coitrees | A very fast interval tree data structure

coitrees is a Rust library. coitrees has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. You can download it from GitHub.

COITrees implements a data structure for very fast overlap queries of a static set of integer intervals, with genomic intervals in mind. Borrowing from cgranges, this data structure stores intervals in contiguous memory, but improves query performance by storing the nodes in in-order van Emde Boas layout layout. Computing the layout requires some extra time and memory, but improves average cache locality for queries of the tree. If the interval set is relatively large, and a sufficiently large number of queries are performed, it tends to out-perform other data structures. The SortedQuerent type implements an alternative query strategy that keeps track of the results of the previous query. When a query overlaps the previous one, the results from that previous query can be reused to dramatically accelerate the current one. (In the benchmarks, this is the --sorted option.). In the avx branch, a variation is implemented that groups intervals into chunks of 8 and searches using AVX instructions, which speeds things up somewhat, especially when in comes to counting. Make sure to set RUSTFLAGS="-Ctarget-cpu=ARCH" where ARCH is e.g. haswell or znver2 or some architecture that supports AVX and AVX2.