sgkit-dev sgkit issues - Githubissues

sgkit-dev / sgkit

Scalable genetics toolkit

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

Apache License 2.0

235 stars 32 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Run tests using Zarr Python v3

#1277 tomwhite closed 2 weeks ago
1
Drop Python 3.9

#1276 tomwhite closed 2 weeks ago
0
Don't use local functions to wrap numba functions

#1275 tomwhite closed 2 weeks ago
0
Use sgkit.distarray for PCA

#1274 tomwhite opened 3 weeks ago
1
Remove use of `dask.array.ma` in PCA in favour of array API compliant functions

#1272 tomwhite closed 1 month ago
0
Disable failing GPU build

#1271 tomwhite closed 1 month ago
0
GPU build is failing

#1270 tomwhite closed 1 month ago
0
Fix windows wheels test

#1269 tomwhite closed 1 month ago
0
Windowing fails for datasets where contigs lack variant sites

#1268 percyfal opened 1 month ago
1
Dask 2024.8.1 and later is very slow

#1267 tomwhite opened 1 month ago
7
Benchmarking Numba vs JAX

#1266 tomwhite opened 1 month ago
4
Remove VCF support

#1264 tomwhite closed 1 month ago
1
Test on Python 3.12

#1263 tomwhite closed 1 month ago
5
Use sgkit.distarray for gwas_linear_regression

#1262 tomwhite closed 1 month ago
0
Install dask[dataframe] explicitly to fix upstream error

#1261 tomwhite opened 2 months ago
2
Use sgkit.distarray for sample_stats and hardy_weinberg_test

#1259 tomwhite closed 2 months ago
0
Use vcf2zarr in GWAS tutorial notebook

#1258 tomwhite closed 2 months ago
3
Update GWAS tutorial to use vcf2zarr

#1257 tomwhite closed 2 months ago
0
Update actions/upload-artifact to v4 in .github/workflows

#1256 tomwhite closed 2 months ago
0
Use sgkit.distarray for count_variant_alleles and variant_stats

#1255 tomwhite closed 2 months ago
0
Run test_count_call_alleles on Cubed (alternative approach)

#1254 tomwhite closed 2 months ago
5
Bump actions/download-artifact from 2 to 4.1.7 in /.github/workflows

#1253 dependabot[bot] closed 2 months ago
0
Disable validation workflow

#1252 jeromekelleher closed 2 months ago
1
Disable validation workflow

#1251 jeromekelleher closed 2 months ago
1
Run `test_count_call_alleles` on Cubed

#1249 tomwhite closed 2 months ago
4
Pin Dask to fix slow main build

#1248 tomwhite closed 2 months ago
1
Main build is very slow and times out

#1247 tomwhite closed 2 months ago
0
Deprecate VCF write functions

#1245 tomwhite closed 1 month ago
2
Unclear how to overwrite a dataset

#1243 hyanwong opened 4 months ago
2
No page at https://sgkit-dev.github.io

#1242 hyanwong opened 4 months ago
0
Displaying alleles when using `sgkit.display_genotypes(ds)`

#1240 hyanwong opened 4 months ago
0
Numpy 2 testing

#1237 tomwhite closed 2 months ago
1
Release 0.9.0

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

#1234 tomwhite closed 2 months ago
3
Deprecate functions for reading VCF

#1233 tomwhite closed 4 months ago
0
Deprecate functions for reading VCF

#1232 tomwhite closed 4 months ago
1
Unblock upstream build which now requires Python>=3.10

#1231 tomwhite closed 5 months ago
0
Pin to Zarr < 3

#1230 tomwhite closed 5 months ago
0
Add 'matching' method option to identity_by_state

#1229 timothymillar closed 4 months ago
3
Minor fixes for Numpy 2

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

#1227 timothymillar closed 4 months ago
0
Run tests against Zarr 3

#1226 tomwhite closed 2 weeks ago
4
Main build failing with 'RuntimeWarning: overflow encountered in scalar subtract'

#1225 tomwhite closed 5 months ago
0
Update docs to say "Scalable genetics toolkit"

#1223 jeromekelleher opened 5 months ago
0
simulate_genotype_call_dataset creates alleles as byte strings

#1222 hyanwong opened 5 months ago
1
simulate_genotype_call_dataset creates duplicate alleles

#1221 hyanwong opened 5 months ago
0
ImportError: dlopen[...]: symbol not found in flat namespace '_bcf_float_missing' - sgkit-vcf requirements are not installed

#1220 simonharnqvist closed 6 months ago
4
Genome accessibility/callability

#1219 mufernando opened 6 months ago
4
Python 3.11,3.12 conda install fails.

#1218 benjeffery opened 6 months ago
0
Fix wheel test on macOS

#1217 tomwhite closed 6 months ago
3