Add option to force sorting.
Add option to force sorting.

Files can still have the sort flag in the header, but become
unsorted, this lets us force sorting of a file.

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