[Bioperl-l] frac_aligned_query returning results >1.

Chris Fields cjfields at uiuc.edu
Fri Mar 2 08:33:08 EST 2007


On Mar 2, 2007, at 5:25 AM, Sendu Bala wrote:

> Chris Fields wrote:
>> This is related to a reported bug:
>> http://bugzilla.open-bio.org/show_bug.cgi?id=2193
>> The relevant code used to tile HSPs is a bit brittle and  
>> sometimes  leads to errors like this.  The error (which is  
>> actually a thrown  exception) is wrapped in an eval block and  
>> converted to a warn for  that reason.  I'm not familiar with the  
>> tiling algorithm used, maybe  Steve can add some input?
>
> Depending on what exactly you're talking about here, I may have re- 
> written that algorithm. Nice to know the bug survived ;)

Yep, I saw your commits (revs. 1.16, 1.17, 1.19, and 1.20).  I can  
check code prior to that to see if it changes anything for better or  
worse or gets rid of the bug (prob. later today or tomorrow), though  
I can't see why your revisions would make it worse.  If anything  
they're now more accurate.

Thiago can also try; just pull up a revision prior to the ones listed  
above and see if it helps:

http://code.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/ 
Search/SearchUtils.pm?cvsroot=bioperl

Jason had previously indicted problems with tiling (i.e. similar  
exceptions were thrown) prior to your commits so I don't think your  
changes are related, but one never knows.

Chris



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