Examples with VcfGnomad com.github.lindenb.jvarkit.tools.gnomad.VcfGnomad used on opensource projects

Example 1 with VcfGnomad

use of com.github.lindenb.jvarkit.tools.gnomad.VcfGnomad in project jvarkit by lindenb.

the class TestNg01 method testVcfGnomad.

@Test
public void testVcfGnomad() throws IOException {
    final File manifest = new File(TEST_RESULTS_DIR, "gnomad.manifest");
    PrintWriter pw = new PrintWriter(manifest);
    pw.println("exome\t*\tsrc/test/resources/gnomad.exomes.r2.0.1.sites.vcf.gz");
    pw.println("genome\t1\tsrc/test/resources/gnomad.genomes.r2.0.1.sites.1.vcf.gz");
    pw.flush();
    pw.close();
    Assert.assertEquals(0, new VcfGnomad().instanceMain(new String[] { "-o", JETER_VCF.getPath(), "-m", manifest.getPath(), VCF01 }));
    assertIsVcf(JETER_VCF);
    Assert.assertTrue(JETER_VCF.delete());
    Assert.assertTrue(manifest.delete());
}