[Bioperl-l] not recognizing hsp in a hit

[Steve Chervitz]

On Thu, Apr 7, 2011 at 2:28 AM, Dave Messina <David.Messina at sbc.su.se>wrote:

> I should also say: I wouldn't be surprised if the blast-style output that
> Blat produces is slightly nonstandard and causes our parser to make
> mistakes. By the way, which version of Blat are you using?
>
> It looks like Jim Kent has taken Blat at least semi-commercial:
> http://www.kentinformatics.com/products.html
> If there's a new version of blat, I don't think BioPerl has seen it yet.
>
> Can anyone confirm or deny recent Blat output format changes?
>

It's not recent, but this might possibly be the culprit:

blat quirk in -blast output mode:
https://lists.soe.ucsc.edu/pipermail/genome/2008-April/016211.html

Steve