Skip to content

Issues: sgkit-dev/sgkit

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
34 Open 36 Closed
34 Open 36 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
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

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 opened Mar 7, 2024 by timothymillar
3
Sequential VCF parsing IO Issues related to reading and writing common third-party file formats
#1183 opened Feb 5, 2024 by hammer
@jeromekelleher
1
read_plink from cloud storage IO Issues related to reading and writing common third-party file formats
#1150 opened Dec 2, 2023 by hammer
1
Single-step VCF to Zarr conversion IO Issues related to reading and writing common third-party file formats
#1131 opened Sep 20, 2023 by tomwhite
Alternative execution engines for VCF conversion IO Issues related to reading and writing common third-party file formats
#1130 opened Sep 20, 2023 by tomwhite
5
Can we use KvikIO? IO Issues related to reading and writing common third-party file formats
#1127 opened Sep 7, 2023 by hammer
Utilities to help with and/or automatically select VCF ingestion parameters IO Issues related to reading and writing common third-party file formats
#1123 opened Sep 4, 2023 by benjeffery
1
Test with Zarr V3 IO Issues related to reading and writing common third-party file formats upstream Used when our build breaks due to upstream changes
#1118 opened Aug 23, 2023 by tomwhite
Remove contigs dataset attribute data representation Issues related to how data is represented: data types, data structures, indexes, access methods, etc IO Issues related to reading and writing common third-party file formats
#1058 opened Apr 5, 2023 by tomwhite
Copy contigs from attribute to array in load_dataset IO Issues related to reading and writing common third-party file formats
#1057 opened Apr 5, 2023 by tomwhite 0.9.1
@benjeffery
Support quantitative trait values in plink IO Issues related to reading and writing common third-party file formats
#1023 opened Feb 14, 2023 by tomwhite
Write pedigree data to VCF IO Issues related to reading and writing common third-party file formats
#1014 opened Jan 30, 2023 by timothymillar
Read pedigree data from VCF IO Issues related to reading and writing common third-party file formats
#1013 opened Jan 30, 2023 by timothymillar
1
Document reading tabular pedigree formats into sgkit documentation Improvements or additions to documentation IO Issues related to reading and writing common third-party file formats
#1012 opened Jan 30, 2023 by timothymillar
3
Write family information in write_plink IO Issues related to reading and writing common third-party file formats
#1010 opened Jan 30, 2023 by tomwhite
3
Populate parent_id variable in read_plink IO Issues related to reading and writing common third-party file formats
#1009 opened Jan 30, 2023 by tomwhite
2
Make sample_id from plink reader unique IO Issues related to reading and writing common third-party file formats
#1008 opened Jan 30, 2023 by tomwhite
4
Improve control over float formatting in VCF writer enhancement New feature or request IO Issues related to reading and writing common third-party file formats
#966 opened Nov 22, 2022 by tomwhite
1
Can't convert VCF fields not defined in the header IO Issues related to reading and writing common third-party file formats
#728 opened Oct 6, 2021 by tomwhite
1
Port GFF3 I/O methods of scikit-allel to sgkit? IO Issues related to reading and writing common third-party file formats
#657 opened Aug 31, 2021 by hammer
Can't read remote VCF files over https on Linux IO Issues related to reading and writing common third-party file formats
#645 opened Aug 2, 2021 by tomwhite
VCF file zoo IO Issues related to reading and writing common third-party file formats
#478 opened Mar 4, 2021 by hammer
2
Extract additional metadata from VCF files data representation Issues related to how data is represented: data types, data structures, indexes, access methods, etc IO Issues related to reading and writing common third-party file formats
#464 opened Feb 14, 2021 by hammer
3
Genetics data IO performance stats/doc documentation Improvements or additions to documentation IO Issues related to reading and writing common third-party file formats performance
#437 opened Jan 12, 2021 by ravwojdyla
9
Document and test vcf_to_zarr's variant order guarantees documentation Improvements or additions to documentation IO Issues related to reading and writing common third-party file formats
#425 opened Dec 17, 2020 by tomwhite
ProTip! Type g i on any issue or pull request to go back to the issue listing page.