Fixed disambiguation for STAR alignments
Merge pull request #318 from mjafin/master

Fixed disambiguation for STAR alignments
v0.7.7 release. Final commit includes pointers to latest conda version of pysam + makes pandas an optional soft import in feature counts
Provide 0.7.7 conda package of bcbio-nextgen. Update Dockerfile to match latest security fixes in bcbio-nextgen-vm
Use bcftools and vcflib for splitting variants into SNPs and Indels and merging samples back together. #294 Clarify and test for correct usage of various merging functions.
Avoid using newer pysam from binstars which causes issues on CentOS. Fixes #319
Improved fix for pysam on CentOS, use up to date pysam package compiled on CentOS 5 from bcbio binstar channel. #319
Move selection of single samples from multi-sample VCFs to bcftools instead of GATK. #294
Normalize input BED files with overlapping regions as part of processing pipeline to avoid out of order errors from downstream callers like FreeBayes. Fixes #320
Normalize input BED files with overlapping regions as part of processing pipeline to avoid out of order errors from downstream callers like FreeBayes. Fixes #320
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