[Bioperl-l] Generic Blast parsing issue

[CALLEY_JOHN_N@Lilly.com]

I'm not sure if this is a bug or a missing feature. I'm a long time user 
of the old Blast.pm module. I recently showed a colleague how to set 
things up and suggested that he use the new generic SearchIO feature 
instead of doing things the old way. Unfortunately he needs the offset of 
the HSP in the query and hit sequences. In the Blast.pm module this is 
accessible via the $hsp->range or $hsp->start methods. In the GenericHSP 
object there are no direct equivalents, but there is the get_aln call. 
Since SimpleAlign uses LocatableSeqs internally I hoped that the start and 
end maintained there, might have what I needed. Unfortunately, they are 
always set to 1 and the length of the sequence. Is this a bug? Or a 
misunderstanding on my part? Do I need to give up on using the generic 
modules?

Thanks,
  John Calley