[Bioperl-l] cigar string in GenericHSP

[Marc Logghe]

Hi Bob,
> 
> what about the reportwriter methods? am i missing something here?
No, you're OK. 

> 
> on a separate note, it appears from code that I'm writing that using 
> Bio::Tools::Run::StandAloneBlast to run local blast generates 
> GenericHit and GenericHSP objects, not the Blast specific ones. E.g. 
> print $hit->raw_hit_data throws an error. This method is present in 
> Bio::Search::Hit::blast but not Bio::Search::GenericHit. Am I doing 
> something wrong?
I don't think so. I asked myself the same question a while ago. My
conclusion was (correct me if I am wrong here) that you end up with a
Bio::Search::Hit::blast hit object when having run psi blast, the GenericHit
objects you get after parsing a 'normal' blast.
Cheers,
Marc