Metadata-Version: 2.1
Name: lanctools
Version: 0.3.0
Summary: Tools for working with phased local ancestry data stored in the `.lanc` file format
Author-Email: Franklin Ockerman <frank.ockerman@gmail.com>
License: MIT
Project-URL: Homepage, https://github.com/frankp-0/lanctools
Project-URL: Documentation, https://lanctools.readthedocs.io
Project-URL: Repository, https://github.com/frankp-0/lanctools
Project-URL: Issues, https://github.com/frankp-0/lanctools/issues
Requires-Python: >=3.10
Requires-Dist: numba>=0.63.1
Requires-Dist: numpy>=2.2.6
Requires-Dist: pandas>=2.3.3
Requires-Dist: pgenlib>=0.93.0
Requires-Dist: typer>=0.20.1
Provides-Extra: dev
Requires-Dist: ipython>=8.37.0; extra == "dev"
Requires-Dist: pytest>=9.0.2; extra == "dev"
Requires-Dist: pytest-cov>=7.0.0; extra == "dev"
Provides-Extra: docs
Requires-Dist: mkdocstrings-python>=2.0.1; extra == "docs"
Requires-Dist: zensical>=0.0.17; extra == "docs"
Description-Content-Type: text/markdown

**lanctools** is a python package and command-line tool for working with phased local ancestry data stored in the `.lanc` file format, as defined by Admix-kit [Hou et al., 2024].

`lanctools` is designed to provide **fast local ancestry queries** and convenient conversion from external formats (e.g., FLARE [Browning et al., 2023] and RFMix [Maples et al., 2013]). It focuses on efficient access to `.lanc` data and is **not** intended to replace the full functionality of Admix-kit. Features include:

- Efficient random access to phased local ancestry data
- Local ancestry-masked genotype queries
- Conversion from FLARE and RFMix output to `.lanc` format
- Merging `.lanc` files
- Python API and command-line interface (CLI)

Full documentation can be found [here](https://lanctools.readthedocs.io/en/latest/)

## Development Status

This project is in early development and is only intended for academic use.

Per semantic versioning conventions, anything may change at any time. The API
should not be considered stable, and breaking changes may occur without notice.

## References

- Hou, K. et al. Admix-kit: an integrated toolkit and pipeline for genetic analyses of admixed populations. Bioinformatics 40, btae148 (2024). [paper](https://doi-org.libproxy.lib.unc.edu/10.1093/bioinformatics/btae148) [software](https://github.com/KangchengHou/admix-kit)
- Browning, S. R., Waples, R. K. & Browning, B. L. Fast, accurate local ancestry inference with FLARE. Am J Hum Genet 110, 326–335 (2023). [paper](https://doi.org/10.1016/j.ajhg.2022.12.010) [software](https://github.com/browning-lab/flare)
- Maples, B. K., Gravel, S., Kenny, E. E. & Bustamante, C. D. RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference. Am J Hum Genet 93, 278–288 (2013). [paper](<https://doi.org/10.1016/j.ajhg.2013.06.020>) [software](https://github.com/slowkoni/rfmix)
