Sorry, Galaxy I hit sent by accident in my earlier message. Like I said, I had a question about bed_intersect_basewise.py My first bed file has the following interval: chr22 267 572 and my second bed file has the intervals: chr22 147 267 chr22 267 387 chr22 387 507 chr22 507 627 When I run the program, I get the answer chr22 202 572 But I'm trying to see if there is a way I can get the complement, bases in the second file that don't overlap the first. The desired answer would be: chr22 147 267 chr22 572 627 I know there is a -v option on bed_intersect.py, but I want the equivalent basewise behavior. I was trying to poke around the BinnedBitSet code, and I see there is an invert method, but calling the invert method has some side effects on the rest of the code (either the next_set or next_clear call), and I get a run-time error. The BinnedBitSet code somewhat of a blackbox to me, but I'd appreciate any pointers in the right direction. Thanks for your help, Amit Indap -- Amit Indap