Currently only the basic exon structure and some basic GTF tags are preserved when gffcompare is running in "annotation mode", where a single input transcript file is given (+ a reference annotation) and no merging of input transcripts is requested - and thus the output GTF is named with the prefix .annotated.gtf
Proper implementation would make the "annotation mode" much more useful than it currently is. Issues to keep in mind:
CDS features must be fully preserved
--no-merge option should be automatically activated by default ?
handle GTF tag collisions for the added tags (at least warn about them; better yet: provide renaming options)
Currently only the basic exon structure and some basic GTF tags are preserved when gffcompare is running in "annotation mode", where a single input transcript file is given (+ a reference annotation) and no merging of input transcripts is requested - and thus the output GTF is named with the prefix
.annotated.gtfProper implementation would make the "annotation mode" much more useful than it currently is. Issues to keep in mind:
--no-mergeoption should be automatically activated by default ?