outline of translation tool and the first test
now finds starts and stops of locations
Added base alignments to use for HIV translations. Will need to add more when we do full genome translations
add an ungapping tool
pep-8 fix
fails, but at least it does so correctly :)
refactored how I do the alignments, still needs work!
now works properly!
now tests to make sure V3 is gettable
added extensive documentation
Merge branch 'feature/transtool' into develop