The Nested Containment List for Python. Basically an immutable interval-tree that is super-fast for both construction and lookups. - hunt-genes/ncls
Finally, nested containment list in Python:
, and GenomicsRanges in Python:
. This was what python badly needed for years.
Nested containment lists are quite a bit faster than interval trees for range overlap operations. Not quite fair as I'm comparing a Python implementation to a Cython one, but dropping in NCLS (
) lead to a ~30 fold speed up. Paper: