Fix for the complexity plot if there are not enough reads.
Fix resources for expression level quantification.

These steps now use more cores appropriately when they are available.
Updated with complexity changes, STAR and fusion support.
Correctly handle preparation of pre-aligned BAM files when sorting and coordinate specification needed. Thanks to Severine Catreux.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen