Package htsjdk.variant.variantcontext

Examples of htsjdk.variant.variantcontext.GenotypeBuilder

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        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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        Allele[] alleles = new Allele[ploidy];
       
        for (int i=0; i < ploidy; i++)
            alleles[i] = Allele.NO_CALL;
       
        return new GenotypeBuilder(name, Arrays.asList(alleles)).PL(gls).make();
    }                             
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    @Test
    public void testMinMedian() {
        //TODO - might be better to make this test use a data provider?
        final HomRefBlock band = new HomRefBlock(vc, 10, 20, HomoSapiensConstants.DEFAULT_PLOIDY);
        final GenotypeBuilder gb = new GenotypeBuilder("NA12878");
        gb.alleles(vc.getAlleles());

        int pos = vc.getStart();
        band.add(pos++, gb.DP(10).GQ(11).PL(new int[]{0,11,100}).make());
        Assert.assertEquals(band.getStop(), pos - 1);
        assertValues(band, 10, 10, 11, 11);

        band.add(pos++, gb.DP(11).GQ(10).PL(new int[]{0,10,100}).make());
        Assert.assertEquals(band.getStop(), pos - 1);
        assertValues(band, 10, 11, 10, 11);

        band.add(pos++, gb.DP(12).GQ(12).PL(new int[]{0,12,100}).make());
        Assert.assertEquals(band.getStop(), pos - 1);
        assertValues(band, 10, 11, 10, 11);

        band.add(pos++, gb.DP(13).GQ(15).PL(new int[]{0,15,100}).make());
        Assert.assertEquals(band.getStop(), pos - 1);
        band.add(pos++, gb.DP(14).GQ(16).PL(new int[]{0,16,100}).make());
        Assert.assertEquals(band.getStop(), pos - 1);
        band.add(pos++, gb.DP(15).GQ(17).PL(new int[]{0,17,100}).make());
        Assert.assertEquals(band.getStop(), pos - 1);
        band.add(pos++, gb.DP(16).GQ(18).PL(new int[]{0,18,100}).make());
        Assert.assertEquals(band.getStop(), pos - 1);
        assertValues(band, 10, 13, 10, 15);
        Assert.assertEquals(band.getSize(), pos - vc.getStart());
        Assert.assertTrue(Arrays.equals(band.getMinPLs(), new int[]{0,10,100}));
    }
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    }

    @Test
    public void testBigGQIsCapped() {
        final HomRefBlock band = new HomRefBlock(vc, 10, 20, HomoSapiensConstants.DEFAULT_PLOIDY);
        final GenotypeBuilder gb = new GenotypeBuilder("NA12878");
        gb.alleles(vc.getAlleles());

        band.add(vc.getStart(), gb.DP(1000).GQ(1000).PL(new int[]{0,10,100}).make());
        assertValues(band, 1000, 1000, 99, 99);
    }
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    }

    @Test(expectedExceptions = IllegalArgumentException.class)
    public void testBadAdd() {
        final HomRefBlock band = new HomRefBlock(vc, 10, 20, HomoSapiensConstants.DEFAULT_PLOIDY);
        final GenotypeBuilder gb = new GenotypeBuilder("NA12878");

        band.add(vc.getStart() + 10, gb.DP(10).GQ(11).PL(new int[]{0,10,100}).make());
    }
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        // Apply filters to the necessary genotypes
        builder.noGenotypes();
        final List<Genotype> newGenotypes = new ArrayList<Genotype>(ctx.getNSamples());
        for (final Genotype gt : ctx.getGenotypes()) {
            final GenotypeBuilder gtBuilder = new GenotypeBuilder(gt);
            final List<String> filters = gtFilterStrings.get(gt.getSampleName());

            if (filters == null || filters.isEmpty()) {
                gtBuilder.filter(PASS_FILTER);
            }
            else {
                gtBuilder.filters(filters);
            }
            newGenotypes.add(gtBuilder.make());
        }
        builder.genotypes(newGenotypes);

        return builder.make();
    }
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        testGenotypeConcordanceDetermineState(vcFiltered, TruthState.VC_FILTERED, vcFiltered, CallState.VC_FILTERED, 0, 0);

        // Filtering on the genotype
        final List<String> gtFilters = new ArrayList<String>(Arrays.asList("WICKED"));
        final List<Allele> alleles3 = makeUniqueListOfAlleles(Aref, C);
        final Genotype gt3 = new GenotypeBuilder(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, C)).filters(gtFilters).make();
        final VariantContext vcGtFiltered = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, alleles3).genotypes(gt3).make();

        testGenotypeConcordanceDetermineState(vcGtFiltered, TruthState.GT_FILTERED, vcNotFiltered, CallState.HET_REF_VAR1, 0, 0);
        testGenotypeConcordanceDetermineState(vcNotFiltered, TruthState.HET_REF_VAR1, vcGtFiltered, CallState.GT_FILTERED, 0, 0);
        testGenotypeConcordanceDetermineState(vcGtFiltered, TruthState.GT_FILTERED, vcGtFiltered, CallState.GT_FILTERED, 0, 0);
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        final List<Allele> allelesNormal = makeUniqueListOfAlleles(Aref, C);
        final Genotype gtNormal = GenotypeBuilder.create(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, C));
        final VariantContext vcNormal = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, allelesNormal).genotypes(gtNormal).make();

        final List<Allele> allelesLowDp = makeUniqueListOfAlleles(Aref, C);
        final Genotype gtLowDp = new GenotypeBuilder(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, C)).DP(4).make();
        final VariantContext vcLowDp = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, allelesLowDp).genotypes(gtLowDp).make();

        testGenotypeConcordanceDetermineState(vcLowDp, TruthState.LOW_DP, vcNormal, CallState.HET_REF_VAR1, 0, 20);
        testGenotypeConcordanceDetermineState(vcLowDp, TruthState.HET_REF_VAR1, vcLowDp, CallState.HET_REF_VAR1, 0, 2);
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        final List<Allele> allelesNormal = makeUniqueListOfAlleles(Aref, C);
        final Genotype gtNormal = GenotypeBuilder.create(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, C));
        final VariantContext vcNormal = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, allelesNormal).genotypes(gtNormal).make();

        final List<Allele> allelesLowGq = makeUniqueListOfAlleles(Aref, C);
        final Genotype gtLowGq = new GenotypeBuilder(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, C)).GQ(4).make();
        final VariantContext vcLowGq = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, allelesLowGq).genotypes(gtLowGq).make();

        testGenotypeConcordanceDetermineState(vcLowGq, TruthState.LOW_GQ, vcNormal, CallState.HET_REF_VAR1, 20, 0);
        testGenotypeConcordanceDetermineState(vcLowGq, TruthState.HET_REF_VAR1, vcLowGq, CallState.HET_REF_VAR1, 2, 0);
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Related Classes of htsjdk.variant.variantcontext.GenotypeBuilder

  • org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.GeneralPloidyAFCalculationModelUnitTest
  • org.broadinstitute.gatk.utils.gvcf.GVCFWriter
  • org.broadinstitute.gatk.utils.gvcf.HomRefBlockUnitTest
  • picard.vcf.filter.FilterApplyingVariantIterator
  • picard.vcf.GenotypeConcordanceTest
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