Skip to content

Use bioframe inside skgenome #982

@etal

Description

@etal

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.

Metadata

Metadata

Assignees

No one assigned

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions