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213 Open 472 Closed
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Issues list

Run tests against NumPy 2 upstream Used when our build breaks due to upstream changes
#1234 opened Jun 24, 2024 by tomwhite
2
Run tests against Zarr 3 upstream Used when our build breaks due to upstream changes
#1226 opened Jun 17, 2024 by tomwhite
2
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
1
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
Sequential VCF parsing IO Issues related to reading and writing common third-party file formats
#1183 opened Feb 5, 2024 by hammer
@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
Document how to use save_dataset to overwrite existing files
#1173 opened Jan 19, 2024 by hyanwong
1
"missing_pct" misnamed in simulate_genotype_call_dataset
#1172 opened Jan 19, 2024 by hyanwong
Iterating through variants
#1171 opened Jan 19, 2024 by hyanwong
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