Geo Pertea

- [ ] implement a greedy algorithm to iteratively assemble intron-compatible transfrags in decreasing order of their "structural overlap score" - [ ] when a reference annotation is given (`-r`),...

Agreed, I'm still trying to figure out the best way to easily share the gclib code across multiple projects while coordinating release, tagging etc with git. gclib is quite eclectic...

Wow - thank you so much for taking the time to provide a (possible and very likely) explanation for that puzzling behavior! I've never been able to reproduce the problem...

I realized I ignored ehhill's error because it really looked like a basic user error in which the `-i` option was somehow misused.. Clearly the `-i` option should be immediately...

OK, maybe I jumped the gun here assuming that you (and ehhill) used the `-i` option when perhaps you didn't. In any case, I need details about the exact command...

Really? Are you really going to argue that you just don't see a duplicate ID _gene29892_ in those first two lines of your ref.gff quote you're showing here ? :)...

Leaving aside the cheeky fun I had with my reply above, it turns out that in fact I was in the wrong there -- not about the duplicate IDs, but...

Not precisely, at the moment, unfortunately. But you can glean some info about the _transcripts_ owning those novel introns or exons by looking at the "class codes" provided in the...

This is an issue related to the internal representation of coordinates as a 32bit integer. I will have to update my code to use 64 bit instead, in order to...

Can you point me to that `Ath_genomic.gff` file so I can check/debug this ? Also, I see this is a conda version of gffread, what does `gffread --version` show?