Examples of makeSourceFromStream()

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

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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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