Examples with VCFStripAnnotations com.github.lindenb.jvarkit.tools.vcfstripannot.VCFStripAnnotations used on opensource projects

Example 1 with VCFStripAnnotations

use of com.github.lindenb.jvarkit.tools.vcfstripannot.VCFStripAnnotations in project jvarkit by lindenb.

the class TestNg01 method testVCFStripAnnotations.

@Test
public void testVCFStripAnnotations() throws IOException {
    final File output = new File(TEST_RESULTS_DIR, "jeter.vcf");
    Assert.assertEquals(0, new VCFStripAnnotations().instanceMain(new String[] { "-o", output.getPath(), "--exclude", "INFO/CSQ,ID,FILTER/*", "src/test/resources/ExAC.r1.sites.vep.vcf.gz" }));
    Assert.assertTrue(streamVcf(output).count() > 0L);
    Assert.assertTrue(streamVcf(output).filter(V -> V.hasAttribute("CSQ")).count() == 0L);
    Assert.assertTrue(streamVcf(output).filter(V -> V.hasID()).count() == 0L);
    Assert.assertTrue(streamVcf(output).filter(V -> V.isFiltered()).count() == 0L);
    Assert.assertTrue(output.delete());
}