sgkit-dev sgkit issues - Githubissues

sgkit-dev / sgkit

Scalable genetics toolkit

https://sgkit-dev.github.io/sgkit

Apache License 2.0

217 stars 32 forks source link

issues

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Numpy 2 testing

#1237 tomwhite opened 1 week ago
0
Release 0.9.0

#1235 tomwhite closed 4 days ago
4
Run tests against NumPy 2

#1234 tomwhite opened 1 week ago
2
Deprecate functions for reading VCF

#1233 tomwhite closed 1 week ago
0
Deprecate functions for reading VCF

#1232 tomwhite closed 1 week ago
1
Unblock upstream build which now requires Python>=3.10

#1231 tomwhite closed 1 week ago
0
Pin to Zarr < 3

#1230 tomwhite closed 1 week ago
0
Add 'matching' method option to identity_by_state

#1229 timothymillar closed 1 day ago
3
Minor fixes for Numpy 2

#1228 timothymillar closed 2 weeks ago
5
Option to calculate IBS probabilities via allele matching

#1227 timothymillar closed 1 day ago
0
Run tests against Zarr 3

#1226 tomwhite opened 2 weeks ago
2
Main build failing with 'RuntimeWarning: overflow encountered in scalar subtract'

#1225 tomwhite closed 2 weeks ago
0
Update docs to say "Scalable genetics toolkit"

#1223 jeromekelleher opened 4 weeks ago
0
simulate_genotype_call_dataset creates alleles as byte strings

#1222 hyanwong opened 4 weeks ago
1
simulate_genotype_call_dataset creates duplicate alleles

#1221 hyanwong opened 4 weeks ago
0
ImportError: dlopen[...]: symbol not found in flat namespace '_bcf_float_missing' - sgkit-vcf requirements are not installed

#1220 simonharnqvist closed 1 month ago
4
Genome accessibility/callability

#1219 mufernando opened 1 month ago
1
Python 3.11,3.12 conda install fails.

#1218 benjeffery opened 1 month ago
0
Fix wheel test on macOS

#1217 tomwhite closed 2 months ago
3
Release 0.8.0

#1216 tomwhite closed 1 month ago
2
MemoryError: Allocation failed (probably too large) with ped.compute()

#1213 fouerghi opened 2 months ago
7
Move docs to sgkit.dev

#1212 hammer opened 3 months ago
0
Update project email address

#1211 hammer closed 3 months ago
0
`vcf_to_zarr` raises error instead of truncating INFO fields of length `R`

#1210 timothymillar opened 4 months ago
3
read_plink returns bytes for variant_alleles not unicode

#1209 jeromekelleher opened 4 months ago
0
Partial changes for VCF Character S->U

#1208 jeromekelleher opened 4 months ago
0
Mixed-ploidy VanRaden GRM

#1207 timothymillar opened 4 months ago
0
Fix xarray repr in doctests

#1205 tomwhite closed 4 months ago
3
Change in Xarray repr is causing doctest failures

#1204 tomwhite closed 4 months ago
0
partition_into_regions: tabix index returns illegal region with multiple contigs

#1203 jeromekelleher opened 4 months ago
0
partition_into_regions: CSI indexed BCFs return empty regions

#1202 jeromekelleher opened 4 months ago
0
partition_into_regions: CSI indexed VCFs have incorrect sequence names

#1201 jeromekelleher opened 4 months ago
0
partition_into_regions returns empty region for all contigs in header

#1200 jeromekelleher closed 4 months ago
5
Avoid disabling jit on guvectorised functions

#1199 timothymillar closed 3 months ago
3
Cannot round-trip explicitly set missing INFO values in VCF

#1197 jeromekelleher closed 4 months ago
3
vcf_writer emitting incorrect missing values for INFO fields

#1196 jeromekelleher closed 4 months ago
0
read_scikit_allel_vcfzarr returns string pad values instead of missing for INFO fields

#1195 jeromekelleher opened 4 months ago
0
Numba cache masking compile warnings and deprecations

#1194 jeromekelleher closed 3 months ago
7
Irrelavant change for build

#1193 jeromekelleher closed 4 months ago
1
VCF parser returning FILL instead of MISSING values

#1192 jeromekelleher closed 4 months ago
0
Turn off numba cache by default

#1191 jeromekelleher closed 4 months ago
3
Errors in missing vs pad values in VCF

#1190 jeromekelleher closed 4 months ago
9
Genealogical relatedness greater than 1

#1188 fouerghi closed 4 months ago
3
Do chunk sizes have to be the same for all variables in a given dimension?

#1186 jeromekelleher opened 5 months ago
1
Two-pass non-Dask VCF conversion

#1185 jeromekelleher closed 4 months ago
3
Upgrade sphinx to fix build

#1184 tomwhite closed 5 months ago
2
Sequential VCF parsing

#1183 hammer opened 5 months ago
1
`sgkit.regenie` review. Work in progress

#1182 jdstamp opened 5 months ago
0
`sgkit.genee` improvements

#1181 jdstamp opened 5 months ago
0
genee review: sgkit implementation limitations

#1180 jdstamp opened 5 months ago
1