[Bioperl-l] Bug #2936

[Fields, Christopher J]

Sure, a pull request would be good.  I suggest making sure you are in sync with the 'master' branch first, but I don't think you'll run into conflicts with that.  

My guess is we'll need to pull this into a branch and test rigorously first if it is to go into a bioperl 1.6.  One of the (many?) problems with Bio::Location is that it assumes all features are on linear chromosomes, so there is quite a bit of logic/magic built-in with that assumption that tends to be wrong (e.g. sort order of sublocations and so on, which breaks split locations).  

Frankly, I think we could really simplify this logic so that it is less magic, less fuzzy, and it would bite us in the ass a lot less, but of course this breaks backcompat.  So, my feeling is such fixes would be handled better in a BioPerl v2.

chris

On Mar 15, 2013, at 9:26 AM, Francisco J. Ossandón <fossandonc at hotmail.com> wrote:

> Hello,
> 
> Around 2 weeks ago I posted comments and a fix for Bug #2936, but haven't
> received any feedback yet.
> 
> https://redmine.open-bio.org/issues/2936
> 
> 
> 
> Probably everybody is busy, so I would like to ask only if the proposed fix
> is acceptable. If the fix were fine, I could prepare changes in my forked
> repo, add tests (in "t/Seq/PrimarySeq.t"???) and make a pull request. What
> do you think?
> 
> 
> 
> Cheers,
> 
> 
> 
> --
> 
> Francisco J. Ossandon
> 
> Bioinformatician.
> 
> Ph.D. Candidate, University Andres Bello.
> 
> Center for Bioinformatics and Genome Biology,
> 
> Fundacion Ciencia para la Vida.
> 
> Santiago, Chile.
> 
> <http://www.cienciavida.cl/CBGB.htm> www.cienciavida.cl/CBGB.htm
> 
> 
> 
> 
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