Error if sgkit sample data is unphased #784
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benjeffery
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Codecov Report
@@ Coverage Diff @@
## main #784 +/- ##
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Coverage 93.32% 93.32%
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Files 17 17
Lines 5571 5571
Branches 990 990
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Hits 5199 5199
Misses 246 246
Partials 126 126
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jeromekelleher
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Dec 7, 2022
tests/test_sgkit.py
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| @@ -48,3 +50,42 @@ def test_sgkit_dataset(tmp_path): | |||
| samples = tsinfer.SgkitSampleData(tmp_path / "data.zarr") | |||
| inf_ts = tsinfer.infer(samples) | |||
| assert np.array_equal(ts.genotype_matrix(), inf_ts.genotype_matrix()) | |||
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| def test_sgkit_unphased(tmp_path): | |||
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This looks like four tests. Also you wouldnt' need to rmtree by doing this.
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@jeromekelleher Review changes made - should be good to go. |
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@Mergifyio rebase |
✅ Branch has been successfully rebased |
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Fixes #772
This is doing unnecessary checks as not all sites may be used - but this is the simplest approach. If we think there are common use cases where used are only using a subset of sites and the rest are unphased, then could consider only checking used sites.