[gt-users] gff3 parser

[Gordon Gremme]

> ok. now i understand that problem, but not quite the solution.
> where would it keep the GtCstrTable? as an additional field on the
> GtGFF3Visitor struct?
> or on the GtGFF3Instream?

I would put it into the GtGFF3Visitor. That is, the IDs are changed
when they are shown via the GtGFF3OutStream and not when they are read
in via the GtGFF3InStream.


> and then, the option will be a boolean in tools/gt_gff3.c like: -keepids

Correct. I would pass it through to the GtGFF3Visitor similar to the
method gt_gff3_out_stream_set_fasta_width().


> so i think i can add an arg to gff3_parser.c
> gt_gff3_parser_parse_genome_nodes and parse_regular_gff3_line
> for the GtCstrTable *used_ids. then in parse_regular_gff3_line, it
> modifies the id attribute if it's in used_ids already.

No, I would rather put this functionality in the GtGFF3Vistitor (as
described above).

Happy coding,

Gordon