[Bioperl-l] Bio::Index::Fastq indexing options

[Chris Fields]

Evan,

I don't think it was performance-related, just that no one has had time to really work on it (the main dev behind the push for this, Mark Jensen, is still around but has been very busy with his new job).  I do know (from my own attempts at implementing this) a few roadblocks were the use of DB_File-specific constants in some modules.

If you or anyone else wants to work on this feel free, it would be more than welcome.

chris

I fully support a move to either AnyDBM_File or DBD::SQLite specifically.
On Jul 11, 2011, at 1:33 PM, Evan Staton wrote:

> Hi bioperl-l,
> 
> I have been experimenting with Bio::Index::Fastq, and I realize from
> previous conversations<http://lists.open-bio.org/pipermail/bioperl-l/2011-February/034530.html>
> on
> the list that this module will not work efficiently with the scale of Fastq
> files being produced by modern sequencing instruments. Based on that
> conversation, it appears that the module uses DB_File currently and it was
> mentioned that AnyDBM_File could be used to allow the use of SQLite. Has any
> progress been made towards this goal? I am aware there are other indexing
> solutions, and I would offer to help out but it appears this transition has
> already been worked out in detail on the
> HOWTO<http://www.bioperl.org/wiki/HOWTO:SQLite_for_BioPerl_indexing>
> page.
> However, I don't see the changes reflected in github for this module. I was
> curious if the performance improvements did not justify making changes for
> this module or if there were other explanations.
> 
> Sorry if I missed relevant conversations on the topic, but I'd like to help
> with this if I can.
> 
> Thanks,
> 
> Evan
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