Package htsjdk.variant.variantcontext

Examples of htsjdk.variant.variantcontext.VariantContextBuilder

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    private VariantReviewSource source;

    @Before
    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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            List<htsjdk.variant.variantcontext.Allele> alleleList = new ArrayList<htsjdk.variant.variantcontext.Allele>(variant.getAlternateAlleles().size() + 1);
            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();
        }
    }
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            }
        }

        if (vcfWriter != null && writeVariant) {
            if (!vcComp.hasAttribute("callStatus")) {
                vcfWriter.add(new VariantContextBuilder(vcComp).attribute("callStatus", call.isCalledAlt(callConf) ? "ALT" : "REF").make());
            }
            else
                vcfWriter.add(vcComp);
        }
        return counter;
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     * is no variant-context to be output into the VCF.
     */
    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
        gb.GQ(block.getMedianGQ());
        gb.DP(block.getMedianDP());
        gb.attribute(MIN_DP_FORMAT_FIELD, block.getMinDP());
        gb.PL(block.getMinPLs());

        // This annotation is no longer standard
        //gb.attribute(MIN_GQ_FORMAT_FIELD, block.getMinGQ());

        return vcb.genotypes(gb.make()).make();
    }
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                    lod = Double.valueOf(lodString);
                } catch (NumberFormatException e) {
                    throw new UserException("Encountered a malformed record in the input recal file. The lod is unreadable for the record at: " + vc );
                }

                VariantContextBuilder builder = new VariantContextBuilder(vc);

                // Annotate the new record with its VQSLOD and the worst performing annotation
                builder.attribute(VariantRecalibrator.VQS_LOD_KEY, lod);
                builder.attribute(VariantRecalibrator.CULPRIT_KEY, recalDatum.getAttribute(VariantRecalibrator.CULPRIT_KEY));
                if ( recalDatum.hasAttribute(VariantRecalibrator.POSITIVE_LABEL_KEY))
                    builder.attribute(VariantRecalibrator.POSITIVE_LABEL_KEY, true);
                if ( recalDatum.hasAttribute(VariantRecalibrator.NEGATIVE_LABEL_KEY))
                    builder.attribute(VariantRecalibrator.NEGATIVE_LABEL_KEY, true);

                final String filterString = generateFilterString(lod);

                if( filterString.equals(VCFConstants.PASSES_FILTERS_v4) ) {
                    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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    @DataProvider(name = "TestMakeAlleleConditionalContexts")
    public Object[][] makeTestMakeAlleleConditionalContexts() {
        List<Object[]> tests = new ArrayList<Object[]>();

        final VariantContextBuilder root = new VariantContextBuilder("x", "1", 1, 1, Arrays.asList(A));
        final VariantContextBuilder vcAC = new VariantContextBuilder(root).alleles(Arrays.asList(A, C));
        final VariantContextBuilder vcAG = new VariantContextBuilder(root).alleles(Arrays.asList(A, G));
        final VariantContextBuilder vcACG = new VariantContextBuilder(root).alleles(Arrays.asList(A, C, G));
        final VariantContextBuilder vcAGC = new VariantContextBuilder(root).alleles(Arrays.asList(A, G, C));

        final Genotype gACG = makePL( 0, 1, 2, 3, 4, 5);
        final Genotype gAGC = makePL( 0, 4, 5, 1, 3, 2);
        final Genotype gACcombined = makePL(0, 2, 5);
        final Genotype gACcombined2 = makePL(0, 1, 4);
        final Genotype gAGcombined = makePL(0, 4, 9);

        // biallelic
        tests.add(new Object[]{vcAC.genotypes(gACcombined).make(), Arrays.asList(vcAC.genotypes(gACcombined).make())});

        // tri-allelic
        tests.add(new Object[]{vcACG.genotypes(gACG).make(), Arrays.asList(vcAC.genotypes(gACcombined).make(), vcAG.genotypes(gAGcombined).make())});
        tests.add(new Object[]{vcAGC.genotypes(gAGC).make(), Arrays.asList(vcAG.genotypes(gAGcombined).make(), vcAC.genotypes(gACcombined2).make())});

        return tests.toArray(new Object[][]{});
    }
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        // create dummy alleles to be used
        final List<Allele> alleles = Arrays.asList(Allele.create("N", true), Allele.create("<VQSR>", false));

        for( final VariantDatum datum : data ) {
            VariantContextBuilder builder = new VariantContextBuilder("VQSR", datum.loc.getContig(), datum.loc.getStart(), datum.loc.getStop(), alleles);
            builder.attribute(VCFConstants.END_KEY, datum.loc.getStop());
            builder.attribute(VariantRecalibrator.VQS_LOD_KEY, String.format("%.4f", datum.lod));
            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 int[] ac = new int[testBuilder.numAltAlleles];
                ac[0] = 1;
                final VariantContext vc = testBuilder.makeACTest(ac, 0, nonTypePL);

                for ( final int position : MathUtils.log10LinearRange(0, vc.getNSamples(), 0.1) ) {
                    final VariantContextBuilder vcb = new VariantContextBuilder(vc);
                    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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        for (VariantContext vc : vcs) {

            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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        }
        final GenomeLoc loc = genomeLocParser.createGenomeLoc(artificialContig,locStart+offset,locStart+offset);
        final ReferenceContext referenceContext = new ReferenceContext(genomeLocParser,loc,window,windowBases.getBytes());

        final VariantContext vc = new VariantContextBuilder("test", artificialContig, locStart+offset, locStart+offset+alleles.get(0).length()-1, alleles).make();
        final Pair<VariantContext,Integer> result = LeftAlignAndTrimVariants.alignAndWrite(vc,referenceContext);
        Assert.assertTrue(result.second == (offset>0?1:0));
        Assert.assertEquals(result.first.getStart(), locStart);

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