Package htsjdk.variant.variantcontext

Examples of htsjdk.variant.variantcontext.VariantContextBuilder

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                    // for each eval in the track
                    for ( VariantContext eval : evalSetBySample ) {
                        // deal with ancestral alleles if requested
                        if ( eval != null && aastr != null ) {
                            eval = new VariantContextBuilder(eval).attribute("ANCESTRALALLELE", aastr).make();
                        }

                        // for each comp track
                        for ( final RodBinding<VariantContext> compRod : comps ) {
                            // no sample stratification for comps
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        return 0;
    }

    /** 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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        if (gtFilterStrings.keySet().containsAll(variantSamples)) {
            filterStrings.add(ALL_GTS_FILTERED);
        }

        // Make a builder and set the site level filter appropriately
        final VariantContextBuilder builder = new VariantContextBuilder(ctx);
        if (filterStrings.isEmpty()) {
            builder.passFilters();
        }
        else {
            builder.filters(filterStrings);
        }

        // 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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  private static VariantContext buildVariantContext(final String source, final String contig, final long start) {
    final Collection<Allele> alleles = new ArrayList<Allele>();
    alleles.add(Allele.create("AAAA", true));
    alleles.add(Allele.create("AAGG", false));
    return new VariantContextBuilder(source, contig, start, start + 3, alleles).make();
  }
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    public void testGenotypeConcordanceDetermineState(final Allele truthAllele1, final Allele truthAllele2, final TruthState expectedTruthState,
                                                      final Allele callAllele1, final Allele callAllele2, final CallState expectedCallState) throws Exception {
        final List<Allele> truthAlleles = makeUniqueListOfAlleles(truthAllele1, truthAllele2);
        final Genotype truthGt = GenotypeBuilder.create(TRUTH_SAMPLE_NAME, Arrays.asList(truthAllele1, truthAllele2));

        final VariantContext truthVariantContext = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, truthAlleles).genotypes(truthGt).make();

        final List<Allele> callAlleles = makeUniqueListOfAlleles(callAllele1, callAllele2);
        final Genotype callGt = GenotypeBuilder.create(CALL_SAMPLE_NAME, Arrays.asList(callAllele1, callAllele2));
        final VariantContext callVariantContext = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, callAlleles).genotypes(callGt).make();

        testGenotypeConcordanceDetermineState(truthVariantContext, expectedTruthState, callVariantContext, expectedCallState, 0, 0);
    }
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    @Test
    public void testGenotypeConcordanceDetermineStateNull() throws Exception {
        final List<Allele> alleles = makeUniqueListOfAlleles(Aref, C);
        final Genotype gt1 = GenotypeBuilder.create(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, C));
        final VariantContext vc1 = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, alleles).genotypes(gt1).make();

        testGenotypeConcordanceDetermineState(null, TruthState.MISSING, null, CallState.MISSING, 0, 0);
        testGenotypeConcordanceDetermineState(vc1, TruthState.HET_REF_VAR1, null, CallState.MISSING, 0, 0);
        testGenotypeConcordanceDetermineState(null, TruthState.MISSING, vc1, CallState.HET_REF_VAR1, 0, 0);
    }
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        final Set<String> filters = new HashSet<String>(Arrays.asList("BAD!"));

        // Filtering on the variant context
        final List<Allele> alleles1 = makeUniqueListOfAlleles(Aref, C);
        final Genotype gt1 = GenotypeBuilder.create(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, C));
        final VariantContext vcFiltered = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, alleles1).genotypes(gt1).filters(filters).make();

        final List<Allele> alleles2 = makeUniqueListOfAlleles(Aref, T);
        final Genotype gt2 = GenotypeBuilder.create(TRUTH_SAMPLE_NAME, Arrays.asList(Aref, T));
        final VariantContext vcNotFiltered = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, alleles2).genotypes(gt2).make();

        testGenotypeConcordanceDetermineState(vcFiltered, TruthState.VC_FILTERED, vcNotFiltered, CallState.HET_REF_VAR1, 0, 0);
        testGenotypeConcordanceDetermineState(vcNotFiltered, TruthState.HET_REF_VAR1, vcFiltered, CallState.VC_FILTERED, 0, 0);
        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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    @Test
    public void testGenotypeConcordanceDetermineStateDp() throws Exception {
        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);

        testGenotypeConcordanceDetermineState(vcNormal, TruthState.HET_REF_VAR1, vcLowDp, CallState.LOW_DP, 0, 20);
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    @Test
    public void testGenotypeConcordanceDetermineStateGq() throws Exception {
        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);

        testGenotypeConcordanceDetermineState(vcNormal, TruthState.HET_REF_VAR1, vcLowGq, CallState.LOW_GQ, 20, 0);
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