Isolate calculation of callable regions to parallelizable process so it occurs within docker containers containing pybedtools. Identify soft requirements not needed by bcbio-nextgen-vm
Merge pull request #330 from mjafin/master

Support Appistry SomaticIndelDetector and bundle with calls to MuTect
Use the sample name not the lane name for featureCounts.

Also returns the sample name instead of the lane name from
Tophat/STAR. Closes #333. Thanks to @mjafin.
Write merge list files inside transaction directory to prevent race conditions #324
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen