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
Merge remote-tracking branch 'upstream/master' into vcf-somatic-fix
Handle correctly the result from INFO tag adjustment: PyVCF writes
uncompressed, so we have to compress the result ourselves
Sequencer support: ensure nglims retrieved flowcell matches inputs; avoiding fuzzy matches. Correctly prepare names for input YAML files. Avoid large amount of regional splitting for default standard pipelines
Sequencer support: server side fixes, handle nglims name inputs and avoid java PrintReads bamprep unless doing variant calling
Added danielevo to contributors list.
fixed typo
Add exclusion of telomere/centromere regions to structural variation calling. Fix sv type calling in delly. Use samtools for lumpy samblaster prep to provide better error messages
Improvements for structural variation detection: pass original alignment outputs directly to lumpy to avoid issues with extra non-mapping reads passed via combining analysis/no-analysis regions. Parallelize lumpy analysis to take advantage of multiple cores
Rework batched regional variant calling to cleanup code. Avoids special cases for tumor/normal and makes batch-level filtering explicit. Work towards support for GATK gVCF squaring off approaches
Merge pull request #350 from lbeltrame/vcf-somatic-fix

Add SOMATIC flag for FreeBayes records
Add PyVCF as a soft dependency to support VCF manipulation. #350
Avoid including Python warnings in version output. Fixes #397
TGen user page additions. Check my formatting, I think I got it right...?
Needed space in begining as to not ital, also fix AAC url/name
fixed some words
fixed some words
I love git

Merge branch 'master' of https://github.com/caddymob/bcbio-nextgen

Conflicts:
	docs/contents/introduction.rst