Examples with BufferedVCFReader com.github.lindenb.jvarkit.variant.vcf.BufferedVCFReader used on opensource projects

Example 6 with BufferedVCFReader

use of com.github.lindenb.jvarkit.variant.vcf.BufferedVCFReader in project jvarkit by lindenb.

the class VcfGnomadExomeVsGenome method isVariantIn.

boolean isVariantIn(final VariantContext ctx, final BufferedVCFReader reader) {
    final String ctg = this.ctgNameConverter.apply(ctx.getContig());
    if (StringUtils.isBlank(ctg))
        return false;
    try (CloseableIterator<VariantContext> iterE = reader.query(new SimpleInterval(ctg, ctx.getStart(), ctx.getEnd()))) {
        while (iterE.hasNext()) {
            final VariantContext ctx2 = iterE.next();
            if (ctx.getStart() != ctx2.getStart())
                continue;
            if (!ctx.getReference().equals(ctx2.getReference()))
                continue;
            final Set<Allele> alt2 = ctx2.getAlternateAlleles().stream().filter(A -> AcidNucleics.isATGC(A)).collect(Collectors.toSet());
            if (ctx.getAlternateAlleles().stream().anyMatch(A -> alt2.contains(A)))
                return true;
        }
    }
    return false;
}

Example 7 with BufferedVCFReader

use of com.github.lindenb.jvarkit.variant.vcf.BufferedVCFReader in project jvarkit by lindenb.

the class BamToHaplotypes method beforeSam.

@Override
protected int beforeSam() {
    this.vcfReader = VCFReaderFactory.makeDefault().open(this.vcfFile, true);
    this.bufferedVCFReader = new BufferedVCFReader(this.vcfReader, this.buffSizeInBp);
    this.bufferedVCFReader.setSimplifier(V -> simplify(V));
    return 0;
}