[Bioperl-l] PullHSP bug

Hilmar Lapp hlapp at gmx.net
Thu Dec 4 10:12:38 EST 2008

On Dec 2, 2008, at 9:40 PM, Chris Fields wrote:

> It appears the problem boils down to a small inconsistency with the  
> way blank IDs are handled between the two BLAST parsers.  The  
> regular blast parser explicitly sets this to '', while blast_pull  
> leaves it undef.  When one constructs a LocatableSeq w/o an ID it  
> dies, but '' works, hence the problem.  I don't think using '' is a  
> real solution though (seems like something added to silence errors).

I agree. Using '' where a value is expected is an ugly kludge. Is it  
possible to fix this?

: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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