Package htsjdk.variant.vcf

Examples of htsjdk.variant.vcf.VCFFormatHeaderLine

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    @Override
    public List<String> getKeyNames() { return Collections.singletonList(STRAND_BIAS_BY_SAMPLE_KEY_NAME); }

    @Override
    public List<VCFFormatHeaderLine> getDescriptions() { return Collections.singletonList(new VCFFormatHeaderLine(getKeyNames().get(0), 4, VCFHeaderLineType.Integer, "Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.")); }
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    @Override
    public void initialize(final AnnotatorCompatible walker, final GenomeAnalysisEngine toolkit, final Set<VCFHeaderLine> headerLines) {
        boolean hasSBBSannotation = false;
        for ( final VCFHeaderLine line : headerLines) {
            if ( line instanceof VCFFormatHeaderLine) {
                final VCFFormatHeaderLine formatline = (VCFFormatHeaderLine)line;
                if ( formatline.getID().equals(StrandBiasBySample.STRAND_BIAS_BY_SAMPLE_KEY_NAME) ) {
                    hasSBBSannotation = true;
                    break;
                }
            }
        }
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    }

    public List<String> getKeyNames() { return Arrays.asList("AB"); }

    public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(new VCFFormatHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "Allele balance for each het genotype")); }
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    }

    public List<String> getKeyNames() { return Arrays.asList(VCFConstants.MAPPING_QUALITY_ZERO_KEY); }

    public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(
            new VCFFormatHeaderLine(getKeyNames().get(0), 1,
                    VCFHeaderLineType.Integer, "Number of Mapping Quality Zero Reads per sample")); }
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        final FilterApplyingVariantIterator iterator = new FilterApplyingVariantIterator(in.iterator(), variantFilters, genotypeFilters);

        final VariantContextWriter out = new VariantContextWriterBuilder().setOutputFile(OUTPUT).build();
        final VCFHeader header = in.getFileHeader();
        header.addMetaDataLine(new VCFFilterHeaderLine("AllGtsFiltered", "Site filtered out because all genotypes are filtered out."));
        header.addMetaDataLine(new VCFFormatHeaderLine("FT", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Genotype filters."));
        for (final VariantFilter filter : variantFilters) {
            for (final VCFFilterHeaderLine line : filter.headerLines()) {
                header.addMetaDataLine(line);
            }
        }
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Related Classes of htsjdk.variant.vcf.VCFFormatHeaderLine

  • org.broadinstitute.gatk.tools.walkers.annotator.AlleleBalanceBySample
  • org.broadinstitute.gatk.tools.walkers.annotator.MappingQualityZeroBySample
  • org.broadinstitute.gatk.tools.walkers.annotator.StrandBiasBySample
  • org.broadinstitute.gatk.tools.walkers.annotator.StrandBiasTest
  • picard.vcf.filter.FilterVcf
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