Examples of makeSourceFromStream()

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

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            originalLineIterator.next();
            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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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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        final File outputVCFAnn = executeTest("testStrandBiasBySample re-annotation of FisherStrand", specAnn).getFirst().get(0);

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

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        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);

        while( lineIterator.hasNext() && lineIteratorAnn.hasNext() ) {
            final String line = lineIterator.next();
            Assert.assertFalse(line == null);
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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        // confirm that the QD values are present in the new file for all biallelic variants
        // 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));
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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        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);

        while( lineIterator.hasNext() && lineIteratorAnn.hasNext() ) {
            final String line = lineIterator.next();
            Assert.assertFalse(line == null);
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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    public void testSimpleComparison() {
        Pair<VariantContext,VariantContext> data = getData1();
        VariantContext eval = data.getFirst();
        VariantContext truth = data.getSecond();
        VCFCodec codec = new VCFCodec();
        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
        VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader,null);
        metrics.update(eval,truth);
        Assert.assertEquals(eval.getGenotype("test1_sample2").getType().ordinal(), 2);
        Assert.assertEquals(truth.getGenotype("test1_sample2").getType().ordinal(),1);
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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        Pair<VariantContext,VariantContext> data = getData1();
        VariantContext eval = data.getFirst();
        VariantContext truth = data.getSecond();
        VCFCodec codec = new VCFCodec();
        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
        VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader,null);
        metrics.update(eval,truth);
        Assert.assertEquals(eval.getGenotype("test1_sample2").getType().ordinal(), 2);
        Assert.assertEquals(truth.getGenotype("test1_sample2").getType().ordinal(),1);
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getnMismatchingAlt(),0);
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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    public void testMismatchingAlleleInAlleleSubset() {
        Pair<VariantContext,VariantContext> data = getData2();
        VariantContext eval = data.getFirst();
        VariantContext truth = data.getSecond();
        VCFCodec codec = new VCFCodec();
        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
        VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader,null);
        metrics.update(eval,truth);
        Assert.assertEquals(eval.getGenotype("test1_sample2").getType().ordinal(), 2);
        Assert.assertEquals(truth.getGenotype("test1_sample2").getType().ordinal(),2);
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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        Pair<VariantContext,VariantContext> data = getData2();
        VariantContext eval = data.getFirst();
        VariantContext truth = data.getSecond();
        VCFCodec codec = new VCFCodec();
        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
        VCFHeader compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
        ConcordanceMetrics metrics = new ConcordanceMetrics(evalHeader,compHeader,null);
        metrics.update(eval,truth);
        Assert.assertEquals(eval.getGenotype("test1_sample2").getType().ordinal(), 2);
        Assert.assertEquals(truth.getGenotype("test1_sample2").getType().ordinal(),2);
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getnMismatchingAlt(),1);
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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        // now flip them around

        eval = data.getSecond();
        truth = data.getFirst();
        codec = new VCFCodec();
        evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
        compHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_1_HEADER))));
        metrics = new ConcordanceMetrics(evalHeader,compHeader,null);
        metrics.update(eval,truth);
        Assert.assertEquals(eval.getGenotype("test1_sample2").getType().ordinal(), 2);
        Assert.assertEquals(truth.getGenotype("test1_sample2").getType().ordinal(),2);
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