Add REJECT filter to non-somatic records in VarScan2

Like the work done in FreeBayes, this patch adds a REJECT filter to
non-somatic records (i.e., everything with a Somatic Status - SS - not
equal to 2) produced by VarScan2.

It includes some duplicated code from FreeBayes, which could be moved to
vcfutils.
updated URL
the config file for the system is called bcbio_system.yaml
updated URL for freebayes
add yeast genome
Update bcbio conda build to support latest bcbio-nextgen-vm. Clean up Dockerfile
upgrade to a more recent genome for sacCer 2 => 3
Bug fix for correctly grouping multi-caller/multi-batch variant calls
Joint squaring off: add initial integration with bcbio-nextgen-recall, needs additional work to handle regional calling
Easier prep for custom genomes.

This hooks until the cloudbiolinux preparation stuff and is
super hacky but as a place to get started making this a little bit
easier.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Remove development code.
Merge pull request #448 from kern3020/master

enable sacCer2, update urls and fixes some typos
Joint/batch calling: Merge regional batches into single final batch. Correctly reconstitute orignal variation files if calling and joint calling both done. Feed joint callers into gemini database creation instead of initial calls
Fix joint calling test data to use correct ploidy and have additional reference call tests
Integrate LOFTEE VEP plugin from @konradjk to support annotating predicted loss of function variations
pass extra args (for example, --pdb) to the testrunner
Merge pull request #450 from jwm/testrunner_passthrough_extra_args

pass extra args (for example, --pdb) to the testrunner
fix for #451
Wrap some of the longer lines.