[Bioperl-l] coordinate issue with Bio::SearchIO::psl

[Jason Stajich]

good catch Elliott -  I thought I had finally squashed it but apparently
not.  Will take a look when I get a chance - may be helpful if you can
submit a bug and an example psl file and script which give the wrong
answer in case someone else wants to take a crack at it.


On Tue, 23 Mar 2004, Elliott H Margulies wrote:

> Dear BioPerl Developers:
>
> I have been evaluating the use of BioPerl for parsing BLASTZ lav
> output. To do this, I convert the lav output to 'psl' format with Jim
> Kent's lavToPsl program.
>
> When I report some stats about the alignments from within BioPerl, I
> notice that lengths and stop positions are 1 *greater* than they should
> be.
>
> I'm pretty sure this is a reflection of the fact that psl output is in
> the infamous half-open zero-based coordinate system and not simply
> zero-based closed intervals.
>
> Please let me know how I can help facilitate this fix, if it is in fact
> confirmed to be true.
>
> Regards,
> Elliott
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu