Added test bowtie2 indicies.
Added a couple of requirements.
Merge branch 'master' of github.com:roryk/bipy
Fixed sh dependency to grab my beta version for now.
Cleanup.
Initial commit of script for doing paired analysis with edgeR.
Added locate to find input files to utils.
Bug fix for combine_pairs to recognize 1/2 based on _1 and _2 not just 1/2.
Added unit tests for locate and combine_pairs.
Merge branch 'master' of github.com:roryk/bipy
Slightly better documentation, work in progress.
Update README.md
Fix bug in fix_RPKM_count caused by pandas updated API.
Added unit test for fix_RPKM_count_file.
Merge branch 'master' of github.com:roryk/bipy
Freezing pysam version since pysam 0.7.2 is broken.
Fix to actually pass options.
combine_pair handles single ended files correctly.
Fix for handling single end files.
Fixed typo.