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Issues list

Run tests against Zarr 3 upstream Used when our build breaks due to upstream changes
#1226 opened Jun 17, 2024 by tomwhite updated Jul 11, 2024
3
Run tests against NumPy 2 upstream Used when our build breaks due to upstream changes
#1234 opened Jun 24, 2024 by tomwhite updated Jun 25, 2024
2
Update docs to say "Scalable genetics toolkit"
#1223 opened Jun 7, 2024 by jeromekelleher updated Jun 7, 2024
simulate_genotype_call_dataset creates duplicate alleles bug Something isn't working
#1221 opened Jun 7, 2024 by hyanwong updated Jun 7, 2024
simulate_genotype_call_dataset creates alleles as byte strings bug Something isn't working
#1222 opened Jun 7, 2024 by hyanwong updated Jun 7, 2024
1
Genome accessibility/callability
#1219 opened May 22, 2024 by mufernando updated May 23, 2024
1
Python 3.11,3.12 conda install fails.
#1218 opened May 15, 2024 by benjeffery updated May 15, 2024
partition_into_regions: tabix index returns illegal region with multiple contigs bug Something isn't working
#1203 opened Mar 3, 2024 by jeromekelleher updated Apr 29, 2024 0.9.1
partition_into_regions: CSI indexed BCFs return empty regions bug Something isn't working
#1202 opened Mar 3, 2024 by jeromekelleher updated Apr 29, 2024 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 updated Apr 29, 2024 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 updated Apr 29, 2024 0.9.1
Set SGKIT_DISABLE_NUMBA_CACHE=1 by default bug Something isn't working
#1156 opened Dec 14, 2023 by jeromekelleher updated Apr 29, 2024 0.9.1
3
MemoryError: Allocation failed (probably too large) with ped.compute()
#1213 opened Apr 8, 2024 by fouerghi updated Apr 21, 2024
7
Move docs to sgkit.dev documentation Improvements or additions to documentation
#1212 opened Mar 29, 2024 by hammer updated Mar 29, 2024
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 updated Mar 7, 2024
3
read_plink returns bytes for variant_alleles not unicode bug Something isn't working
#1209 opened Mar 6, 2024 by jeromekelleher updated Mar 6, 2024
Mixed-ploidy VanRaden GRM enhancement New feature or request
#1207 opened Mar 4, 2024 by timothymillar updated Mar 4, 2024
Don't display attributes expanded for dataset enhancement New feature or request
#1157 opened Dec 14, 2023 by jeromekelleher updated Feb 9, 2024 0.9.1
5
Parts of work redone when a dask worker dies
#1154 opened Dec 5, 2023 by benjeffery updated Feb 9, 2024 0.9.1
2
"show source" for function in docs shows rst code documentation Improvements or additions to documentation
#1117 opened Aug 22, 2023 by jeromekelleher updated Feb 9, 2024 0.9.1
Use contig_id and filter_id arrays instead of attributes in write_vcf bug Something isn't working
#1101 opened Jul 8, 2023 by timothymillar updated Feb 9, 2024 0.9.1
@benjeffery
1
vcf_to_zarr creates zero-sized first chunk which results in incorrect dtype. bug Something isn't working upstream Used when our build breaks due to upstream changes
#1090 opened May 18, 2023 by benjeffery updated Feb 9, 2024 0.9.1
@benjeffery
8
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 updated Feb 9, 2024 0.9.1
@benjeffery
Tests should use process-based dask
#1051 opened Mar 9, 2023 by benjeffery updated Feb 9, 2024 0.9.1
3
Do chunk sizes have to be the same for all variables in a given dimension?
#1186 opened Feb 5, 2024 by jeromekelleher updated Feb 5, 2024
1
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