bgen -

2025-05-09

• enable reading bgen files by streaming from stdin

- C++
Published by jeremymcrae about 1 year ago

bgen -

2024-12-02

• fixed issue reading metadata containing whitespace characters

- C++
Published by jeremymcrae over 1 year ago

bgen -

### 2024-07-20

• optimized writing 8-bit genotypes

- C++
Published by jeremymcrae over 1 year ago

bgen -

2024-06-25

• fixed issue with empty list

- C++
Published by jeremymcrae over 1 year ago

bgen - v1.7.0

2024-06-25

• changed .withrsids() and .atpositions() to always return lists, which allows those methods to return multiple variants if multiple matches exist, or empty list if none exist

- C++
Published by jeremymcrae about 2 years ago

bgen -

2024-05-01

• fixed minor bugs
• avoid chance of heap overflow

- C++
Published by jeremymcrae about 2 years ago

bgen -

2024-01-24

• allow copying variants into a new bgen file without parsing

- C++
Published by jeremymcrae about 2 years ago

bgen - v1.6.1

2024-01-10

• fixed bug writing 1-bit encoded genotypes

- C++
Published by jeremymcrae over 2 years ago

bgen - v1.6.0

2024-01-09

• faster probabilities and dosages by avoiding copying float arrays

- C++
Published by jeremymcrae over 2 years ago

bgen - v1.5.9

2023-11-07

• bfile.rsids() and bfile.chroms() return in same order as in bgen file

- C++
Published by jeremymcrae over 2 years ago

bgen - v1.5.8

2023-11-02

• removed a deprecated python module import
• documented BgenWriter

- C++
Published by jeremymcrae over 2 years ago

bgen - v1.5.7

2023-10-27

• faster haplotype probabilities for 8-bit data
• quicker numpy array generation

- C++
Published by jeremymcrae over 2 years ago

bgen - v1.5.6

2023-10-24

• sped up parsing phased probabilities

- C++
Published by jeremymcrae over 2 years ago

bgen - 2023-10-16

sped up parsing phased probabilities when ploidy is constant

- C++
Published by jeremymcrae almost 3 years ago

bgen -

2023-04-03

• now can write bgen files in addition to reading
• faster decoding of zstd compressed genotypes by -O2 compiler option

- C++
Published by jeremymcrae over 3 years ago

bgen -

2023-03-10

• added fast dosage code for aarch64 (ARM) hardware

- C++
Published by jeremymcrae over 3 years ago

bgen -

2023-02-31

• added prebuilt windows packages
  • avoid creating Variant objects multiple times in python
  • fixed some compiler differences between linux and windows
  • only open ifstream in binary mode to prevent file seeking differences on windows

- C++
Published by jeremymcrae over 3 years ago

bgen -

2022-09-21

• handle if x86_64, but without AVX2
• add testing and package creation for macosx

- C++
Published by jeremymcrae almost 4 years ago

bgen -

2022-09-16

• capture and handle error while obtaining phased status if underlying data is not ready
• added method to get alt allele dosage from variant
• fixed issue if using dosage in numpy array after variant object is deleted

- C++
Published by jeremymcrae almost 4 years ago

bgen -

2022-06-03

• improved propagation of errors while reading data from filesystem

- C++
Published by jeremymcrae almost 4 years ago

bgen -

2022-06-03

• propagate c++ exceptions into python exceptions, enables handling variant errors on unstable filesystems
• use fixed width types in c++ code

- C++
Published by jeremymcrae almost 4 years ago

bgen -

2022-02-14

fixed bug assigning missing genotypes to samples

- C++
Published by jeremymcrae over 4 years ago

bgen -

2020-07-15

• fixed bug with dosage on layout=1
• cleaned up function documentation

- C++
Published by jeremymcrae almost 6 years ago

bgen -

2020-07-13

• use vectorized operations to calculate ref allele dosage from probabilties

- C++
Published by jeremymcrae almost 6 years ago

bgen -

2020-07-10

Only use vectorized operations on relevant hardware.

- C++
Published by jeremymcrae almost 6 years ago

bgen -

2020-07-10

Fixed bug from uninitialized variables.

- C++
Published by jeremymcrae almost 6 years ago

bgen -

2020-07-10

• Use vectorized operations to speed up calculating minor allele dosage
• sped up parsing probabilities with bgen layout=1
• refactored parsing probabilities and dosages

- C++
Published by jeremymcrae almost 6 years ago

bgen -

2020-09-01

Fixed a memory leak, which occurred when the minor allele dosage and probabilities were both calculated for a variant.

- C++
Published by jeremymcrae almost 6 years ago

bgen -

2020-07-02

• sped up parsing missingness when the ploidy is the same for all samples by checking 8 samples simultaneously, and only checking individual samples if any appear missing. Checking missingness under these conditions is now 3X faster than before.
• Optimized parsing probabilities when all samples are diploid with two alleles, and probabilities are encoded with 8 bits. This is now 2.5X faster than the standard method for calculating probabilities.

- C++
Published by jeremymcrae about 6 years ago

bgen -

2020-06-23

• fixed source distribution on pypi
• allow getting variant with next(bfile)

- C++
Published by jeremymcrae about 6 years ago

bgen -

2020-06-18

• use travis.ci for building wheels for pypi upload
• tests built wheels for python 3.6, 3.7, 3.8
• only uploads new version to pypi for commits with git tag

- C++
Published by jeremymcrae about 6 years ago

bgen -

2020-06-16

• fixed issue with 0000 magic number in header
• slightly faster parsing of ploidy states

- C++
Published by jeremymcrae about 6 years ago

bgen -

2020-06-10

• reuse probabilities and minor allele dosage if computed previously
• sped up minor allele dosage by avoiding numpy copy operation
• can fetch variants within a genomic region if bgen index file is present

- C++
Published by jeremymcrae about 6 years ago

bgen -

2020-06-04 - faster probabilities

• sped up parsing probabilities by avoiding an integer multiplication
• sped up parsing ploidy and missingness states
• sped up setting sample IDs

- C++
Published by jeremymcrae about 6 years ago

bgen -

2020-06-03 - minor fixes

• sped up calculating minor allele dosage
• simplified parsing genotype probabilities

- C++
Published by jeremymcrae about 6 years ago

bgen -

2020-06-01 - minor fixes

• sped up loading sample IDs from sample file
• fixed BgenFile context handling
• fixed bug with iteration if all variants loaded into memory
• added unit tests for minor allele dosage

- C++
Published by jeremymcrae about 6 years ago

bgen -

2020-05-28 - sped up parsing probabilities

• calculates genotype probabilities from integer representation to float probability with multiplies, which can be faster than divides

- C++
Published by jeremymcrae about 6 years ago

bgen -

2020-05-14 - fixed index issue

• fixed issue with bgenix indexes when multiprocessing

- C++
Published by jeremymcrae about 6 years ago

bgen -

2020-05-21 - fix memory leak

• avoid memory leak when repeatedly getting probabilities/dosages from same variant

- C++
Published by jeremymcrae about 6 years ago

bgen -

2020-05-27 - minor fixes

• sped up setting ploidy when all samples have same ploidy
• sped up getting minor allele dosage by determining minor allele from subset of samples

- C++
Published by jeremymcrae about 6 years ago

bgen - v1.1.3

2020-05-14 - improved use of index files

• more efficient iteration through bgen files
• added functions to get variants from bgen by position or rsid

- C++
Published by jeremymcrae about 6 years ago

bgen -

• fixed bug with python3.6 sqlite.connect() not accepting Path-like objects

- C++
Published by jeremymcrae about 6 years ago

bgen -

• fixed str decode error when logging sample_path

- C++
Published by jeremymcrae about 6 years ago

bgen - v1.1.0

2020-05-04 - now can use index files

• now can use bgenix index files to speed opening bgen files and slicing out variants
• fixed bugs with parsing ploidy states
• added continuous testing on OSX

- C++
Published by jeremymcrae about 6 years ago

bgen - v1.0.0 initial release

#### 2020-04-27 - released with basic functionality - open bgen files - parse variants - extract genotype data - extract minor allele dosage for biallelic variants - iterate through variants in bgen file - can exclude unwanted variants - can pickle/unpickle variants for distributed compute

- C++
Published by jeremymcrae about 6 years ago