Metadata-Version: 2.1
Name: bgen-reader
Version: 4.0.9
Summary: Bgen file format reader
License: MIT
Author: Danilo Horta
Author-email: horta@ebi.ac.uk
Requires-Python: >=3.10,<4.0
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Provides-Extra: docs
Requires-Dist: appdirs (>=1.4.4,<2.0.0)
Requires-Dist: cachetools (>=5.5.0,<6.0.0)
Requires-Dist: cbgen (>=1.0.6,<2.0.0)
Requires-Dist: dask[array,bag,dataframe,delayed] (>=2024.10.0,<2025.0.0)
Requires-Dist: limix-sphinx-theme (>=0.0.4,<0.0.5) ; extra == "docs"
Requires-Dist: numpy (>=2.1.2,<3.0.0)
Requires-Dist: pandas (>=2.2.3,<3.0.0)
Requires-Dist: requests (>=2.32.3,<3.0.0)
Requires-Dist: sphinx (>=8.1.3,<9.0.0) ; extra == "docs"
Requires-Dist: sphinx-rtd-theme (>=3.0.1,<4.0.0) ; extra == "docs"
Requires-Dist: texttable (>=1.7.0,<2.0.0)
Requires-Dist: tqdm (>=4.66.5,<5.0.0)
Requires-Dist: xarray (>=2024.10.0,<2025.0.0)
Description-Content-Type: text/markdown

# bgen-reader

A [bgen file format](http://www.well.ox.ac.uk/~gav/bgen_format/) reader.

Bgen is a file format for storing large genetic datasets.
It supports both unphased genotypes and phased haplotype data with variable
ploidy and number of alleles. It was designed to provides a compact data
representation without sacrificing variant access performance.

This python package is a wrapper around the [bgen library](https://github.com/limix/bgen),
a low-memory footprint reader that efficiently reads bgen files.
It fully supports the bgen format specifications: 1.2 and 1.3;
as well as their optional compressed formats.

## Install

It can be installed via [conda](https://conda.io/docs/)

```bash
conda install -c conda-forge bgen-reader
```

Or via pip

```bash
pip install bgen-reader
```

## Documentation

Please, refer to [https://bgen-reader.readthedocs.io](https://bgen-reader.readthedocs.io).


## Troubleshooting

### fatal error: bgen.h: No such file or directory

This means that bgen C library is not installed (or could not be found). Please,
follow the instructions in <https://github.com/limix/bgen> to install it, and try
installing bgen-reader again.

## Problems

If you encounter any issue, please, [submit it](https://github.com/limix/bgen-reader-py/issues/new).

## Authors

* [Danilo Horta](https://github.com/horta)

## License

This project is licensed under the [MIT License](https://raw.githubusercontent.com/limix/bgen-reader-py/main/LICENSE.md).

