starting to get along with including BamM
This looks like it's going to work
Tested on my datasets. The integration seems to work so far
GroopM still uses BamTyper for extraction so I need to finish BamM
before the integration is complete

Good enough for peeps to test and try get around the bug for now
added BamM to dependencies
Finished merging BamM with GroopM
made changes to match new BamM
added help for when bamm sucks
import sys!
Minor bug fixes.

Moving 0.3.0 into the main stream
Merge branch 'master' of https://github.com/minillinim/GroopM