Tophat2 support, vcf splitter by chromosome, some utilities.

chapmanb / bcbb

Incubator for useful bioinformatics code, primarily in Python and R

http://bcbio.wordpress.com

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Tophat2 support, vcf splitter by chromosome, some utilities. #64

Closed roryk closed 11 years ago

roryk commented 11 years ago

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.

chapmanb commented 11 years ago

Awesome, thanks Rory. Tophat in bcbio-nextgen is suffering from bitrot, so happy to have you rip out and replace with your TopHat2 code.

For splitting, the only change I made was to move the functionality into it's own namespace. Otherwise, looks great. Thanks again.