Bgen file format reader

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Project description

bgen-reader

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A bgen file 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, 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.

Questions? Please, visit the bgen-reader forum 💬.

Install

It can be installed via conda

conda install -c conda-forge bgen-reader

Or via pip

pip install bgen-reader

Documentation

Please, refer to 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.

Authors

License

This project is licensed under the MIT License.

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