[Bioperl-l] question about in-between overlapping exact location
Jason Stajich
jason at bioperl.org
Tue May 5 22:06:50 UTC 2009
George -
I don't think the location type is taken into account in the overlap
code testing code. Would you expect 2..3 and 3..5 to overlap?
-jason
On May 5, 2009, at 2:42 PM, George Hartzell wrote:
>
> I was surprised to see that:
>
> $ins = Bio::Location::Simple->new(-start => 2,
> -end => 3,
> -location_type => 'IN-BETWEEN',
> );
> $start = Bio::Location::Simple->new(-start => 3,
> -end => 5);
>
> print "Wow!\n" if $start->overlaps($ins);
>
> To my mind they would only overlap if the insertion were 3^4 or 4^5.
>
> Is my mental model of in-between's overlapping exact's wrong, or could
> the code be improved (I'm happy to make a change, but...)?
>
> g.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
Jason Stajich
jason at bioperl.org
More information about the Bioperl-l
mailing list