Add SOMATIC flag for FreeBayes records

Initial step to address issue #317, but it is not hooked yet to the pipeline
Merge branch 'master' into vcf-somatic-fix
Hook the somatic fixing to Freebayes's paired pipeline and make the move
be in place
Fixes for nglims-based sample preparation: correctly specify upload directory for Galaxy, handle controls, and avoid passing empty fastq files through
Improvements for Galaxy upload: handle creation of missing Galaxy database libraries, support nglims-based specifications, avoid uploading indexes
Entry point for creating validation plots from existing CSV files
fixed typo
Merge pull request #388 from kern3020/master

fixed typo
Ensure de-duplication occurs on Standard processing pipeline if specified
Add min_allele_fraction that customizes minimum detection ratio for tumor/normal calling. Used in MuTect indel detection but not generally yet. Provide hook to get tumor algorithm configuration #314
Do not merge nglims samples based on descriptions, only on unique names. Set parameters for standard nglims post-analysis to include de-duplication.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Update mutect.py

I had a copy-paste typo on line 114, apologies
Merge pull request #390 from mjafin/patch-2

Update mutect.py
Improve plotting of validation calls to handle whole genome inputs. Generalize plot normalization to keep consistent differences across plots.
Add proper NM and MD tags to STAR alignments.

Thanks to @mjafin for the suggestion.
Restore AS tag to STAR alignments.
Handle new evaluation-based approach to writing concordant files in bcbio.variation. Back compatible with older versions
Ensure multiple callers are correctly merged for split BAMs. Thanks to @mjafin
Clean up directory preparation code in main function. Ensure pack information passed along with docker and AWS wrapped bcbio runs