Package htsjdk.variant.variantcontext

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

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    public void setUp() throws Exception {
        super.setUp();
        VariantContextBuilder builder = new VariantContextBuilder();
        //Convert from exclusive end to inclusive end
        builder.start(start + 1).stop(end).chr(chr).alleles(alleles);
        VariantContext vc = builder.make();
        mvc = VariantReviewSource.createMVC(allele0, allele1, callsetName, vc, truthStatus, false);

        int errorsResetting = 0;
        try {
            errorsResetting = resetDB();
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            alleleList.add(htsjdk.variant.variantcontext.Allele.create(variant.getReference(), true));
            for (Allele all : variant.getAlternateAlleles()) {
                alleleList.add(htsjdk.variant.variantcontext.Allele.create(all.getBases(), false));
            }
            VariantContextBuilder vcb = new VariantContextBuilder(variant.getID(), variant.getChr(), variant.getStart(), variant.getEnd(), alleleList);
            return vcb.make();
        }
    }

    /**
     * @author Jim Robinson
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                    builder.passFilters();
                } else {
                    builder.filters(filterString);
                }

                final VariantContext outputVC = builder.make();
                if( !EXCLUDE_FILTERED || outputVC.isNotFiltered() ) {
                    vcfWriter.add( outputVC );
                }
            } else { // valid VC but not compatible with this mode, so just emit the variant untouched
                vcfWriter.add( vc );
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            builder.attribute(VariantRecalibrator.CULPRIT_KEY, (datum.worstAnnotation != -1 ? annotationKeys.get(datum.worstAnnotation) : "NULL"));

            if ( datum.atTrainingSite ) builder.attribute(VariantRecalibrator.POSITIVE_LABEL_KEY, true);
            if ( datum.atAntiTrainingSite ) builder.attribute(VariantRecalibrator.NEGATIVE_LABEL_KEY, true);

            recalWriter.add(builder.make());
        }
    }
}
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                    final List<Genotype> genotypes = new ArrayList<Genotype>(vc.getGenotypes());
                    Collections.rotate(genotypes, position);
                    vcb.genotypes(genotypes);

                    timer.start();
                    final AFCalculationResult resultTracker = calc.getLog10PNonRef(vcb.make(), HomoSapiensConstants.DEFAULT_PLOIDY, testBuilder.numAltAlleles, priors);
                    final long runtime = timer.getElapsedTimeNano();

                    final List<Object> columns = new LinkedList<Object>(coreValues);
                    columns.addAll(Arrays.asList(runtime, resultTracker.getnEvaluations(), nonTypePL, position));
                    report.addRowList(columns);
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            if ( vc.isPolymorphicInSamples() && hasPLs(vc) ) {
                synchronized (UG_engine) {
                    final VariantContextBuilder builder = new VariantContextBuilder(UG_engine.calculateGenotypes(vc)).filters(vc.getFiltersMaybeNull());
                    VariantContextUtils.calculateChromosomeCounts(builder, false);
                    vc = builder.make();
                }
            }

            vcfWriter.add(vc);
        }
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    public void testAssembleRefAndSNP(final ReadThreadingAssembler assembler, final GenomeLoc loc, final int nReadsToUse, final int variantSite) {
        final byte[] refBases = seq.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases();
        final Allele refBase = Allele.create(refBases[variantSite], true);
        final Allele altBase = Allele.create((byte)(refBase.getBases()[0] == 'A' ? 'C' : 'A'), false);
        final VariantContextBuilder vcb = new VariantContextBuilder("x", loc.getContig(), variantSite, variantSite, Arrays.asList(refBase, altBase));
        testAssemblyWithVariant(assembler, refBases, loc, nReadsToUse, vcb.make());
    }

    @Test(dataProvider = "AssembleIntervalsWithVariantData")
    public void testAssembleRefAndDeletion(final ReadThreadingAssembler assembler, final GenomeLoc loc, final int nReadsToUse, final int variantSite) {
        final byte[] refBases = seq.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases();
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        final byte[] refBases = seq.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases();
        for ( int deletionLength = 1; deletionLength < 10; deletionLength++ ) {
            final Allele refBase = Allele.create(new String(refBases).substring(variantSite, variantSite + deletionLength + 1), true);
            final Allele altBase = Allele.create(refBase.getBases()[0], false);
            final VariantContextBuilder vcb = new VariantContextBuilder("x", loc.getContig(), variantSite, variantSite + deletionLength, Arrays.asList(refBase, altBase));
            testAssemblyWithVariant(assembler, refBases, loc, nReadsToUse, vcb.make());
        }
    }

    @Test(dataProvider = "AssembleIntervalsWithVariantData")
    public void testAssembleRefAndInsertion(final ReadThreadingAssembler assembler, final GenomeLoc loc, final int nReadsToUse, final int variantSite) {
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        final byte[] refBases = seq.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases();
        for ( int insertionLength = 1; insertionLength < 10; insertionLength++ ) {
            final Allele refBase = Allele.create(refBases[variantSite], false);
            final Allele altBase = Allele.create(new String(refBases).substring(variantSite, variantSite + insertionLength + 1), true);
            final VariantContextBuilder vcb = new VariantContextBuilder("x", loc.getContig(), variantSite, variantSite + insertionLength, Arrays.asList(refBase, altBase));
            testAssemblyWithVariant(assembler, refBases, loc, nReadsToUse, vcb.make());
        }
    }

    private void testAssemblyWithVariant(final ReadThreadingAssembler assembler, final byte[] refBases, final GenomeLoc loc, final int nReadsToUse, final VariantContext site) {
        final String preRef = new String(refBases).substring(0, site.getStart());
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        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 )
                throw new IllegalArgumentException("Expected to remove variant context from the event map but remove said there wasn't any element there: " + merged);
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