Package htsjdk.variant.variantcontext

Examples of htsjdk.variant.variantcontext.VariantContextBuilder

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        context = new ReferenceContext(genomeLocParser, locus, (byte)'A');
        A = Allele.create("A", true);
        C = Allele.create("C");
        G = Allele.create("G");
        T = Allele.create("T");
        AC_SNP = new VariantContextBuilder("x", "chr1", START_POS, START_POS, Arrays.asList(A, C)).make();
        AG_SNP = new VariantContextBuilder("x", "chr1", START_POS, START_POS, Arrays.asList(A, G)).make();
        AT_SNP = new VariantContextBuilder("x", "chr1", START_POS, START_POS, Arrays.asList(A, T)).make();
        span10_10 = makeSpan(10, 10);
        span1_20 = makeSpan(1, 20);
        span10_20 = makeSpan(10, 20);
    }
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     * Test code that creates VariantContexts
     */
    @Test()
    public void testWithVariantContext() throws Exception {
        final List<Allele> alleles = Arrays.asList(Allele.create("A", true), Allele.create("C"));
        final VariantContext vc = new VariantContextBuilder("test", "1", 10, 10, alleles).make();
        Assert.assertTrue(vc.getAlleles().size() >= 0);
        // TODO -- add some tests that use VariantContext
    }
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        final Allele h1refAllele = Allele.create(ref, true);
        final Allele h1altAllele = Allele.create(alt, false);
        final ArrayList<Allele> alleles = new ArrayList<Allele>();
        alleles.add(h1refAllele);
        alleles.add(h1altAllele);
        final VariantContext vc = new VariantContextBuilder().alleles(alleles).loc("1", loc, loc + h1refAllele.getBases().length - 1).make();
        h.setAlignmentStartHapwrtRef(0);
        h.setCigar(cigar);
        final Haplotype h1 = h.insertAllele(vc.getReference(), vc.getAlternateAllele(0), loc, vc.getStart());
        final Haplotype h1expected = new Haplotype(newHap.getBytes());
        Assert.assertEquals(h1, h1expected);
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        Assert.assertEquals(loc.getStop(), feature.getEnd());
    }

    @Test
    public void testCreationFromVariantContext() {
        final VariantContext feature = new VariantContextBuilder("x", "chr1", 1, 5, Arrays.asList(Allele.create("AAAAA", true))).make();
        final GenomeLoc loc = genomeLocParser.createGenomeLoc(feature);
        Assert.assertEquals(loc.getContig(), feature.getChr());
        Assert.assertEquals(loc.getStart(), feature.getStart());
        Assert.assertEquals(loc.getStop(), feature.getEnd());
    }
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            filters.add("TooManyHomVars");
            numHomVarViolations++;
            isViolation = true;
        }

        VariantContextBuilder builder = new VariantContextBuilder(vContext).filters(filters);
        numRecords++;

        // add the info fields
        builder.attribute("NoCallPct", String.format("%.1f", 100.0 * noCallProp));
        builder.attribute("HomRefPct", String.format("%.1f", 100.0 * homRefProp));
        builder.attribute("HomVarPct", String.format("%.1f", 100.0 * homVarProp));
        builder.attribute("HetPct", String.format("%.1f", 100.0 * hetProp));
        builder.attribute("HW", String.format("%.2f", hwScore));
        Collection<Allele> altAlleles = vContext.getAlternateAlleles();
        int altAlleleCount = altAlleles.size() == 0 ? 0 : vContext.getCalledChrCount(altAlleles.iterator().next());
        if ( !isViolation && altAlleleCount > 0 )
            numTrueVariants++;
        builder.attribute(VCFConstants.ALLELE_COUNT_KEY, String.format("%d", altAlleleCount));
        builder.attribute(VCFConstants.ALLELE_NUMBER_KEY, String.format("%d", vContext.getCalledChrCount()));

        return builder.make();
    }
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        if ( ! isSingleton && hasChrCountAnnotations ) {
            // nothing to update
            return vcsub;
        } else {
            // have to do the work
            VariantContextBuilder builder = new VariantContextBuilder(vcsub);

            if ( isSingleton )
                builder.attribute(VariantEval.IS_SINGLETON_KEY, true);

            if ( ! hasChrCountAnnotations )
                VariantContextUtils.calculateChromosomeCounts(builder, true);

            return builder.make();
        }
    }
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    public VariantContext annotateRsID(final List<VariantContext> vcsAtLoc, final VariantContext vcToAnnotate ) {
        final String rsID = getRsID(vcsAtLoc, vcToAnnotate);

        // add the ID if appropriate
        if ( rsID != null ) {
            final VariantContextBuilder vcb = new VariantContextBuilder(vcToAnnotate);

            if ( ! vcToAnnotate.hasID() ) {
                return vcb.id(rsID).make();
            } else if ( ! vcToAnnotate.getID().contains(rsID) ) {
                return vcb.id(vcToAnnotate.getID() + VCFConstants.ID_FIELD_SEPARATOR + rsID).make();
            } // falling through to return VC lower down
        }

        // nothing to do, just return vc
        return vcToAnnotate;
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    public VariantContext annotateOverlap(final List<VariantContext> overlapTestVCs, final String attributeKey, VariantContext vcToAnnotate) {
        if ( overlapBindings.isEmpty() ) return vcToAnnotate;

        final boolean overlaps = overlaps(overlapTestVCs, vcToAnnotate);
        if ( overlaps ) {
            return new VariantContextBuilder(vcToAnnotate).attribute(attributeKey, true).make();
        } else {
            return vcToAnnotate;
        }
    }
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                continue;

            if ( mergedVC.hasAllele(GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE) )
                throw new UserException("CombineVariants should not be used to merge gVCFs produced by the HaplotypeCaller; use CombineGVCFs instead");

            final VariantContextBuilder builder = new VariantContextBuilder(mergedVC);
            // re-compute chromosome counts
            VariantContextUtils.calculateChromosomeCounts(builder, false);

            if ( minimalVCF )
                GATKVariantContextUtils.pruneVariantContext(builder, Arrays.asList(SET_KEY));
            final VariantContext vc = builder.make();
            if( !EXCLUDE_NON_VARIANTS || vc.isPolymorphicInSamples() )
                vcfWriter.add(builder.make());
        }

        return vcs.isEmpty() ? 0 : 1;
    }
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            // check whether the strand flips, and if so reverse complement everything
            if ( fromInterval.isPositiveStrand() != toInterval.isPositiveStrand() && vc.isPointEvent() ) {
                vc = GATKVariantContextUtils.reverseComplement(vc);
            }

            vc = new VariantContextBuilder(vc).loc(toInterval.getSequence(), toInterval.getStart(), toInterval.getStart() + length).make();

            if ( RECORD_ORIGINAL_LOCATION ) {
                vc = new VariantContextBuilder(vc)
                        .attribute("OriginalChr", fromInterval.getSequence())
                        .attribute("OriginalStart", fromInterval.getStart()).make();
            }

            if ( originalVC.isSNP() && originalVC.isBiallelic() && GATKVariantContextUtils.getSNPSubstitutionType(originalVC) != GATKVariantContextUtils.getSNPSubstitutionType(vc) ) {
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Related Classes of htsjdk.variant.variantcontext.VariantContextBuilder

  • org.broad.igv.plugin.mongovariant.VariantReviewTest
  • org.broad.igv.variant.vcf.VCFVariant
  • org.broadinstitute.gatk.engine.refdata.RefMetaDataTrackerUnitTest
  • org.broadinstitute.gatk.tools.walkers.annotator.VariantOverlapAnnotator
  • org.broadinstitute.gatk.tools.walkers.annotator.VariantOverlapAnnotatorUnitTest
  • org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AFCalculatorPerformanceTest$AnalyzeBySingletonPosition
  • org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.IndependentAllelesDiploidExactAFCalculatorUnitTest
  • org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotyperEngineUnitTest
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeResolver
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.LocalAssemblyEngineUnitTest
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