Examples of VCFHeaderLine

Examples of htsjdk.variant.vcf.VCFHeaderLine

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                ", maxGQ=" + maxGQ +
                '}';
    }

    public VCFHeaderLine toVCFHeaderLine() {
        return new VCFHeaderLine("GVCFBlock", "minGQ=" + getGQLowerBound() + "(inclusive),maxGQ=" + getGQUpperBound() + "(exclusive)");
    }
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Examples of htsjdk.variant.vcf.VCFHeaderLine

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                selectedTypes.add(t);

        }

        Set<VCFHeaderLine> headerLines = new HashSet<VCFHeaderLine>();
        headerLines.add(new VCFHeaderLine("source", "ValidationSiteSelector"));
        vcfWriter.writeHeader(new VCFHeader(headerLines));

    }
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Examples of htsjdk.variant.vcf.VCFHeaderLine

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                1, Arrays.asList(""));
        spec.disableShadowBCF();
        final File vcf = executeTest("testGATKVersionInVCF", spec).first.get(0);
        final VCFCodec codec = new VCFCodec();
        final VCFHeader header = (VCFHeader) codec.readActualHeader(codec.makeSourceFromStream(new FileInputStream(vcf)));
        final VCFHeaderLine versionLine = header.getMetaDataLine(GATKVCFUtils.GATK_COMMAND_LINE_KEY);
        Assert.assertNotNull(versionLine);
        Assert.assertTrue(versionLine.toString().contains("SelectVariants"));
    }
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Examples of htsjdk.variant.vcf.VCFHeaderLine

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        testEngine1.setWalker(walker1);

        final GenomeAnalysisEngine testEngine2 = new GenomeAnalysisEngine();
        testEngine2.setWalker(walker2);

        final VCFHeaderLine line1 = GATKVCFUtils.getCommandLineArgumentHeaderLine(testEngine1, Collections.EMPTY_LIST);
        logger.warn(line1);
        Assert.assertNotNull(line1);
        Assert.assertEquals(line1.getKey(), GATKVCFUtils.GATK_COMMAND_LINE_KEY);
        for ( final String field : Arrays.asList("Version", "ID", "Date", "CommandLineOptions"))
            Assert.assertTrue(line1.toString().contains(field), "Couldn't find field " + field + " in " + line1.getValue());
        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));
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Examples of htsjdk.variant.vcf.VCFHeaderLine

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        if ( header.isWriteEngineHeaders() ) {
            // skip writing the command line header if requested
            if ( ! skipWritingCommandLineHeader && header.isWriteCommandLine() ) {
                // Always add the header line, as the current format allows multiple entries
                final VCFHeaderLine commandLineArgHeaderLine = GATKVCFUtils.getCommandLineArgumentHeaderLine(engine, argumentSources);
                vcfHeader.addMetaDataLine(commandLineArgHeaderLine);
            }

            if ( UPDATE_CONTIG_HEADERS )
                vcfHeader = GATKVCFUtils.withUpdatedContigs(vcfHeader, engine);
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