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Add option to specify num_alleles when using solve_num_mismatches #386

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merged 1 commit into from
Nov 6, 2024

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szhan
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@szhan szhan commented Nov 6, 2024

Fix #385

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szhan commented Nov 6, 2024

I didn't update match_recombinant because it is marked for removal.

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szhan commented Nov 6, 2024

Also, in the tests, num_alleles is hard-coded to 5, because the functions are calling match_tsinfer with default option of deletions_as_missing, which is False.

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let's default to n=5 in the signature to minimise breakage. It's really not going to matter much, as it's just very slightly altering the proba of choosing a recomb vs not.

sc2ts/inference.py Outdated Show resolved Hide resolved
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I'm going to move the solving for mu/rho given num mismatches into match_tsfiner, so don't worry too much about details here.

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szhan commented Nov 6, 2024

I'm passing a specific value for num_alleles in match_samples because deletions_as_missing is specified.

@jeromekelleher jeromekelleher merged commit ddafdc4 into jeromekelleher:main Nov 6, 2024
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Scaling mutation rate in solve_num_mismatches
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