A Python package implementing ARG-Needle and ASMC-clust genealogical inference.
Use
pip install arg_needle
to install from PyPI, and
pip install .
to install from a local clone.
Please see the ARG-Needle manual for all usage instructions and documentation.
- Bump the version number in pyproject.toml and CMakeLists.txt
- Update RELEASE_NOTES.md
- Push changes and check that all GitHub workflows pass
- Tag the commit in Git using syntax
vX.Y.Z - Make a release on GitHub, which should trigger a new build that will upload Python wheels to PyPI
arg-needle has been developed by Brian C. Zhang with support from Fergus Cooper, Árni Freyr Gunnarsson, and Pier Francesco Palamara.
The files src/hashing/FileUtils.cpp and src/hashing/FileUtils.hpp are adapted from analogous files in the Eagle software, which can be found at https://github.com/poruloh/Eagle/tree/master/src. Eagle was developed by Po-Ru Loh and released under the GNU General Public License v3.0 (GPLv3). Its license can be found under the 3rd_party/ directory.
If you use this software, please cite:
B. C. Zhang, A. Biddanda, Á. F. Gunnarsson, F. Cooper, P. F. Palamara, Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits. Nature Genetics, 2023.