https://github.com/limix/bgen-reader-py
A BGEN file format reader.
https://github.com/limix/bgen-reader-py
Last synced: 6 months ago
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A BGEN file format reader.
- Host: GitHub
- URL: https://github.com/limix/bgen-reader-py
- Owner: limix
- License: mit
- Created: 2017-06-15T07:18:08.000Z (almost 8 years ago)
- Default Branch: main
- Last Pushed: 2024-10-28T12:01:16.000Z (7 months ago)
- Last Synced: 2024-10-28T12:50:05.425Z (7 months ago)
- Language: Python
- Homepage:
- Size: 1.2 MB
- Stars: 10
- Watchers: 3
- Forks: 3
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
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README
# 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 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).