[qob] Fix IBD and enable tests #14062
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patrick-schultz
previously requested changes
Jan 4, 2024
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Thanks for fixing this!
Do we need to set the seed in the tests here?
No need. This ensures all tests using hail's randomness are deterministic.
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| def random_dataset(): | |||
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I'd suggest making this a fixture:
@pytest.fixture(scope=module)
def ds():
...Then each test that wants to use it adds an argument of the same name:
def test_ibd_default_arguments(ds):
plink_results = plinkify(ds)
...The scope=module caches the result of the function to avoid recomputing it over the duration of the test module. In this case it doesn't save that much, because it's only caching the construction of the IR, but that's probably slightly better than recomputing it each time.
patrick-schultz
approved these changes
Jan 5, 2024
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CHANGELOG: Fixed bugs in the identity by descent implementation for Query on Batch
This PR fixes #14052. There were two bugs in how we compute IBD. In addition, the tests weren't running in QoB and the test dataset we were using doesn't have enough variability to catch errors. I used Balding Nichols generated data instead. Do we need to set the seed in the tests here?