Examples with VcfBurdenFilterGenes com.github.lindenb.jvarkit.tools.burden.VcfBurdenFilterGenes used on opensource projects

Example 1 with VcfBurdenFilterGenes

use of com.github.lindenb.jvarkit.tools.burden.VcfBurdenFilterGenes in project jvarkit by lindenb.

the class TestNg01 method testVcfBurdenFilterGenes.

@Test
public void testVcfBurdenFilterGenes() throws IOException {
    final File tmp = File.createTempFile("_tmp", ".txt", TEST_RESULTS_DIR);
    PrintWriter pw = new PrintWriter(tmp);
    pw.println("ISG15");
    pw.flush();
    pw.close();
    final File output = new File(TEST_RESULTS_DIR, "jeter.vcf");
    Assert.assertEquals(0, new VcfBurdenFilterGenes().instanceMain(new String[] { "-o", output.getPath(), "--genes", tmp.getPath(), "--filter", "ABCD", "src/test/resources/ExAC.r1.sites.vep.vcf.gz" }));
    Assert.assertTrue(streamVcf(output).count() > 0L);
    Assert.assertTrue(output.delete());
    tmp.delete();
}