GTF parsing assumes gene_id and gene_name

[JosephLalli]

I'm encountering issues using a gtf file downloaded from NCBI. While the gtf specification is a nightmare, from what I can tell the NCBI believes that gene_id is required, but gene_name is not. They use the label "gene" for the equivalent piece of information.

Because g2gtools assumes any line without a gene name is invalid, it is unable to convert any of the NCBI gtfs I am providing.

Is it possible to remove the gene_name requirement? I understand it is useful when working with Ensembl gtfs, so maybe retain them as an optional piece of data to track.

(NCBI source: ncbi.nlm.nih.gov/genbank/genomes_gff)

[mattjvincent]

Do you have an example gtf file you are trying to convert? Are you sure your vci file is accurate?