Add AlienTrimmer to program provenance.
Start of replacing RNA-SeQC with some custom plots.

Coverage calculation for 100 random genes to replace the
coverage calculation in RNA-SeQC.

Need to implement exon/intron/coding summaries as well.
Use pysam for calculation of sample coverage, removing dependence on GATK CallableLoci. Work towards chanjo integration for coverage
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Fix filename length bug in template workflow.
Update configuration.rst

Added star as one of the aligner options. Added mutect as one of the variant calling options.
Merge pull request #323 from porterjamesj/patch-5

Fix filename length bug in template workflow.
Merge pull request #325 from mjafin/patch-1

Update configuration.rst
Use bgzipped and tabix indexed VCFs throughout the pipeline instead of uncompressed VCFs.
Use -f flag to tabix to overwrite existing indices. Handles race conditions when indexing the same file in multiple concurrent processes. Fixes #326
Fix UnboundLocalError when running freebayes in paired mode

The defintion of config was inside the if, and hence it was skipped if
the file already existed, leading to errors
Merge pull request #327 from lbeltrame/fix-unboundlocalerror

Fix UnboundLocalError when running freebayes in paired mode
Ensure we have a recent pysam version to avoid index out of bound errors. Fixes #328. Drop old dependencies no longer needed in 0.7.7
Additional GATK cleanup: remove unused variant evaluation code. Remove todo for ReducedReads since it will be gone in GATK 3.0
Remove hack to avoid too small regions when subsetting BED files by regions, since this is now handled cleanly within  and can cause improper BED regions. Fixes #329
Overview cartoon of bcbio-nextgen-vm and bcbio-nextgen Docker components
Appistry mutect SomaticIndelDetector support added.
Combining muTect SNPs and SID InDels correctly using combine_variants
Added splice junction read support
MuTect versioning for appistry and subsequent application of SomaticIndelDetector