[Bioperl-l] Bioperl-ext and Staden Package

Chris Fields cjfields at uiuc.edu
Thu Nov 23 09:12:20 EST 2006

On Nov 23, 2006, at 4:46 AM, Squig at web.de wrote:

> Hello,
> I have a short question concerning bioperl-ext and the io_lib from  
> the staden package.
> Are there plans to fix bioperl-ext so it could be used with the  
> actual version of io_lib (at the moment 1.10.1)?

This is one of the things tentatively planned but there have been no  
volunteers for it.

> Myself has no experience in evoking externally written c - code  
> from perl. But I think the changes to the io_lib - api are very  
> well documented so a fix shouldn't be to hard for somebody with  
> experience in this field. Please correct me if I'm totally wrong.
> Here you find the changes, you have to scroll a little bit down to  
> "Changes".
> https://sourceforge.net/project/shownotes.php? 
> release_id=340318&group_id=100316
> If you think I could give a helping hand, please let me know.
> With kind regards,
> Stefan

Any help would be greatly appreciated!  There are tests included with  
bioperl-ext which you can add to or modify if needed.  You can post  
patches for any changed code to bugzilla.  Here's a HOWTO:


Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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