[Bioperl-l] Bio::Tools::BPlite::HSP - percentage IDs

[Paul Gordon]

> Hmm, I really hadn't ever looked at that code - What are the arguments for
> or against.  
> 
> We can have a flag be twiddled to determine whether or not to use
> subject or query, but are both technically correct? 

I think both are useful (e.g. one may only be interested in hits matching
> 90% of both query and subject).  How about keeping the percent method 
deprecated with the same for backward compatibility (lack of a switch
choosing one behaviour seems icky) and introducing percent_subject and
percent_query to unambiguously define the functionality?

My CDN$0.02.:-)