Metadata-Version: 2.2
Name: threads-arg
Version: 0.2.1
Summary: Highly scalable inference of ancestral recombination graphs (ARGs)
Author: Threads Developers
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Requires-Python: >=3.9
Requires-Dist: click
Requires-Dist: xarray
Requires-Dist: h5py
Requires-Dist: pandas
Requires-Dist: numba
Requires-Dist: numpy
Requires-Dist: tszip
Requires-Dist: arg-needle-lib==1.1.3
Requires-Dist: cyvcf2
Requires-Dist: ray
Requires-Dist: pgenlib
Requires-Dist: tqdm
Provides-Extra: dev
Requires-Dist: pytest; extra == "dev"
Description-Content-Type: text/markdown

# Threads

This software implements the Threads algorithm, described in

`Á. F. Gunnarsson, J. Zhu, B. C. Zhang, Z. Tsangalidou, A. Allmont, P. Palamara. A scalable approach for genome-wide inference of ancestral recombination graphs. bioRxiv, 2024.`

The user manual for threads can be found [here](https://palamaralab.github.io/software/threads/).

## Installation

```sh
pip install threads_arg
```
# threads Release Notes

## [0.2.1] - 2025-06-03

### Added

- VCF conversion backwards compatibility (#76)
- Add Linux ARM platform to Python wheels (#82)

## [0.2.0] - 2025-04-29

### Added

- Optimised imputation (#28)
- Variant mapping (#38)
- Upgrade to numpy 2.0 (#39)
- Consistent SHAPEIT format for regions (#42)
- Ability to write impute output directly to stdout (#42)
- Allele age estimation and data consistency (#51)

### Fixed

- Fix os.sched_getaffinity macOS error (#49)

## [0.1.0] - 2024-07-04

### Added

- Initial version of threads
