Skip to content

Issues: sgkit-dev/sgkit

Beta
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Clear current search query, filters, and sorts
193 Open 515 Closed
193 Open 515 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Assigned to nobody Loading
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

ImportError: cannot import name 'vcf2zarr' from 'bio2zarr' bug Something isn't working upstream Used when our build breaks due to upstream changes
#1308 by tomwhite was closed Apr 14, 2025
2
2
Wheels always have 0.0.0 version number bug Something isn't working process + tools
#1306 by tomwhite was closed Apr 7, 2025
1
Release 0.10.0
#1304 by tomwhite was closed Apr 8, 2025
2
Wheels build is broken github_actions Pull requests that update GitHub Actions code good first issue Good for newcomers help wanted Extra attention is needed process + tools
#1302 by tomwhite was closed Apr 7, 2025
1
Unit test failures under Zarr Python 3.0.2 IO Issues related to reading and writing common third-party file formats upstream Used when our build breaks due to upstream changes
#1290 by tomwhite was closed Feb 25, 2025
1
Unit tests failures under Cubed bug Something isn't working
#1284 by tomwhite was closed Feb 10, 2025
1
1
Fix CI for Zarr Python v3 upstream Used when our build breaks due to upstream changes
#1283 by tomwhite was closed Jan 14, 2025
1
Chunked pedigree kinship
#1280 by timothymillar was closed Jan 13, 2025
1
@timothymillar
GPU build is failing process + tools
#1270 by tomwhite was closed Oct 14, 2024
1
Benchmarking Numba vs JAX performance
#1266 by tomwhite was closed Feb 10, 2025
4
Update GWAS tutorial to use vcf2zarr documentation Improvements or additions to documentation IO Issues related to reading and writing common third-party file formats
#1257 by tomwhite was closed Sep 17, 2024
1
Main build is very slow and times out upstream Used when our build breaks due to upstream changes
#1247 by tomwhite was closed Sep 2, 2024
1
Deprecate VCF write functions documentation Improvements or additions to documentation IO Issues related to reading and writing common third-party file formats
#1245 by tomwhite was closed Oct 11, 2024
2
Release 0.9.0
#1235 by tomwhite was closed Jul 1, 2024
4
Run tests against NumPy 2 upstream Used when our build breaks due to upstream changes
#1234 by tomwhite was closed Sep 2, 2024
1
3
Deprecate functions for reading VCF IO Issues related to reading and writing common third-party file formats
#1232 by tomwhite was closed Jun 27, 2024
1
1
Option to calculate IBS probabilities via allele matching enhancement New feature or request
#1227 by timothymillar was closed Jul 4, 2024
1
Run tests against Zarr 3 upstream Used when our build breaks due to upstream changes
#1226 by tomwhite was closed Nov 5, 2024
1
4
Main build failing with 'RuntimeWarning: overflow encountered in scalar subtract' bug Something isn't working upstream Used when our build breaks due to upstream changes
#1225 by tomwhite was closed Jun 19, 2024
1
@timothymillar
ImportError: dlopen[...]: symbol not found in flat namespace '_bcf_float_missing' - sgkit-vcf requirements are not installed
#1220 by simonharnqvist was closed May 23, 2024
4
Release 0.8.0 process + tools
#1216 by tomwhite was closed May 7, 2024
2
MemoryError: Allocation failed (probably too large) with ped.compute()
#1213 by fouerghi was closed Jan 13, 2025
1
8
vcf_to_zarr raises error instead of truncating INFO fields of length R bug Something isn't working IO Issues related to reading and writing common third-party file formats
#1210 by timothymillar was closed May 7, 2025
5
Change in Xarray repr is causing doctest failures upstream Used when our build breaks due to upstream changes
#1204 by tomwhite was closed Mar 4, 2024
1
partition_into_regions: tabix index returns illegal region with multiple contigs bug Something isn't working
#1203 by jeromekelleher was closed May 7, 2025 0.9.1
1
ProTip! Find all open issues with in progress development work with linked:pr.