Examples of addMetaDataLine()

Examples of htsjdk.variant.vcf.VCFHeader.addMetaDataLine()

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        Assert.assertTrue(line1.toString().contains("ID=" + testEngine1.getWalkerName()));

        final VCFHeaderLine line2 = GATKVCFUtils.getCommandLineArgumentHeaderLine(testEngine2, Collections.EMPTY_LIST);
        logger.warn(line2);

        header.addMetaDataLine(line1);
        final Set<VCFHeaderLine> lines1 = header.getMetaDataInInputOrder();
        Assert.assertTrue(lines1.contains(line1));

        header.addMetaDataLine(line2);
        final Set<VCFHeaderLine> lines2 = header.getMetaDataInInputOrder();
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Examples of htsjdk.variant.vcf.VCFHeader.addMetaDataLine()

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        header.addMetaDataLine(line1);
        final Set<VCFHeaderLine> lines1 = header.getMetaDataInInputOrder();
        Assert.assertTrue(lines1.contains(line1));

        header.addMetaDataLine(line2);
        final Set<VCFHeaderLine> lines2 = header.getMetaDataInInputOrder();
        Assert.assertTrue(lines2.contains(line1));
        Assert.assertTrue(lines2.contains(line2));
    }
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Examples of htsjdk.variant.vcf.VCFHeader.addMetaDataLine()

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        final VCFFileReader in = new VCFFileReader(INPUT, false);
        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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Examples of htsjdk.variant.vcf.VCFHeader.addMetaDataLine()

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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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Examples of htsjdk.variant.vcf.VCFHeader.addMetaDataLine()

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        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);
            }
        }

        out.writeHeader(in.getFileHeader());
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