made bwa tool and tools/__init__ 80-complete
Merge branch 'master' of github.com:broadinstitute/viral-ngs into hml-80-complete

Conflicts:
	tools/__init__.py
	tools/bwa.py
fixing tabs + 80 completeness in tools/__init__.py and util/file.py.  passes all tests locally for python 2 and 3
more tab replacement and general code cleanup
retab and 80-completeness of taxon_filter
massive tab replacement, but didn't bother with 80-complete-ness
more 80-complete files
Merge pull request #22 from broadinstitute/hml-80-complete

Hml 80 complete
Merged master into irwin-taxon_filter.
Use filecmp for file comparison in test.assert_equal_contents.