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

Example 26 with VCFReader

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

the class TestSupport method createRandomPedigreeFromFile.

public Path createRandomPedigreeFromFile(final String vcfFile) throws IOException {
    class TmpSample {

        String fam = "F1";

        String name;

        String father = "0";

        String mother = "0";

        int sex = 0;

        int status = 0;
    }
    int status = 0;
    final Path vcfIn = Paths.get(vcfFile);
    final VCFReader r = VCFReaderFactory.makeDefault().open(vcfIn, false);
    final VCFHeader header = r.getHeader();
    r.close();
    final List<String> samples = new ArrayList<>(header.getSampleNamesInOrder());
    final List<TmpSample> ped = new ArrayList<>();
    if (samples.isEmpty())
        return null;
    while (!samples.isEmpty()) {
        final TmpSample indi = new TmpSample();
        indi.name = samples.remove(0);
        indi.fam = ped.stream().filter(P -> P.father.equals(indi.name) || P.mother.equals(indi.name)).map(P -> P.fam).findFirst().orElse("F" + this.random.nextInt());
        if (ped.stream().anyMatch(P -> P.father.equals(indi.name))) {
            indi.sex = 1;
        } else if (ped.stream().anyMatch(P -> P.mother.equals(indi.name))) {
            indi.sex = 2;
        } else {
            indi.sex = this.random.nextBoolean() ? 1 : 2;
        }
        // TODO
        indi.sex = 0;
        if (random.nextBoolean()) {
            final List<String> remain = new ArrayList<>(samples);
            if (!remain.isEmpty()) {
                indi.father = remain.remove(0);
            } else {
                indi.father = "0";
            }
            if (!remain.isEmpty()) {
                indi.mother = remain.remove(0);
            } else {
                indi.mother = "0";
            }
        } else {
            indi.father = "0";
            indi.mother = "0";
        }
        indi.status = (status++) % 2;
        ped.add(indi);
    }
    final Path pedFile = createTmpPath(".ped");
    final PrintWriter pw = new PrintWriter(Files.newBufferedWriter(pedFile));
    for (TmpSample ts : ped) {
        pw.print(ts.fam);
        pw.print('\t');
        pw.print(ts.name);
        pw.print('\t');
        pw.print(ts.father);
        pw.print('\t');
        pw.print(ts.mother);
        pw.print('\t');
        pw.print(ts.sex);
        pw.print('\t');
        pw.print(ts.status);
        pw.println();
    }
    pw.flush();
    pw.close();
    return pedFile;
}

Example 27 with VCFReader

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

the class TestSupport method wc.

public long wc(final Path f) throws IOException {
    if (f.getFileName().toString().endsWith(".bam") || f.getFileName().toString().endsWith(".sam")) {
        final SamReader sr = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).open(f);
        final SAMRecordIterator iter = sr.iterator();
        final long n = iter.stream().count();
        iter.close();
        sr.close();
        return n;
    } else if (f.getFileName().toString().endsWith(".vcf") || f.getFileName().toString().endsWith(".vcf.gz")) {
        final VCFReader sr = VCFReaderFactory.makeDefault().open(f, false);
        final CloseableIterator<VariantContext> iter = sr.iterator();
        final long n = iter.stream().count();
        iter.close();
        sr.close();
        return n;
    }
    final BufferedReader br = IOUtils.openPathForBufferedReading(f);
    final long n = br.lines().count();
    br.close();
    return n;
}

Example 28 with VCFReader

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

the class VcfPeekAfTest method testACAN01.

public void testACAN01() throws IOException {
    try {
        String vcfin = support.resource("test_vcf01.vcf");
        String vcfdb = vcfin;
        Path out = support.createTmpPath(".vcf");
        Assert.assertEquals(new VcfPeekAf().instanceMain(new String[] { "-o", out.toString(), "--peeker", "ACAN", "--treshold", "0.5", "--database", vcfdb, vcfin }), 0);
        support.assertIsVcf(out);
        try (VCFReader r1 = VCFReaderFactory.makeDefault().open(out, false)) {
            Assert.assertEquals(r1.iterator().stream().filter(V -> V.getNAlleles() == 2 && V.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY)).filter(V -> V.getAttributeAsDouble(VCFConstants.ALLELE_FREQUENCY_KEY, 1.0) > 0.5).count(), 0L);
        }
    } finally {
        support.removeTmpFiles();
    }
}

Example 29 with VCFReader

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

the class VcfPeekAfTest method testGT01.

public void testGT01() throws IOException {
    try {
        String vcfin = support.resource("test_vcf01.vcf");
        String vcfdb = vcfin;
        Path out = support.createTmpPath(".vcf");
        Assert.assertEquals(new VcfPeekAf().instanceMain(new String[] { "-o", out.toString(), "--peeker", "GT", "--treshold", "0.5", "--database", vcfdb, vcfin }), 0);
        support.assertIsVcf(out);
        try (VCFReader r1 = VCFReaderFactory.makeDefault().open(out, false)) {
            Assert.assertEquals(r1.iterator().stream().filter(V -> V.getNAlleles() == 2 && V.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY)).filter(V -> V.getAttributeAsDouble(VCFConstants.ALLELE_FREQUENCY_KEY, 1.0) > 0.5).count(), 0L);
        }
    } finally {
        support.removeTmpFiles();
    }
}

Example 30 with VCFReader

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

the class VcfPeekAfTest method testAF02.

public void testAF02() throws IOException {
    try {
        final String fname = "THEFILTER";
        String vcfin = support.resource("test_vcf01.vcf");
        String vcfdb = vcfin;
        Path out = support.createTmpPath(".vcf");
        Assert.assertEquals(new VcfPeekAf().instanceMain(new String[] { "-o", out.toString(), "--peeker", "AF", "--treshold", "0.5", "--database", vcfdb, "--filter", fname, vcfin }), 0);
        support.assertIsVcf(out);
        try (VCFReader r1 = VCFReaderFactory.makeDefault().open(out, false)) {
            CloseableIterator<VariantContext> iter = r1.iterator();
            while (iter.hasNext()) {
                VariantContext ctx = iter.next();
                if (ctx.getNAlleles() != 2)
                    continue;
                if (!ctx.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY))
                    continue;
                double af = ctx.getAttributeAsDouble(VCFConstants.ALLELE_FREQUENCY_KEY, 1.0);
                if (af <= 0.5) {
                    Assert.assertFalse(ctx.getFilters().contains(fname));
                } else {
                    Assert.assertTrue(ctx.getFilters().contains(fname));
                }
            }
            iter.close();
        }
    } finally {
        support.removeTmpFiles();
    }
}