[Bioperl-l] Bio::Index::Fastq - Interface for indexing (multiple) fastq files failure

[Chris Fields]

On Wed, 2010-04-07 at 19:09 +0100, Peter wrote:
> On Wed, Apr 7, 2010 at 6:56 PM, Chris Fields <cjfields at illinois.edu> wrote:
> >Peter wrote:...
> >
> > I think this is a good idea for ODBA-based modules, but Bio::Index::*
> > modules aren't ODBA-compliant (at least that I know of); it's a simple
> > key-value hash pairing I believe.  Bio::Flat* are ODBA-compliant,
> > though, so it's worth exploring this.
> >
> > chris
> 
> I didn't appreciate BioPerl had more than one indexing back end
> (Bio::Index versus Bio::Flat).
> 
> Peter

Yes, which makes it more confusing unfortunately (there is actually a
third commonly-used one, Bio::DB::Fasta).  We should try moving towards
ODBA compliance, maybe integrating some of the speedups that
Bio::DB::Fasta uses for our purposes.  

chris