Package htsjdk.variant.vcf

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

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        // confirm that the call is the correct one
        final VCFCodec codec = new VCFCodec();
        final FileInputStream s = new FileInputStream(outputVCF);
        final LineIterator lineIterator = codec.makeSourceFromStream(new PositionalBufferedStream(s));
        codec.readHeader(lineIterator);
        final String line = lineIterator.next();
        Assert.assertFalse(line == null);
        final VariantContext vc = codec.decode(line);
        Assert.assertTrue(vc.isBiallelic());
        Assert.assertTrue(vc.getReference().basesMatch("ATGTATG"));
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        final File outputVCF = executeTest("testMultiAllelics", spec).getFirst().get(0);

        final VCFCodec codec = new VCFCodec();
        final FileInputStream originalStream = new FileInputStream(MultiAllelicsTest);
        final LineIterator originalLineIterator = codec.makeSourceFromStream(new PositionalBufferedStream(originalStream));
        codec.readHeader(originalLineIterator);
        int numOriginalRecords = 0;
        while ( originalLineIterator.hasNext() ) {
            originalLineIterator.next();
            numOriginalRecords++;
        }
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            numOriginalRecords++;
        }

        final FileInputStream newStream = new FileInputStream(outputVCF);
        final LineIterator newLineIterator = codec.makeSourceFromStream(new PositionalBufferedStream(newStream));
        codec.readHeader(newLineIterator);
        int numNewRecords = 0;
        while ( newLineIterator.hasNext() ) {
            newLineIterator.next();
            numNewRecords++;
        }
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        // confirm that the FisherStrand values are identical for the two pipelines
        final VCFCodec codec = new VCFCodec();
        final FileInputStream s = new FileInputStream(outputVCF);
        final LineIterator lineIterator = codec.makeSourceFromStream(new PositionalBufferedStream(s));
        codec.readHeader(lineIterator);

        final VCFCodec codecAnn = new VCFCodec();
        final FileInputStream sAnn = new FileInputStream(outputVCFAnn);
        final LineIterator lineIteratorAnn = codecAnn.makeSourceFromStream(new PositionalBufferedStream(sAnn));
        codecAnn.readHeader(lineIteratorAnn);
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        codec.readHeader(lineIterator);

        final VCFCodec codecAnn = new VCFCodec();
        final FileInputStream sAnn = new FileInputStream(outputVCFAnn);
        final LineIterator lineIteratorAnn = codecAnn.makeSourceFromStream(new PositionalBufferedStream(sAnn));
        codecAnn.readHeader(lineIteratorAnn);

        while( lineIterator.hasNext() && lineIteratorAnn.hasNext() ) {
            final String line = lineIterator.next();
            Assert.assertFalse(line == null);
            final VariantContext vc = codec.decode(line);
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        // QD values won't be identical because some filtered reads are missing during re-annotation

        final VCFCodec codec = new VCFCodec();
        final FileInputStream s = new FileInputStream(outputVCF);
        final LineIterator lineIterator = codec.makeSourceFromStream(new PositionalBufferedStream(s));
        codec.readHeader(lineIterator);

        final VCFCodec codecAnn = new VCFCodec();
        final FileInputStream sAnn = new FileInputStream(outputVCFAnn);
        final LineIterator lineIteratorAnn = codecAnn.makeSourceFromStream(new PositionalBufferedStream(sAnn));
        codecAnn.readHeader(lineIteratorAnn);
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        codec.readHeader(lineIterator);

        final VCFCodec codecAnn = new VCFCodec();
        final FileInputStream sAnn = new FileInputStream(outputVCFAnn);
        final LineIterator lineIteratorAnn = codecAnn.makeSourceFromStream(new PositionalBufferedStream(sAnn));
        codecAnn.readHeader(lineIteratorAnn);

        while( lineIterator.hasNext() && lineIteratorAnn.hasNext() ) {
            final String line = lineIterator.next();
            Assert.assertFalse(line == null);
            final VariantContext vc = codec.decode(line);
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