Package htsjdk.variant.variantcontext

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

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        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();
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        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());
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        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 )
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        // 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++;
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        // 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));
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        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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        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();
    }

    private double hardyWeinbergCalculation(VariantContext vc) {
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        } 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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