@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); }