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

219 Open 479 Closed
219 Open 479 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

Chunked pedigree kinship
#1280 opened Dec 15, 2024 by timothymillar
@timothymillar
Add separate function for Watterson's theta
#1279 opened Dec 5, 2024 by percyfal
2
Diversity calculations on windowed datasets generate lots of unmanaged memory
#1278 opened Dec 5, 2024 by percyfal
8
Windowing fails for datasets where contigs lack variant sites bug Something isn't working
#1268 opened Oct 10, 2024 by percyfal
5
Dask 2024.8.1 and later is very slow performance upstream Used when our build breaks due to upstream changes
#1267 opened Oct 7, 2024 by tomwhite
8
Benchmarking Numba vs JAX performance
#1266 opened Oct 7, 2024 by tomwhite
4
Unclear how to overwrite a dataset
#1243 opened Jul 26, 2024 by hyanwong
2
No page at https://sgkit-dev.github.io
#1242 opened Jul 26, 2024 by hyanwong
Displaying alleles when using sgkit.display_genotypes(ds)
#1240 opened Jul 25, 2024 by hyanwong
Update docs to say "Scalable genetics toolkit"
#1223 opened Jun 7, 2024 by jeromekelleher
simulate_genotype_call_dataset creates alleles as byte strings bug Something isn't working
#1222 opened Jun 7, 2024 by hyanwong
1
simulate_genotype_call_dataset creates duplicate alleles bug Something isn't working
#1221 opened Jun 7, 2024 by hyanwong
Genome accessibility/callability
#1219 opened May 22, 2024 by mufernando
4
Python 3.11,3.12 conda install fails.
#1218 opened May 15, 2024 by benjeffery
MemoryError: Allocation failed (probably too large) with ped.compute()
#1213 opened Apr 8, 2024 by fouerghi
7
Move docs to sgkit.dev documentation Improvements or additions to documentation
#1212 opened Mar 29, 2024 by hammer
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
read_plink returns bytes for variant_alleles not unicode bug Something isn't working
#1209 opened Mar 6, 2024 by jeromekelleher
Mixed-ploidy VanRaden GRM enhancement New feature or request
#1207 opened Mar 4, 2024 by timothymillar
partition_into_regions: tabix index returns illegal region with multiple contigs bug Something isn't working
#1203 opened Mar 3, 2024 by jeromekelleher 0.9.1
partition_into_regions: CSI indexed BCFs return empty regions bug Something isn't working
#1202 opened Mar 3, 2024 by jeromekelleher 0.9.1
partition_into_regions: CSI indexed VCFs have incorrect sequence names bug Something isn't working
#1201 opened Mar 3, 2024 by jeromekelleher 0.9.1
read_scikit_allel_vcfzarr returns string pad values instead of missing for INFO fields bug Something isn't working
#1195 opened Feb 15, 2024 by jeromekelleher 0.9.1
Do chunk sizes have to be the same for all variables in a given dimension?
#1186 opened Feb 5, 2024 by jeromekelleher
1
genee review: sgkit implementation limitations
#1180 opened Jan 27, 2024 by jdstamp
@hammer @tomwhite
1
ProTip! Exclude everything labeled bug with -label:bug.