FreeBayes: do not call if no BED regions available
FreeBayes: do not call if no BED regions available

When filtering out high depth/repeat regions to improve runtime, avoid
calling when the resulting file is empty. FreeBayes complains about
an empty BED file, so we instead write an empty VCF. Thanks to
@guillermo-carrasco.

chapmanb/bcbio-nextgen,a113n/bcbio-nextgen,biocyberman/bcbio-nextgen,Cyberbio-Lab/bcbio-nextgen,lpantano/bcbio-nextgen,vladsaveliev/bcbio-nextgen,lpantano/bcbio-nextgen,Cyberbio-Lab/bcbio-nextgen,chapmanb/bcbio-nextgen,biocyberman/bcbio-nextgen,vladsaveliev/bcbio-nextgen,mjafin/bcbio-nextgen,mjafin/bcbio-nextgen,gifford-lab/bcbio-nextgen,a113n/bcbio-nextgen,mjafin/bcbio-nextgen,gifford-lab/bcbio-nextgen,brainstorm/bcbio-nextgen,gifford-lab/bcbio-nextgen,vladsaveliev/bcbio-nextgen,a113n/bcbio-nextgen,lpantano/bcbio-nextgen,biocyberman/bcbio-nextgen,brainstorm/bcbio-nextgen,Cyberbio-Lab/bcbio-nextgen,brainstorm/bcbio-nextgen,chapmanb/bcbio-nextgen,lbeltrame/bcbio-nextgen,lbeltrame/bcbio-nextgen,lbeltrame/bcbio-nextgen