@anbangx @JavierJia so the problem as I see it is you have certain parameters that you only use in 1) generating the expected file and 2) running the test cases.  You don't want to make them command-line options since they aren't in use in any other case.

We could make it so you can specify arbitrary settings through the driver.  Something like `-extraSetting genomix.tipAdd.length=50` or perhaps `-S key=value` for short?  Or perhaps you could specify an additional .xml conf file on the command line and we just slurped up any settings inside of it?  Then you could keep all the special test settings in the `JobGenerator` where they were before but use its output for both test cases (as they were before) and driver jobs.