[Bioperl-l] experimental Bio::Search::Tiling implementation
Mark A. Jensen
maj at fortinbras.us
Wed May 20 07:46:43 EDT 2009
Re: refactor-- I'll have a go at the relevant Bio::Search::[Hit | HSP] modules
and put the modified files in the right places in bioperl-dev.
(BTW: development may slow down a tad, due to $job, but never fear.)
----- Original Message -----
From: "Chris Fields" <cjfields at illinois.edu>
To: "Sendu Bala" <bix at sendu.me.uk>
Cc: "BioPerl List" <bioperl-l at lists.open-bio.org>; "Mark A. Jensen"
<maj at fortinbras.us>
Sent: Tuesday, May 19, 2009 9:14 PM
Subject: Re: [Bioperl-l] experimental Bio::Search::Tiling implementation
> On May 19, 2009, at 7:07 PM, Sendu Bala wrote:
>> Steve Chervitz wrote:
>>> Great work. My SearchUtils tiling function has been lingering for far
>>> too long (at least a decade).
>> I actually reworked it a little from revisions r10199 to r11247.
>> Mark: tricky.wublast and frac_problems.blast were the test files that had
>> problems that needed solving.
>> The corresponding tests were in SearchIO.t but have since (hopefully!) been
>> moved to another test file somewhere.
> They should be in t/SearchIO/blast.t; the SearchIO tests were split up based
> on format. Was there a bug linked to these that need to be merged with
> Mark: great work! I suppose the next step is to try refactoring the relevant
> methods in HSPI's to see what happens.
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