## 9/20/19 - Maybe add max_ends list to the Lapper. Then binary search for upper bounds like AIList does, and iterate backwards checking against the max_end to deteremine overlap... It could make the hopper actually work as well since binary searches in a local area would be useful ## 9/3/19 - Added a worst case mode to allow for setting max misses and then recalculating the binary search from there. I think that for anything except maybe whole chromosome intervals, it's faster to not use it. - Updated docs ## 9/2/19 - Corrected the range on the IterFind to properly stop looking once stop has been hit. - Added benchmarks for find and seek - Sped up the intesection method when we know that overlaps have been merged. - Figure out the possible speedup with miss counting!! - Fix up docs to include features list / make less block of text ## 9/1/19 - Corrected the intersection_and_union function to work regardless of the comparison direction. It's a little slower now and in need of benchmarking. I think there is a gain to be had if we know that both lappers have had overlaps merged, I'm just now sure how to make it work yet. - Copy the version of intersect_and_union from chromcomp, it works and is faster - Next big todo: add benchmarking! ## 8/31/19 - Moved a bunch of functionality in, like merge overlaps and detect intersects and coverage calculation. - I would like to add some whole Lapper functions like a union an intersect. -- did this... but needs fine tuning - I would like to add benchmarks and identify the slow stuff - Something is now really slow I think. Like maybe the coverage calculation. Bench it and see. I also think the checked_sub might be slowing things down. -- figured it out. HashSet was a dumb idea for calculation of coverage and has been changed to be faster.