[Bioperl-l] Bio::Index::Fastq indexing options
cjfields at illinois.edu
Mon Jul 11 22:19:21 UTC 2011
On Jul 11, 2011, at 2:47 PM, Peter Cock wrote:
> On Mon, Jul 11, 2011 at 7:48 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> Forgot to mention, for more info on this, see:
>> This is also filed in Redmine as a bug I believe.
> We've got SQLite based indexing for Biopython's SeqIO module,
> and I'd be keen to try and share the same format (table names,
> column names etc). I view this as an extension to the existing
> flat file and BDB backends for OBDA - what I did for Biopython
> with SQLite was very much inspired by that design.
I think this is a good plan to follow, at least makes the end-point index less reliant on a specific implementation.
> If any BioPerl folk are at the CodeFest this week before BOSC,
> this could be a good project:
Unfortunately I'm not going this year, but maybe open an IRC channel or something similar so we can participate? (though the time difference may limit that somewhat). I am making active plans for attending next year, though.
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