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Sample alleles without replacement in simulate_genotype_call_dataset - #1353
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jeromekelleher merged 1 commit intoOct 12, 2026
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rs.choice drew alleles independently, so a variant could repeat the same allele (e.g. two "T" alleles with seed=1, sgkit-dev#1221). Draw without replacement when n_allele fits the base alphabet; sampling stays unchanged above it.
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LGTM, thanks @barlowa124 !
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Closes #1221.
Per-variant alleles in
simulate_genotype_call_datasetare drawnindependently, allowing the same base twice in one allele list. With
seed=1two sites came out as[T, T], producing malformed variantsfor downstream tooling.
When
n_allelefits the base alphabet the draw now happens withoutreplacement. Larger requests keep the previous behavior. The new test
checks allele uniqueness per variant on the reporter's parameters and
test_testing.pypasses.