Fixes #1 . Now filters gff annotations to only include CDS types (just like roary). Then assigns new orders to the locus tags for each seqid. This should prevent genomic islands being erroneously interrupted by missing tRNA, rRNA etc.
No longer writes out individual fastas for each island unless requested with "--split_islands"
No longer writes out individual gffs for each island. ( no way to request this at the moment)
Writes out a combined dataframe containing the annotation info, pangenome info, and island info for all islands, islands_pangenome_gff.csv .
Fixes #1 . Now filters gff annotations to only include CDS types (just like roary). Then assigns new orders to the locus tags for each seqid. This should prevent genomic islands being erroneously interrupted by missing tRNA, rRNA etc.
No longer writes out individual fastas for each island unless requested with "--split_islands" No longer writes out individual gffs for each island. ( no way to request this at the moment) Writes out a combined dataframe containing the annotation info, pangenome info, and island info for all islands, islands_pangenome_gff.csv .