Examples of htsjdk.variant.variantcontext.VariantContextBuilder.stop()

Class htsjdk.variant.variantcontext.VariantContextBuilder

Examples of htsjdk.variant.variantcontext.VariantContextBuilder.stop()

htsjdk.variant.variantcontext.VariantContextBuilder.stop()

    private VariantContext blockToVCF(final HomRefBlock block) {
        if ( block == null ) return null;


        final VariantContextBuilder vcb = new VariantContextBuilder(block.getStartingVC());
        vcb.attributes(new HashMap<String, Object>(2)); // clear the attributes
        vcb.stop(block.getStop());
        vcb.attribute(VCFConstants.END_KEY, block.getStop());


        // create the single Genotype with GQ and DP annotations
        final GenotypeBuilder gb = new GenotypeBuilder(sampleName, GATKVariantContextUtils.homozygousAlleleList(block.getRef(),block.getPloidy()));
        gb.noAD().noPL().noAttributes(); // clear all attributes

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                alt = Allele.create(vc1.getAlternateAllele(0).getDisplayString() + vc2.getAlternateAllele(0).getDisplayString().substring(1), false);
            } else {
                // we're dealing with a deletion, so we patch the ref
                ref = vc2.getReference();
                alt = vc1.getAlternateAllele(0);
                b.stop(vc2.getEnd());
            }
        } else {
            final VariantContext insertion = vc1.isSimpleInsertion() ? vc1 : vc2;
            final VariantContext deletion  = vc1.isSimpleInsertion() ? vc2 : vc1;
            ref = deletion.getReference();

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        } else {
            final VariantContext insertion = vc1.isSimpleInsertion() ? vc1 : vc2;
            final VariantContext deletion  = vc1.isSimpleInsertion() ? vc2 : vc1;
            ref = deletion.getReference();
            alt = insertion.getAlternateAllele(0);
            b.stop(deletion.getEnd());
        }


        return b.alleles(Arrays.asList(ref, alt)).make();
    }

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        final byte[] refBases = Arrays.copyOfRange(ref, refStartOffset, refEndOffset + 1);
        final byte[] hapBases = AlignmentUtils.getBasesCoveringRefInterval(refStartOffset, refEndOffset, haplotype.getBases(), haplotype.getAlignmentStartHapwrtRef(), haplotype.getCigar());


        final VariantContextBuilder builder = new VariantContextBuilder(first);
        builder.stop(first.getStart() + refBases.length - 1);
        builder.alleles(Arrays.asList(Allele.create(refBases, true), Allele.create(hapBases)));
        final VariantContext block = builder.make();


        // remove all merged events
        for ( final VariantContext merged : neighbors ) {

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