mjafin/disambiguate — pull request #1 by roryk (2013-11-09 09:28:05+00:00)
Title: Small refactor for some things

Hi Miika,

I refactored this a little bit, added some test files and added a setup.py so the script can be installed automatically. I changed the way the command line is, a little bit, you can call it the same way as before, but instead of -h and -m for mouse and human, it is just two positional arguments:

disambiguate.py --i TMP_DIR -o OUTPUT_DIR human1.bam mouse1.bam

That way it is not human/mouse specific. Finally I removed the docopt dependency and used argparse instead so we don't have to bring along docopt. What do you think?