Update process_alignment resources to match ipython specifications
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Have final BAM index file in upload directory use the more common .bam.bai extension. Fixes #261
Update genome configuration files to suppoer snpEff databases for rn5, mm9 and canFam3. chapmanb/bcbio-nextgen-vm#3
Cleanup.

Removed unused imports, commented out code and functions that
were never called.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Add novartis presentation slides
Merge branch 'master' of https://github.com/chapmanb/bcbio-nextgen
Reverted count files back to using gene_id solely