CNVkit: re-add cn1, cn2 calculation for WGS
CNVkit: re-add cn1, cn2 calculation for WGS

WGS runs with `-v` had memory issues during segmentation so we dropped
`-v` from call commands as well. However, this is less problematic
in call and needed for allelic CNVs. Fixes #1657

a113n/bcbio-nextgen,a113n/bcbio-nextgen,biocyberman/bcbio-nextgen,brainstorm/bcbio-nextgen,vladsaveliev/bcbio-nextgen,biocyberman/bcbio-nextgen,chapmanb/bcbio-nextgen,vladsaveliev/bcbio-nextgen,a113n/bcbio-nextgen,biocyberman/bcbio-nextgen,lbeltrame/bcbio-nextgen,brainstorm/bcbio-nextgen,lbeltrame/bcbio-nextgen,chapmanb/bcbio-nextgen,chapmanb/bcbio-nextgen,lbeltrame/bcbio-nextgen,vladsaveliev/bcbio-nextgen,brainstorm/bcbio-nextgen