bgen

A BGEN file format reader.

It fully supports the BGEN format specifications 1.2 and 1.3.

Install

You can install it via conda:

conda install -c conda-forge bgen

A second installation option would be to download the latest source and to build it by yourself. It can be as simple as:

curl -fsSL https://git.io/JerYI | GITHUB_USER=limix GITHUB_PROJECT=bgen bash

Under Windows, please, use Git Bash terminal to enter the above command.

Documentation

Refer to documentation for usage and API description.

File specification

The original specification can be found at http://www.well.ox.ac.uk/~gav/bgen_format/. We have also created an alternative, more user-friendly BGEN specification.

Development

Make sure you have the dependencies installed. From terminal, clone the repository and checkout the develop branch:

git clone https://github.com/limix/bgen.git
cd bgen

Create a build folder and compile from there:

mkdir build
cd build
# Configure and generate scripts that will build it
cmake -DCMAKE_BUILD_TYPE=Release ..
# Compile it
cmake --build . --config Release
# Test it
ctest --output-on-failure -C Release

Acknowledgments

• Marc Jan Bonder for bug-reporting and improvement suggestions.
• Yan Wong for bug-reporting and improvement suggestions.
• Carl Kadie for bug-reporting and improvement suggestions.

Authors

• Danilo Horta

License

This project is licensed under the MIT License.