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Issues list

Windowing fails for datasets where contigs lack variant sites bug Something isn't working
#1268 opened Oct 10, 2024 by percyfal
1
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
7
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
Howto: join biallelic SNPs into a single record?
#1179 opened Jan 22, 2024 by hyanwong
1
Variant positions less than one?
#1176 opened Jan 22, 2024 by hyanwong
1
FAQ - mask out duplicate positions
#1174 opened Jan 20, 2024 by hyanwong
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