Metadata-Version: 2.1
Name: bgen-reader
Version: 3.0.2
Summary: Bgen file format reader
Home-page: https://github.com/limix/bgen-reader-py
Author: Danilo Horta
Author-email: horta@ebi.ac.uk
Maintainer: Danilo Horta
Maintainer-email: horta@ebi.ac.uk
License: MIT
Download-URL: https://github.com/limix/bgen-reader-py
Keywords: bgen,reader,genetics
Platform: Windows
Platform: MacOS
Platform: Linux
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Description-Content-Type: text/markdown
Requires-Dist: cachetools (>=3.0.0)
Requires-Dist: cffi (>=1.11.5)
Requires-Dist: cytoolz (>=0.9.0)
Requires-Dist: dask[dataframe,array,delayed,bag] (>=1.0.0)
Requires-Dist: pandas (>=0.23.3)
Requires-Dist: pytest-runner (>=4.2)
Requires-Dist: pytest (>=3.6.3)
Requires-Dist: scipy (>=1.1.0)
Requires-Dist: texttable (>=1.5.0)
Requires-Dist: tqdm (>=4.23.4)
Requires-Dist: xarray (>=0.11.0)

# bgen-reader

[![Travis](https://img.shields.io/travis/limix/bgen-reader-py.svg?style=flat-square&label=linux%20%2F%20macos%20build)](https://travis-ci.org/limix/bgen-reader-py) [![AppVeyor](https://img.shields.io/appveyor/ci/Horta/bgen-reader-py.svg?style=flat-square&label=windows%20build)](https://ci.appveyor.com/project/Horta/bgen-reader-py)

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 vi [conda](https://conda.io/docs/)

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

Or via pip

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

## 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/master/LICENSE.md).


