The ID attribute of CDS and exon features in the output gff3 is missing

[tiramisutes]

Dear, When I correct the gff3 annotation with the gffread (v0.12.6), the ID attributes of CDS and exon in the output results will be lost. How can we maintain this attribute? Here is my run command.

gffread --keep-genes -C -F --keep-exon-attrs -V -H -B -P -g genome.fasta test.gff3

[dariober]

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