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

Example 1 with VcfLoopOverGenes

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

the class TestNg01 method testVcfLoopOverGenes.

@Test
public void testVcfLoopOverGenes() throws IOException {
    final String prefix = "vlog";
    File genes = new File(TEST_RESULTS_DIR, "jeter.genes.txt");
    Assert.assertEquals(0, new VcfLoopOverGenes().instanceMain(new String[] { "-o", genes.getPath(), "-p", prefix, "--snpEffNoIntergenic", VCF01 }));
    Assert.assertTrue(genes.exists());
    Assert.assertEquals(0, new VcfLoopOverGenes().instanceMain(new String[] { "-o", TEST_RESULTS_DIR.getPath(), "-g", genes.getPath(), VCF01 }));
    Assert.assertEquals(0, new VcfLoopOverGenes().instanceMain(new String[] { "-o", genes.getPath(), "--splitMethod", "VariantSlidingWindow", "--variantsWinCount", "50", "--variantsWinShift", "50", "-p", prefix, "--snpEffNoIntergenic", VCF01 }));
    Assert.assertEquals(0, new VcfLoopOverGenes().instanceMain(new String[] { "-o", TEST_RESULTS_DIR.getPath(), "-g", genes.getPath(), VCF01 }));
    Arrays.asList(TEST_RESULTS_DIR.listFiles()).stream().filter(F -> F.getName().startsWith(prefix) && F.getName().endsWith(".vcf")).forEach(F -> F.delete());
}