Suggestion to support syntax for bcftools csq

[Pierre Lindenbaum]

Hi,
thank you for writing gffread.

I just tested the tool to convert the Gencode GTF to GFF3 ( https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_40/GRCh37_mapping/gencode.v40lift37.annotation.gtf.gz ) in order to use it with bcftools csq . Sadly, the generated gff3 is not supported by bcftools.

"Parent=transcript:" not present:

csq expects a prefix like "gene:" , "transcript:" before each ID.

see samtools/bcftools#530

It would be great if there was an option in gffread to add those prefixes.

Thanks !