@Test(expectedExceptions = UserException.CommandLineException.class)
public void testNoArgs() throws Exception {
// making sure that this blows up in a very specific way (UserException.CommandLineException) if
// we give bogus arguments
final ArgumentsBuilder args = new ArgumentsBuilder();
this.runCommandLine(args.getArgsArray());
}
@Test(dataProvider = "filenames")
public void testCountReads(final String fileIn, final String referenceName) throws Exception {
final File ORIG_BAM = new File(getTestDataDir(), fileIn);
final ArgumentsBuilder args = new ArgumentsBuilder();
args.add("--input");
args.add(ORIG_BAM.getAbsolutePath());
if (null != referenceName) {
final File REF = new File(getTestDataDir(), referenceName);
args.add("-R");
args.add(REF.getAbsolutePath());
}
final Object res = this.runCommandLine(args.getArgsArray());
Assert.assertEquals(res, 8l);
}
private void countReads(
final String interval_args,
final String fileName,
final String referenceName,
final long count) {
final File ORIG_BAM = new File(getTestDataDir(), fileName);
final ArgumentsBuilder args = new ArgumentsBuilder();
args.add("--input");
args.add(ORIG_BAM.getAbsolutePath());
if (null != referenceName) {
final File REF = new File(getTestDataDir(), referenceName);
args.add("-R");
args.add(REF.getAbsolutePath());
}
args.add(interval_args);
final Object res = this.runCommandLine(args.getArgsArray());
Assert.assertEquals(res, count);
}