chapmanb/bcbb — pull request #64 by roryk (2013-01-10 22:24:11+00:00)
Title: Tophat2 support, vcf splitter by chromosome, some utilities.

Sorry for the messy pull request, I'm not sure how to split them into separate concerns, maybe pull request from a branch? I couldn't figure out how to test Tophat2 in your setup, but the Tophat unit tests in bipy pass if I use either version of Bowtie with the correct reference version and fails if it is the wrong one.