Examples of makeSourceFromStream()

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

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        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);
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getnMismatchingAlt(),1);
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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    public void testComplex() {
        Pair<VariantContext,VariantContext> data = getData3();
        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(metrics.getGenotypeConcordance("test1_sample1").getnMismatchingAlt(),1);
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getTable()[2][1],0);
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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        Pair<VariantContext,VariantContext> data = getData3();
        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(metrics.getGenotypeConcordance("test1_sample1").getnMismatchingAlt(),1);
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getTable()[2][1],0);
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getTable()[3][3],1);
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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    public void testNoCalls() {
        Pair<VariantContext,VariantContext> data = getData4();
        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(metrics.getGenotypeConcordance("test1_sample2").getnMismatchingAlt(),0);
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getTable()[2][1],0);
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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        Pair<VariantContext,VariantContext> data = getData4();
        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(metrics.getGenotypeConcordance("test1_sample2").getnMismatchingAlt(),0);
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getTable()[2][1],0);
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getTable()[0][2],1);
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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    public void testMissing() {
        Pair<VariantContext,VariantContext> data = getData5();
        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.assertTrue(eval.getGenotype("test1_sample2").getType().equals(GenotypeType.UNAVAILABLE));
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getnMismatchingAlt(),0);
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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        Pair<VariantContext,VariantContext> data = getData5();
        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.assertTrue(eval.getGenotype("test1_sample2").getType().equals(GenotypeType.UNAVAILABLE));
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getnMismatchingAlt(),0);
        Assert.assertEquals(metrics.getGenotypeConcordance("test1_sample2").getTable()[2][1],0);
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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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.makeSourceFromStream()

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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.makeSourceFromStream()

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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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