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

[Elliott H Margulies]

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

-- 
Elliott H. Margulies, Ph.D.
Genome Technology Branch
National Human Genome Research Institute
National Institutes of Health
50 South Dr., MSC 8004
Bldg. 50, Rm. 5527
Bethesda, MD  20892-8004

phone: (301) 594-9210
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