Filter out repeated transcripts properly.
Filter out repeated transcripts properly.

Some malformed GTF files can have multiple transcripts with the
same name, which breaks downstream tools. This keeps just the first
one.

chapmanb/bcbio-nextgen,lpantano/bcbio-nextgen,elkingtonmcb/bcbio-nextgen,a113n/bcbio-nextgen,guillermo-carrasco/bcbio-nextgen,verdurin/bcbio-nextgen,gifford-lab/bcbio-nextgen,mjafin/bcbio-nextgen,vladsaveliev/bcbio-nextgen,mjafin/bcbio-nextgen,biocyberman/bcbio-nextgen,fw1121/bcbio-nextgen,brainstorm/bcbio-nextgen,lbeltrame/bcbio-nextgen,elkingtonmcb/bcbio-nextgen,chapmanb/bcbio-nextgen,guillermo-carrasco/bcbio-nextgen,elkingtonmcb/bcbio-nextgen,lbeltrame/bcbio-nextgen,a113n/bcbio-nextgen,vladsaveliev/bcbio-nextgen,fw1121/bcbio-nextgen,fw1121/bcbio-nextgen,lbeltrame/bcbio-nextgen,chapmanb/bcbio-nextgen,gifford-lab/bcbio-nextgen,verdurin/bcbio-nextgen,hjanime/bcbio-nextgen,hjanime/bcbio-nextgen,vladsaveliev/bcbio-nextgen,lpantano/bcbio-nextgen,brainstorm/bcbio-nextgen,a113n/bcbio-nextgen,biocyberman/bcbio-nextgen,Cyberbio-Lab/bcbio-nextgen,lpantano/bcbio-nextgen,verdurin/bcbio-nextgen,guillermo-carrasco/bcbio-nextgen,gifford-lab/bcbio-nextgen,mjafin/bcbio-nextgen,hjanime/bcbio-nextgen,brainstorm/bcbio-nextgen,Cyberbio-Lab/bcbio-nextgen,Cyberbio-Lab/bcbio-nextgen,biocyberman/bcbio-nextgen