Problems extraction proteins/cds when `?` in strand column even though feature is not gene

[jd3234]

Hi,

we have some gff3s that contain ? in the strand column. These features are not genes (in our case oriC in bacteria). Nonetheless, when I try to extract protein and cds sequences it fails with an error:

gffread r1.gff3 -S -g chromosomes.fasta -y protein.fasta

Error parsing strand (?) from GFF line:
chr1	PRODIGALEXEX	oriC	663246	664269	.	?	.	ID=JMHBPODKGB_1056;Name=origin of replication;product=origin of replication;inference=similar to DNA sequence

Using ? is OK following GFF3 specs (https://github.com/the-sequence-ontology/specifications/blob/master/gff3.md):

Column 7: "strand"
The strand of the feature. + for positive strand (relative to the landmark), - for minus strand, and . for features that are not stranded. In addition, ? can be used for features whose strandedness is relevant, but unknown.

Could it be an option that you ignore the ? and not output protein/cds in such cases or add a parameter to switch that behaviour on? Or is there maybe a way I have not seen in the help?

Many thanks!