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
bcbio/provenance/programs.py fixed for mutect version detection
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.