Examples of readActualHeader()

Examples of htsjdk.variant.vcf.VCFCodec.readActualHeader()

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        sample2_expected[4] = new int[]{0,1,0,0,0,0};

        List<Pair<VariantContext,VariantContext>> data = getData6();

        VCFCodec codec = new VCFCodec();
        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_2_HEADER))));
        VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_2_HEADER))));
        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader,null);

        for ( Pair<VariantContext,VariantContext> contextPair : data ) {
            VariantContext eval = contextPair.getFirst();
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Examples of htsjdk.variant.vcf.VCFCodec.readActualHeader()

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        List<Pair<VariantContext,VariantContext>> data = getData6();

        VCFCodec codec = new VCFCodec();
        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_2_HEADER))));
        VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_2_HEADER))));
        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader,null);

        for ( Pair<VariantContext,VariantContext> contextPair : data ) {
            VariantContext eval = contextPair.getFirst();
            VariantContext comp = contextPair.getSecond();
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Examples of htsjdk.variant.vcf.VCFCodec.readActualHeader()

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                + " -o %s -L 20:61098",
                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.VCFCodec.readActualHeader()

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                + " -o %s",
                1, Arrays.asList(""));
        spec.disableShadowBCF();
        final File vcf = executeTest("testMultipleGATKVersionsInVCF", spec).first.get(0);
        final VCFCodec codec = new VCFCodec();
        final VCFHeader header = (VCFHeader) codec.readActualHeader(codec.makeSourceFromStream(new FileInputStream(vcf)));

        boolean foundHC = false;
        boolean foundSV = false;
        for ( final VCFHeaderLine line : header.getMetaDataInInputOrder() ) {
            if ( line.getKey().equals(GATKVCFUtils.GATK_COMMAND_LINE_KEY) ) {
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