Examples of makeSourceFromStream()

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

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                "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";

    private VCFHeader createHeader(String headerStr) {
        VCFCodec codec = new VCFCodec();
        VCFHeader head = null;
        head = (VCFHeader) codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(headerStr))));
        return head;
    }

    @Test
    public void testHeadersWithSamplesNamesDuplicationThatIsNotAllowed() {
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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    public void testNRD_testNRS_testMargins() {
        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);
        int[][] table = metrics.getOverallGenotypeConcordance().getTable();
        // set up the table
        table[0] = new int[] {30, 12, 7, 5, 6, 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);
        int[][] table = metrics.getOverallGenotypeConcordance().getTable();
        // set up the table
        table[0] = new int[] {30, 12, 7, 5, 6, 0};
        table[1] = new int[] {10, 100, 5, 1, 7, 1};
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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    }

    @Test(enabled=true)
    public void testRobustness() {
        VCFCodec codec = new VCFCodec();
        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_1))));
        VCFHeader disjointCompHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_2))));
        VCFHeader overlapCompHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_3))));
        ConcordanceMetrics disjointMetrics = new ConcordanceMetrics(evalHeader,disjointCompHeader,null);
        ConcordanceMetrics overlapMetrics = new ConcordanceMetrics(evalHeader,overlapCompHeader,null);
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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    @Test(enabled=true)
    public void testRobustness() {
        VCFCodec codec = new VCFCodec();
        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_1))));
        VCFHeader disjointCompHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_2))));
        VCFHeader overlapCompHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_3))));
        ConcordanceMetrics disjointMetrics = new ConcordanceMetrics(evalHeader,disjointCompHeader,null);
        ConcordanceMetrics overlapMetrics = new ConcordanceMetrics(evalHeader,overlapCompHeader,null);

        // test what happens if you put in disjoint sets and start making requests
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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    @Test(enabled=true)
    public void testRobustness() {
        VCFCodec codec = new VCFCodec();
        VCFHeader evalHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_1))));
        VCFHeader disjointCompHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_2))));
        VCFHeader overlapCompHeader = (VCFHeader)codec.readActualHeader(codec.makeSourceFromStream(new PositionalBufferedStream(new StringBufferInputStream(TEST_3_HEADER_3))));
        ConcordanceMetrics disjointMetrics = new ConcordanceMetrics(evalHeader,disjointCompHeader,null);
        ConcordanceMetrics overlapMetrics = new ConcordanceMetrics(evalHeader,overlapCompHeader,null);

        // test what happens if you put in disjoint sets and start making requests
        Assert.assertEquals(0,disjointMetrics.getPerSampleGenotypeConcordance().size());
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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    }

    @Test(enabled = true)
    public void testSites() {
        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);

        List<Pair<VariantContext,VariantContext>> data = getData7();
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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    @Test(enabled = true)
    public void testSites() {
        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);

        List<Pair<VariantContext,VariantContext>> data = getData7();

        int idx = 0;
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Examples of htsjdk.variant.vcf.VCFCodec.makeSourceFromStream()

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        final File outputVCF = executeTest("HCTestDanglingTailMergingForDeletions", spec).getFirst().get(0);

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

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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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