[Biojava-dev] GFF3Reader modification

[Ryan Golhar]

A little bit of both.  I don't see a reason to load the whole file into
memory at once, at least not for all cases.  I've added two functions to
read 1 feature at a time.  Actually, I've added a constructor and a next()
method along two private variables to the class.  Its a pretty simple
change and doesn't affect the existing code.



On Wed, Aug 22, 2012 at 3:48 PM, Scooter Willis <HWillis at scripps.edu> wrote:

> Ryan
>
> Do you need a feature for debugging faster or trying to avoid reading
> everything into memory? Would be great to get performance improvements or
> additional features to handle large GTF/GFF3 files. Let me know if I can
> do anything to help.
>
> Scooter
>
> On 8/22/12 3:40 PM, "Ryan Golhar" <ngsbioinformatics at gmail.com> wrote:
>
> >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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>
>