Package htsjdk.variant.variantcontext

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

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        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());
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                }

                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);
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                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);
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                // 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);
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                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();
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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);
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        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);
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        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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            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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            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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