The ID attribute of CDS and exon features in the output gff3 is missing
tiramisutes opened this issue · comments
I was going to submit this very same issue. Here's a minimal example:
cat x.gff
chr1 . gene 1 10 . + . ID=g1
chr1 . mRNA 1 10 . + . ID=t1;Parent=g1
chr1 . CDS 1 10 . + 0 ID=c1;Parent=t1;ref=ABC
ID of CDS feature is lost even with -F
(keep all GFF attributes) enabled:
gffread --keep-genes -F x.gff
##gff-version 3
# gffread v0.12.7
# gffread --keep-genes -F x.gff
chr1 . gene 1 10 . + . ID=g1
chr1 . mRNA 1 10 . + . ID=t1;Parent=g1
chr1 . CDS 1 10 . + 0 Parent=t1;ref=ABC