SAMProgramRecord pg = result.getFileHeader().getProgramRecords().get(0);
Assert.assertEquals(pg.getProgramGroupId(), "0");
Assert.assertEquals(pg.getProgramVersion(), "1.0");
Assert.assertEquals(pg.getCommandLine(), "align!");
Assert.assertEquals(pg.getProgramName(), "myAligner");
Assert.assertEquals(pg.getProgramGroupId(), "1",
"Program group ID not picked up correctly from aligned BAM");
Assert.assertEquals(pg.getProgramVersion(), "2.0",
"Program version not picked up correctly from aligned BAM");
Assert.assertNull(pg.getCommandLine(),