Skip insert size calculation if --mate-inner-dist is globally set.
Update dependencies to latest versions of numpy/biopython and lock down pyzmq
Update README to display nicely in both pypi and GitHub
Provide workflows as part of toplevel bcbio_nextgen command. Update xprize ensemble workflow to use new structure
Upload variant calling regions to final directory when available. Avoid BAM file upload if not processed. Bug fix for workflows to change into working directory
Fixes for new RNA-seq trimming. Move definitions of supported adapters in-line
Fixes for SGE support; ensure we can find a parallel environment for launching multicore jobs
Release 0.6.1 finalization: improve usage message for bcbio_nextgen, update documentation and requirements, add development installer for upgrade in place
Updates to FreeBayes filtering for 0.9.9 using new defaults. Avoid post-filtering of FreeBayes and rely on single quality filtering
Cleaned up commented out code.
Provide realignment with gkno tools -- bamtools, ogap, bamleftalign.
Forgot to commit this unit test.
Added 'which' which works like unix 'which'.
Updated comment to include bam_align_fn.
Improve clarity of commandlines for piped commands: use string formatting to expose full pipelines run
htseq_count added.

Used for generating raw counts of the number of reads mapping to
features given a BAM file and a GTF file for use with downstream
tools such as DESeq and edgeR.
Made a couple of functions that should not be public private.
Swapped htseq_count output to return a sample dictionary.

Added "count_file" as a field to the sample dictionary.
Made htseq_count transactional.
Excluded unit test data directory and file.

Also added some other random detritus.