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
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