[Bioperl-l] question about in-between overlapping exact location

Jason Stajich jason at bioperl.org
Tue May 5 18:06:50 EDT 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.
>
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Jason Stajich
jason at bioperl.org






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