Bgen file format reader

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Project description

bgen-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

Danilo Horta

License

This project is licensed under the MIT License.

Project details

These details have not been verified by PyPI

Release history Release notifications | RSS feed

This version

4.0.9

Oct 28, 2024

4.0.8

Jun 23, 2021

4.0.7

Nov 5, 2020

4.0.6

Sep 16, 2020

4.0.5

Aug 11, 2020

4.0.4

Apr 8, 2020

4.0.3

Apr 7, 2020

4.0.2

Apr 7, 2020

4.0.1

Apr 7, 2020

4.0.0

Apr 7, 2020

3.0.7

Oct 22, 2019

3.0.6

May 9, 2019

3.0.5

Apr 8, 2019

3.0.4

Feb 2, 2019

3.0.3

Feb 1, 2019

3.0.2

Jan 18, 2019

2.0.9

May 9, 2019

2.0.8

Nov 17, 2018

2.0.7

Oct 8, 2018

2.0.6

Sep 26, 2018

2.0.5

Jul 17, 2018

2.0.4

Jul 12, 2018

2.0.3

Jul 10, 2018

2.0.2

Jul 9, 2018

2.0.1

Jun 14, 2018

2.0.0

Jun 13, 2018

1.1.6

Jun 9, 2018

1.1.5

Jun 9, 2018

1.1.4

Jun 8, 2018

1.1.3

Jun 7, 2018

1.1.2

Apr 5, 2018

1.1.1

Apr 5, 2018

1.1.0

Apr 5, 2018

1.0.4

Jan 28, 2018

1.0.1

Nov 7, 2017

1.0.0

Sep 20, 2017

0.1.17

Aug 30, 2017

0.1.16

Aug 16, 2017

0.1.15

Aug 15, 2017

0.1.14

Aug 14, 2017

0.1.13

Aug 14, 2017

0.1.12

Aug 10, 2017

0.1.11

Aug 10, 2017

0.1.10

Jun 28, 2017

0.1.9

Jun 26, 2017

0.1.8

Jun 26, 2017

0.1.7

Jun 23, 2017

0.1.6

Jun 23, 2017

0.1.5

Jun 23, 2017

0.1.4

Jun 23, 2017

0.1.2

Jun 23, 2017

0.1.1

Jun 23, 2017

0.1.0

Jun 22, 2017

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