Micro cleanup.

Signed-off-by: Nick Semenkovich <semenko@alum.mit.edu>
Drop specific string import

Signed-off-by: Nick Semenkovich <semenko@alum.mit.edu>
autopep8 -i --max-line-length=999 ROSE2_main.py

Signed-off-by: Nick Semenkovich <semenko@alum.mit.edu>
Improve bamliquidator_batch finding, convert some print() functions.

Signed-off-by: Nick Semenkovich <semenko@alum.mit.edu>
More print() conversions & cleanups

Signed-off-by: Nick Semenkovich <semenko@alum.mit.edu>
Fix rankby

Signed-off-by: Nick Semenkovich <semenko@alum.mit.edu>
Utils cleanups & tweaks

Signed-off-by: Nick Semenkovich <semenko@alum.mit.edu>
More utils cleanups

Signed-off-by: Nick Semenkovich <semenko@alum.mit.edu>
Bugfix, I think.

Signed-off-by: Nick Semenkovich <semenko@alum.mit.edu>
Utils tweak

Signed-off-by: Nick Semenkovich <semenko@alum.mit.edu>
Clean & drop unused imports in Utils. Wildcard = evil!

Signed-off-by: Nick Semenkovich <semenko@alum.mit.edu>
More rose print cleanups & tweaks

Signed-off-by: Nick Semenkovich <semenko@alum.mit.edu>
Fix reference
Merge remote-tracking branch 'upstream/master' into rose2-cleanups

Conflicts:
	ROSE2_main.py
Add gitignore
Bugfix and drop wildcard import.
small genemapper cleanup
Autopep8 on rose.
More bugfixes.
Bugfix -- charles can you 2x check this one?