Examples with VCFBed com.github.lindenb.jvarkit.tools.vcfbed.VCFBed used on opensource projects

Example 1 with VCFBed

use of com.github.lindenb.jvarkit.tools.vcfbed.VCFBed in project jvarkit by lindenb.

the class TestNg01 method testVcfBed.

@Test
public void testVcfBed() throws IOException {
    final File output = new File(TEST_RESULTS_DIR, "jeter.vcf");
    for (int i = 0; i < 2; i++) {
        Assert.assertEquals(0, new VCFBed().instanceMain(new String[] { "-o", output.getPath(), "-T", "VCFBED", "-e", "\"chr\"+bed.get(0)+\":\"+bed.getStart()", (i == 0 ? "--map" : "--bed"), "./src/test/resources/toy.bed.gz", TOY_VCF_GZ }));
        assertIsVcf(output);
        Assert.assertTrue(output.delete());
    }
}