Examples with BackLocate com.github.lindenb.jvarkit.tools.backlocate.BackLocate used on opensource projects

Example 1 with BackLocate

use of com.github.lindenb.jvarkit.tools.backlocate.BackLocate in project jvarkit by lindenb.

the class TestNg01 method testBackLocate.

@Test
public void testBackLocate() throws IOException {
    final File tmp1 = new File(TEST_RESULTS_DIR, "jeter0.txt");
    final PrintWriter pw = new PrintWriter(tmp1);
    pw.println("NOTCH2\tP1090M");
    pw.flush();
    pw.close();
    final File output = new File(TEST_RESULTS_DIR, "jeter1.txt");
    Assert.assertEquals(0, new BackLocate().instanceMain(new String[] { "-o", output.getPath(), "-R", "http://genome.cse.ucsc.edu/cgi-bin/das/hg19/", tmp1.getPath() }));
    Assert.assertTrue(Files.lines(output.toPath()).anyMatch(S -> S.contains("120480548")));
    Assert.assertTrue(tmp1.delete());
    Assert.assertTrue(output.delete());
}