[Bioperl-l] SearchIO speed up

Chris Fields cjfields at uiuc.edu
Mon Aug 14 10:01:52 EDT 2006


Sounds good.  We need to make sure that commits to bioperl-live also  
get committed to the experimental branch, correct?  Or at lease make  
sure bioperl-live commits are merged into experimental (and not vice- 


On Aug 14, 2006, at 6:43 AM, Sendu Bala wrote:

> Chris Fields wrote:
>> Here's a couple of  suggestions to get around that if you want to get
>> the code out there for testing:
>> Could this be CVS-tagged to an experimental bioperl branch instead?
>> It could be merged back to the main branch once everybody gets to try
>> it out, and you could commit changes to the branch (tests, scripts,
>> etc) along the way based on suggestions.  Think of this as a test-
>> drive for a new Bioperl release.
> I have created branch 'branch-experimental' and committed the  
> changes there.
> Please test by checking out the experimental branch:
> cvs co -d experimental -r branch-experimental bioperl-live
> I'll probably end up writing a new pull/chunk parser for BLAST, but
> these changes will still speed up the other SearchIO modules. So test
> the speed-up on different kinds of report as well.
> The experimental branch should be used for trying out major
> implementation changes that have the potential to break important and
> substantial parts of bioperl. Everything else should continue to be
> committed to HEAD until the 1.6 branch emerges (sometime next year).
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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