Add REJECT filter to non-somatic records in VarScan2
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.

fw1121/bcbio-nextgen,guillermo-carrasco/bcbio-nextgen,verdurin/bcbio-nextgen,vladsaveliev/bcbio-nextgen,a113n/bcbio-nextgen,hjanime/bcbio-nextgen,mjafin/bcbio-nextgen,vladsaveliev/bcbio-nextgen,brainstorm/bcbio-nextgen,fw1121/bcbio-nextgen,guillermo-carrasco/bcbio-nextgen,a113n/bcbio-nextgen,a113n/bcbio-nextgen,chapmanb/bcbio-nextgen,lbeltrame/bcbio-nextgen,hjanime/bcbio-nextgen,mjafin/bcbio-nextgen,SciLifeLab/bcbio-nextgen,mjafin/bcbio-nextgen,vladsaveliev/bcbio-nextgen,biocyberman/bcbio-nextgen,elkingtonmcb/bcbio-nextgen,gifford-lab/bcbio-nextgen,chapmanb/bcbio-nextgen,biocyberman/bcbio-nextgen,lbeltrame/bcbio-nextgen,elkingtonmcb/bcbio-nextgen,biocyberman/bcbio-nextgen,verdurin/bcbio-nextgen,hjanime/bcbio-nextgen,verdurin/bcbio-nextgen,elkingtonmcb/bcbio-nextgen,lpantano/bcbio-nextgen,SciLifeLab/bcbio-nextgen,lbeltrame/bcbio-nextgen,fw1121/bcbio-nextgen,brainstorm/bcbio-nextgen,Cyberbio-Lab/bcbio-nextgen,gifford-lab/bcbio-nextgen,gifford-lab/bcbio-nextgen,lpantano/bcbio-nextgen,SciLifeLab/bcbio-nextgen,lpantano/bcbio-nextgen,Cyberbio-Lab/bcbio-nextgen,chapmanb/bcbio-nextgen,Cyberbio-Lab/bcbio-nextgen,guillermo-carrasco/bcbio-nextgen,brainstorm/bcbio-nextgen