Package htsjdk.variant.variantcontext

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

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            ref = deletion.getReference();
            alt = insertion.getAlternateAllele(0);
            b.stop(deletion.getEnd());
        }

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

    // TODO -- warning this is an O(N^3) algorithm because I'm just lazy.  If it's valuable we need to reengineer it
    @Requires("getNumberOfEvents() > 0")
    protected void replaceClumpedEventsWithBlockSubstitutions() {
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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 ) {
            if ( remove(merged.getStart()) == null )
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    /** Makes a new VariantContext with only the desired samples. */
    private static VariantContext subsetToSamplesWithOriginalAnnotations(final VariantContext ctx, final Set<String> samples) {
        final VariantContextBuilder builder = new VariantContextBuilder(ctx);
        final GenotypesContext newGenotypes = ctx.getGenotypes().subsetToSamples(samples);
        builder.alleles(ctx.getAlleles());
        return builder.genotypes(newGenotypes).make();
    }
}
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