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.
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.
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-4.0.0-cp38-cp38-win_amd64.whl
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 1d3c4356b3f6311a0343ed1e2e877d1f21e04fecad910394d3a835bb0eea6a31 |
|
| MD5 | 3c047498a3eb4256d0cec0c114ba7152 |
|
| BLAKE2b-256 | b4009e63e865ebd08171f03bbac65f0c2e1629868e3366a03775818e937ffa47 |
Hashes for bgen_reader-4.0.0-cp38-cp38-manylinux2010_x86_64.whl
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 8285a12c20a2bdcb7a97383e73467eae1af578c09958af6670a050fab8976e84 |
|
| MD5 | c69b2bcf7fc2cc2b858f4be52bfefafe |
|
| BLAKE2b-256 | 4bbc0975bf1151cc8e2a7694d1c0f139eb8d589c53833023fce468d0d8e8faee |
Hashes for bgen_reader-4.0.0-cp38-cp38-manylinux1_x86_64.whl
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | bc42d3b077d9cfa0fad8a7f3c4e491a037f59de339821c07dfe5113c177773ec |
|
| MD5 | 66da76b605f9be85c2481b83909af4a3 |
|
| BLAKE2b-256 | 8c7df6e1fb32392b5670de0b377162353eb8ab72a514b4066c4900de46b840a9 |
Hashes for bgen_reader-4.0.0-cp38-cp38-macosx_10_9_x86_64.whl
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | e197a5b74a701c6a5b879cbad433364a1d1870aafaa831b9e592db44e2b21f43 |
|
| MD5 | ed5a5deb6893bd164257c4d0414cd1b0 |
|
| BLAKE2b-256 | 07196c65b83b1cbee984e463fd6dbb073d53c5c86dfc405f3ca16f3ee7ade84e |
Hashes for bgen_reader-4.0.0-cp37-cp37m-win_amd64.whl
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | e9b8d7aff68f88153d446852ca126c6f71dc65d7fef98112ec31be9d48be9c31 |
|
| MD5 | ea5328b9ccd017ec151ba99a6d0ba697 |
|
| BLAKE2b-256 | bd46c2b7ec1247d59f1c4d78418862ebe119b70ffca9ca2367af00f58d31adf7 |
Hashes for bgen_reader-4.0.0-cp37-cp37m-manylinux2010_x86_64.whl
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | cfb17b97b4325dd49c202460a3685c7b5af92e47534ff5131b19ce1d6e154b96 |
|
| MD5 | f3ecef30e5aacf519f60e1a374483c7d |
|
| BLAKE2b-256 | a973e8db5e56a1822ed159573911e5994abc813fa948b4f78168d180e5d65c7d |
Hashes for bgen_reader-4.0.0-cp37-cp37m-manylinux1_x86_64.whl
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 46f0576820d41096aa0365f88b5c34f3f667bbc7d07f7fcfc2e03ef269f67116 |
|
| MD5 | 83f0fac19824a7e3a594965c046de53c |
|
| BLAKE2b-256 | 1a129dfa316598e3bea820b3da78081d1dca8210634a8879aeaac8a58afd3c5b |
Hashes for bgen_reader-4.0.0-cp37-cp37m-macosx_10_9_x86_64.whl
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 4825e93029f0b16846d13bd634f91c38512cd840f853296fa812e432d1aa5939 |
|
| MD5 | b6d044e78f52b979ef42361c882cde69 |
|
| BLAKE2b-256 | 1f4444ada0c58cb874d428292508c91dedbc47d350f9bbb42dbe0b9db69d3cc4 |
