align prep: fix support for symlinking in prepared inputs
align prep: fix support for symlinking in prepared inputs

Avoids re-prep for cases where we have ready to run bgzip
inputs. Part of generalization for merging more input files.

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