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See: https://github.com/open2c/bioframe
Why:
- Improve performance and robustness of the genomic interval arithmetic functions, especially in WGS mode.
- Reduce the maintenance surface area inside CNVkit's codebase.
There are potentially faster options, but:
- pyranges_1.x with ruranges -- evolving fast, too fast, and it brings a Rust dependency.
- polars_bio -- much heavier dependency chain, overkill here.
- scikit-bio -- interval tree is not the native data structure, so it's neither lighter nor faster than bioframe for CNVkit's use case.
Supersedes #476.
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