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read_plink returns 'nan' strings for sample_ids

bugSomething isn't workingSomething isn't working

Status: Open.

#1314 In sgkit-dev/sgkit;

· jeromekelleher opened on May 20, 2025

Windowing fails for datasets where contigs lack variant sites

bugSomething isn't workingSomething isn't working

Status: Open.

#1268 In sgkit-dev/sgkit;

· percyfal opened on Oct 10, 2024

simulate_genotype_call_dataset creates alleles as byte strings

bugSomething isn't workingSomething isn't working

Status: Open.

#1222 In sgkit-dev/sgkit;

· hyanwong opened on Jun 7, 2024

simulate_genotype_call_dataset creates duplicate alleles

bugSomething isn't workingSomething isn't working

Status: Open.

#1221 In sgkit-dev/sgkit;

· hyanwong opened on Jun 7, 2024

read_plink returns bytes for variant_alleles not unicode

bugSomething isn't workingSomething isn't working

Status: Open.

#1209 In sgkit-dev/sgkit;

· jeromekelleher opened on Mar 6, 2024

read_scikit_allel_vcfzarr returns string pad values instead of missing for INFO fields

bugSomething isn't workingSomething isn't working

Status: Open.

#1195 In sgkit-dev/sgkit;

· jeromekelleher opened on Feb 15, 2024

 ·  

0.9.1

Set SGKIT_DISABLE_NUMBA_CACHE=1 by default

bugSomething isn't workingSomething isn't working

Status: Open.

#1156 In sgkit-dev/sgkit;

· jeromekelleher opened on Dec 14, 2023

 ·  

0.9.1

LD prune test is failing due to differences with scikit-allel

bugSomething isn't workingSomething isn't working

Status: Open.

#864 In sgkit-dev/sgkit;

· tomwhite opened on Jun 9, 2022

Xarray serialization warning when saving dataset

bugSomething isn't workingSomething isn't working

upstreamUsed when our build breaks due to upstream changesUsed when our build breaks due to upstream changes

Status: Open.

#853 In sgkit-dev/sgkit;

· tomwhite opened on May 6, 2022

♻️ cirun not shutting down GCE instances

bugSomething isn't workingSomething isn't working

process + tools

Status: Open.

#842 In sgkit-dev/sgkit;

· ravwojdyla opened on Apr 14, 2022

Regenie validation script is broken

bugSomething isn't workingSomething isn't working

Status: Open.

#624 In sgkit-dev/sgkit;

· eric-czech opened on Jul 7, 2021

Dask reshape bug for arrays with fully chunked leading axes

bugSomething isn't workingSomething isn't working

Status: Open.

#456 In sgkit-dev/sgkit;

· ravwojdyla opened on Feb 4, 2021