Take contigs into account for fixed-size windowing #372
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jeromekelleher
approved these changes
Nov 4, 2020
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LGTM @tomwhite , altough it'd be nice to see some more testing of the edge-cases
sgkit/tests/test_window.py
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| np.testing.assert_equal(ds[window_start].values, [0, 2, 4, 6, 8]) | ||
| np.testing.assert_equal(ds[window_stop].values, [2, 4, 6, 8, 10]) | ||
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| with pytest.raises(MergeWarning): | ||
| window(ds, 2, 2) | ||
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| def test_window__multiple_contigs(): | ||
| ds = simulate_genotype_call_dataset(n_variant=15, n_sample=1, n_contig=3) |
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It'd be nice to test this with n_contig=n_variant, so we test the degenerate case.
Also be nice to see what happens when n_variant=1.
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Added in pystatgen/sgkit@399bd04
Merged
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Fixes #335