[Biojava-dev] GFF3Reader modification

[Michael Heuer]

Hello Ryan, Carmelo

I have somewhere on the back burner a wish to support GFF3+GVF and add
low-level streaming APIs to GFF3 parsing as was done for FASTQ
parsing.  Let me know if this sounds useful and I will try to get on
it sooner.

   michael


On Wed, Aug 22, 2012 at 2:48 PM, Carmelo Foti <carmelo.foti86 at gmail.com> wrote:
> Hi Ryan,
>
> I made some changes in the GFF3Reader class, but I had internet issues and
> I could not commit the patch.
> I think it would be better for you to start from the updated version, which
> is a lot faster when using the entire hg19 gtf.
> I'll send you the files as soon as possible
>
> Regards,
> Carmelo Foti
>
> 2012/8/22 Ryan Golhar <ngsbioinformatics at gmail.com>
>
>> Hi all - I'm using the GFF3Reader right now to read in the hg19 GTF file
>> from UCSC.  In debugging my own application, loading the GTF file take a
>> little bit of time. I'd like to make a modification to read each line on
>> demand instead of all at once.  Is this something others would find useful?
>>  If so, I'll submit a patch with my change.
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>>
>
>
>
> --
> Carmelo Foti
> Research assistant
> Politecnico di Torino
> Dipartimento di Automatica e Informatica - EDA Group
> C.so Duca degli Abruzzi 24, 10129 Torino (ITALY)
> Phone: (+39) 011 090 7072
> Fax: (+39) 011 090 7099
> E-mail: carmelo.foti at polito.it
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