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

George Hartzell hartzell at alerce.com
Tue May 5 17:42:19 EDT 2009


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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