limix/bgen-reader-py issues and pull requests

#51 - Indexing bug in documentation

Issue - State: closed - Opened by saulpierotti about 1 month ago - 4 comments

#50 - Conda: Python versions >3.9

Issue - State: closed - Opened by chrisief 10 months ago - 1 comment

#49 - Fix sample files by moving them to a new GitHub repro.

Pull Request - State: closed - Opened by CarlKCarlK about 1 year ago

#48 - example_filepath reports AWS error

Issue - State: closed - Opened by CarlKCarlK about 1 year ago - 4 comments

#47 - Error while creating metafile bgen.metadata

Issue - State: closed - Opened by cnl27 about 1 year ago - 2 comments

#46 - Minor bug in docs

Issue - State: open - Opened by CarlKCarlK over 1 year ago

#45 - bgen-reader no longer working on windows

Issue - State: open - Opened by CarlKCarlK over 2 years ago

#44 - Allow bgen-reader to work with files in read-only directories

Pull Request - State: open - Opened by CarlKCarlK over 2 years ago

#44 - Allow bgen-reader to work with files in read-only directories

Pull Request - State: closed - Opened by CarlKCarlK over 2 years ago

#43 - GitHub Action python-package.yml seems to have rotted

Issue - State: closed - Opened by CarlKCarlK over 2 years ago - 2 comments

#42 - Can't open bgen using symbolic links

Issue - State: open - Opened by jordanero over 2 years ago - 7 comments

#41 - fix issue 40

Pull Request - State: closed - Opened by CarlKCarlK about 3 years ago

#40 - bgen_reader.allele_expectation allocates memory based on unindexed genotype

Issue - State: open - Opened by jordanero over 3 years ago - 3 comments

#39 - ImportError

Issue - State: closed - Opened by cybluetree over 3 years ago - 2 comments

#38 - Saving metadata in different dir as bgen file

Issue - State: closed - Opened by evigorito almost 4 years ago - 8 comments

#37 - index out of range in bgen["variants"]

Issue - State: closed - Opened by ScarlettWang532 almost 4 years ago - 3 comments

#37 - index out of range in bgen["variants"]

Issue - State: closed - Opened by ScarlettWang532 almost 4 years ago - 3 comments

#36 - Empty bgen file might cause division by zero.

Issue - State: open - Opened by horta about 4 years ago

#35 - Could not open genotype

Issue - State: closed - Opened by fbeghini about 4 years ago - 17 comments
Labels: bug

#34 - Update bgen2 to use cbgen

Pull Request - State: closed - Opened by CarlKCarlK about 4 years ago - 1 comment

#34 - Update bgen2 to use cbgen

Pull Request - State: closed - Opened by CarlKCarlK about 4 years ago - 1 comment

#33 - More options for control of behavior in read_genotype

Issue - State: closed - Opened by eric-czech over 4 years ago - 16 comments

#32 - Export infer_metafile_filepath properly

Issue - State: open - Opened by horta over 4 years ago

#31 - Make use of pooch for example files

Issue - State: closed - Opened by horta over 4 years ago
Labels: enhancement

#30 - Feature request: bulk distributed access

Issue - State: open - Opened by tomwhite over 4 years ago - 35 comments

#29 - Library fails on *.bgen files larger than 2Gbtyes (2**31)

Issue - State: closed - Opened by CarlKCarlK over 4 years ago - 2 comments

#28 - Can't figure out dev build on Derbin

Issue - State: closed - Opened by CarlKCarlK over 4 years ago - 2 comments

#27 - ci\before-build-win.bat references bgen install.bat that no longer exists

Issue - State: closed - Opened by CarlKCarlK over 4 years ago - 2 comments

#26 - Just Python 3?

Issue - State: closed - Opened by CarlKCarlK over 4 years ago - 1 comment

#26 - Just Python 3?

Issue - State: closed - Opened by CarlKCarlK over 4 years ago - 1 comment

#25 - read_bgen ignores new file contents

Issue - State: closed - Opened by CarlKCarlK over 4 years ago - 1 comment

#24 - variant position is returning negative numbers

Issue - State: closed - Opened by CarlKCarlK over 4 years ago - 3 comments

#24 - variant position is returning negative numbers

Issue - State: closed - Opened by CarlKCarlK over 4 years ago - 3 comments

#23 - Variant info performance seems slow as # of variants goes to 1M+

Issue - State: closed - Opened by CarlKCarlK over 4 years ago - 8 comments

#22 - Can't retrieve large.bgen test file

Issue - State: closed - Opened by CarlKCarlK over 4 years ago - 5 comments

#21 - pickle error on dask cluster

Issue - State: closed - Opened by jeremymcrae almost 5 years ago - 1 comment

#21 - pickle error on dask cluster

Issue - State: closed - Opened by jeremymcrae almost 5 years ago - 1 comment

#20 - Segmentation fault (core dumped)

Issue - State: closed - Opened by alexanderbuchholz about 5 years ago - 12 comments

#19 - GEN-reader?

Issue - State: closed - Opened by hoangthienan95 about 5 years ago - 6 comments

#19 - GEN-reader?

Issue - State: closed - Opened by hoangthienan95 about 5 years ago - 6 comments

#18 - Suppress "setupterm() failed: TERM=xterm-256color not found in database or too generic" warning

Issue - State: closed - Opened by horta over 5 years ago
Labels: enhancement

#18 - Suppress "setupterm() failed: TERM=xterm-256color not found in database or too generic" warning

Issue - State: closed - Opened by horta over 5 years ago
Labels: enhancement

#17 - RuntimeError: Could not open /path/to/test.bgen.metadata

Issue - State: closed - Opened by torstees over 5 years ago - 3 comments

#16 - Genotypes in probabilities?

Issue - State: open - Opened by Hoeze over 5 years ago - 8 comments
Labels: enhancement

#16 - Genotypes in probabilities?

Issue - State: open - Opened by Hoeze over 5 years ago - 8 comments
Labels: enhancement

#15 - index out of range

Issue - State: closed - Opened by nurfatimaj over 5 years ago - 13 comments

#14 - Lots of issues with python 2.7

Issue - State: closed - Opened by torstees almost 6 years ago - 1 comment

#13 - sporadic error when reading in genotypes

Issue - State: closed - Opened by arminschoech about 6 years ago - 3 comments

#12 - Add sample_file option to read_bgen

Pull Request - State: closed - Opened by HannahVMeyer over 6 years ago

#11 - Error when installing with pip

Issue - State: closed - Opened by dissectroslin over 6 years ago - 4 comments

#10 - Add example for using batches if you want to accessing all the genome

Issue - State: closed - Opened by hyanwong over 6 years ago - 11 comments
Labels: enhancement

#9 - 'bgen_reader._ffi' not found

Issue - State: closed - Opened by seafloor over 6 years ago - 2 comments

#8 - Add support for phased data (and return extra variant information)

Issue - State: closed - Opened by hyanwong over 6 years ago - 42 comments
Labels: enhancement

#7 - I get "Error while storing buffer: Permission denied"

Issue - State: closed - Opened by hyanwong over 6 years ago - 5 comments

GitHub / limix/bgen-reader-py issues and pull requests