QC: correctly calculate VCF stats for inputs without PASS
QC: correctly calculate VCF stats for inputs without PASS

Handles pre-computed inputs that use '.' instead of PASS in filter column.
Also fixes usage for gVCF inputs specified via tools_on in CWL.

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