contamination: more robust checks for skipping
contamination: more robust checks for skipping

Handles complex cases like regional inputs without initial alignment
by doing strict checks for coverage and variant_regions.

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