAlleles, initialContext.getStart()); builder.log10PError(initialContext.getLog10PError());
builder.computeEndFromAlleles(allAlleles, initialContext.getStart()); builder.log10PError(initialContext.getLog10PError());
.chr(loc.getContig()).start(loc.getStart()).computeEndFromAlleles(nonSymbolicAlleles(allelesList), loc.getStart(), loc.getStart()) .genotypes(genotypes).unfiltered().attributes(new TreeMap<>(attributes)).log10PError(CommonInfo.NO_LOG10_PERROR); // we will need to re-genotype later