Strip transcript/gene versions from Gencode GTFs.
Strip transcript/gene versions from Gencode GTFs.

Gencode doesn't have the transcript_version/gene_version attribute and
instead stores the versions as part of the transcript and gene id. We
detect this now and properly strip them off.

Closes #2696.

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