Add code to separate out stdout and stderr in testing

Previously the output of these was merged by redirection.

Signed-off-by: Martin O. Pollard <mp15@sanger.ac.uk>
Make merge take union of commandline and -b inputs and test merge code

Make merge command take union of command line input file and those listed in
-b's fofn.
Add tests for merge code

Signed-off-by: Martin O. Pollard <mp15@sanger.ac.uk>