[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's?
> Mark: great work!  I suppose the next step is to try refactoring the  relevant 
> methods in HSPI's to see what happens.
> chris
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