Default log timestamps to local time instead of UTC. #140. Uses mitsuhiko/logbook#74
Provide better log messaging for expected VQSR failures, avoiding confusing tracebacks in log file. #140
Avoid loading filtered variants into gemini database for recent gemini versions
Provide todo of current pipeline goals and requested features. Fixes #142
Fix for empty read names with Tophat 2.0.9

Just skips them for now, it seems like a rare occurance.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen