Examples with VCFReader htsjdk.variant.vcf.VCFReader used on opensource projects

Example 1 with VCFReader

use of htsjdk.variant.vcf.VCFReader in project jvarkit by lindenb.

the class VcfBurdenFisherHTest method test01.

@Test(dataProvider = "src1", enabled = false)
public void test01(final String inputFile) throws IOException {
    try {
        final VCFReader r0 = VCFReaderFactory.makeDefault().open(new File(inputFile), false);
        final VCFHeader vcfheader = r0.getHeader();
        if (vcfheader.getNGenotypeSamples() < 2) {
            r0.close();
            return;
        }
        final CloseableIterator<VariantContext> iter = r0.iterator();
        final Path inputVcf = support.createTmpPath(".vcf");
        final VariantContextWriter w = VCFUtils.createVariantContextWriter(inputVcf.toFile());
        w.writeHeader(vcfheader);
        iter.stream().filter(V -> V.getAlleles().size() == 2).forEach(V -> w.add(V));
        iter.close();
        w.close();
        r0.close();
        final Path ped = support.createRandomPedigreeFromFile(inputFile);
        if (ped == null) {
            Reporter.getCurrentTestResult().setAttribute("warn", "No Pedigree for " + inputFile);
            return;
        }
        final Path output = support.createTmpPath(".vcf");
        Assert.assertEquals(new VcfBurdenFisherH().instanceMain(new String[] { "-o", output.toString(), "--pedigree", ped.toString() }), 0);
        support.assertIsVcf(output);
    } finally {
        support.removeTmpFiles();
    }
}

Example 2 with VCFReader

use of htsjdk.variant.vcf.VCFReader in project jvarkit by lindenb.

the class VcfFilterNotInPedigreeTest method test01.

@Test(dataProvider = "src1")
public void test01(final String inputFile) throws IOException {
    try {
        final VCFReader r0 = VCFReaderFactory.makeDefault().open(Paths.get(inputFile), false);
        final VCFHeader vcfheader = r0.getHeader();
        if (vcfheader.getNGenotypeSamples() < 1) {
            r0.close();
            return;
        }
        r0.close();
        final Path ped = support.createRandomPedigreeFromFile(inputFile);
        if (ped == null) {
            Reporter.getCurrentTestResult().setAttribute("warn", "No Pedigree for " + inputFile);
            return;
        }
        final Path output = support.createTmpPath(".vcf");
        Assert.assertEquals(new VcfFilterNotInPedigree().instanceMain(new String[] { "-o", output.toString(), "--pedigree", ped.toString(), inputFile.toString() }), 0);
        support.assertIsVcf(output);
    } finally {
        support.removeTmpFiles();
    }
}

Example 3 with VCFReader

use of htsjdk.variant.vcf.VCFReader in project jvarkit by lindenb.

the class Biostar130456Test method test01.

@Test(dataProvider = "src1")
public void test01(final String vcfpath) throws IOException {
    try {
        final VCFReader r = VCFReaderFactory.makeDefault().open(new File(vcfpath), false);
        final Set<String> samples = new HashSet<>(r.getHeader().getSampleNamesInOrder());
        r.close();
        if (samples.isEmpty())
            return;
        final String vcfOut = IOUtils.getDefaultTmpDir().getPath() + File.separatorChar + "tmp.__SAMPLE__.vcf.gz";
        final Path tsvout = support.createTmpPath(".txt");
        Assert.assertEquals(new Biostar130456().instanceMain(new String[] { "-o", tsvout.toString(), "-p", vcfOut, vcfpath }), 0);
        Assert.assertTrue(Files.exists(tsvout));
        for (final String s : samples) {
            final Path vcfIn2 = Paths.get(vcfOut.replaceAll("__SAMPLE__", s));
            support.assertIsVcf(vcfIn2);
            final VCFReader r2 = VCFReaderFactory.makeDefault().open(vcfIn2, false);
            final List<String> samples2 = r2.getHeader().getSampleNamesInOrder();
            r2.close();
            Assert.assertTrue(samples2.size() == 1);
            Assert.assertEquals(samples2.get(0), s);
            Assert.assertTrue(Files.deleteIfExists(vcfIn2));
        }
    } finally {
        support.removeTmpFiles();
    }
}

Example 4 with VCFReader

use of htsjdk.variant.vcf.VCFReader in project jvarkit by lindenb.

the class TestSupport method variantStream.

public Stream<VariantContext> variantStream(final Path vcfFile) {
    final VCFReader r = VCFReaderFactory.makeDefault().open(vcfFile, false);
    final CloseableIterator<VariantContext> iter = r.iterator();
    return iter.stream().onClose(() -> {
        CloserUtil.close(iter);
        CloserUtil.close(r);
    });
}

Example 5 with VCFReader

use of htsjdk.variant.vcf.VCFReader in project jvarkit by lindenb.

the class VCFCompareGTTest method mute.

private Path mute(final Path in) throws IOException {
    Path outVcf = support.createTmpPath(".vcf");
    final VariantContextWriter w = VCFUtils.createVariantContextWriterToPath(outVcf);
    final VCFReader r = VCFReaderFactory.makeDefault().open(in, true);
    w.writeHeader(r.getHeader());
    final CloseableIterator<VariantContext> iter = r.iterator();
    while (iter.hasNext()) {
        final VariantContext ctx = iter.next();
        // ignore some variants
        if (support.random.nextDouble() < 0.1)
            continue;
        w.add(mute(ctx));
    }
    w.close();
    iter.close();
    r.close();
    support.assertIsVcf(outVcf);
    return outVcf;
}