Bgen file format reader
Project description
bgen-reader
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.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distributions
Hashes for bgen_reader-3.0.7-cp37-cp37m-win_amd64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 8382c70fd8ef351084805a081fb9a78688d36d0d58203b57df0229dbd916f9d8 |
|
MD5 | 03def95ae8398f3017f818d0e18650b3 |
|
BLAKE2b-256 | 2362f99041d431573bf8bbab89ef14789f39f19cb3ce386b0a160cb48f5548cd |
Hashes for bgen_reader-3.0.7-cp37-cp37m-manylinux1_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | fd6d5cd0c66c218cf6f9b57c8f67b76f985eb64fd7256c50ecf3adc248c7d498 |
|
MD5 | db6db0b134e611267ac1e42e0edecbb5 |
|
BLAKE2b-256 | 7a94d6f5edf65d9f01138c4c6b339ca95eff0d8c8849dd8b0ad7ca8b66434ae3 |
Hashes for bgen_reader-3.0.7-cp37-cp37m-macosx_10_6_intel.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | ecb4fccda2b9466c907bd46e80a64f0956b470b8fd136c6e0d10b2563958b48a |
|
MD5 | ee0cc3414518ef67b2b7c3462a48245e |
|
BLAKE2b-256 | b30386151005263992887d8254e3522af2d93dec53e47ee0bc7215804e9b308b |
Hashes for bgen_reader-3.0.7-cp36-cp36m-win_amd64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 074fd93857e8034d2a791ca7dc5955123881ecdd6115d3f9033fdbeeee2705f6 |
|
MD5 | 2965c8c6ed33f336c7cc6eae8ab96d6c |
|
BLAKE2b-256 | 369747aebcc370b430476c9507252f502e46a879f7e33baa662b7524919f1d6f |
Hashes for bgen_reader-3.0.7-cp36-cp36m-manylinux1_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 154e23e19b4bb620b82ef387e169c16625b0a04d0d3c11919454484e74b01d24 |
|
MD5 | d32af341cf4d069f8f78a3166ea38597 |
|
BLAKE2b-256 | 4d6bff2eec4d90c2e2ec6954ddece6db486045e81528e6302609dd6d01bde789 |
Hashes for bgen_reader-3.0.7-cp36-cp36m-macosx_10_6_intel.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | ee8ed2ddc1db6ac52310f02c4d830539df6de227eb544c7b90926542395e7c59 |
|
MD5 | 32e8e97194be7d71aa4a276c3c06ab18 |
|
BLAKE2b-256 | 078d5f7272e6f6ef5cc8ae5a24c1f65d638b8c0524cee39b04083e69f3a5cdf0 |