Geo Pertea

Ah, I think `-W` option was supposed to add all transcript attributes for the `-y` but it does not seem to be working currently (it's broken). I can see how...

OK, I just committed to the master branch a few changes which make gffread to append to the FASTA defline, tab-delimited, all the fields the user specifies with the `--table`...

`-r` should take a _chromosome:start-end_ genomic location specification, with an optional strand prefix or suffix, e.g. `-r chr1:9000-12000` should only show transcripts overlapping that genomic range on chr1 (no matter...

I suppose you are talking about specific GFF attributes being lost? Or it's worse -- actual transcript structures?! (that would be a serious bug). If you could give me more...

Having the issue documented/summarized here would be better, so we can keep track of it properly (and github is neater than my mailbox). I was hoping it would be easy...

To address your 2nd point first -- from what you are showing me, no exons were lost -- just their useless IDs were discarded :) Now I recall the contempt...

Thank you for clarifying the purpose of this conversion, I understand better the issue now. Merging UTR features into exons does not affect the splice sites at all (and not...

Currently it's just plain alphabetical (and case sensitive), but there could/should be an option there for the other sorting methods (lexicographical?) -- thank you for the sort command example, I'll...

I agree, it does look inconsistent and it's likely buggy. There are a few confusing issues here, looking back at the code I wrote for those options, I noticed that:...

What is the source of that gff3 file -- may I see a chunk of it (or the whole file) ? I suspect it has a non-standard format and maybe...