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astheeggeggs / lshmm

code to run Li and Stephens
MIT License
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Add tests for `set_emission_probabilities` when `prob_mutation` is not specified #70

Closed szhan closed 3 months ago

szhan commented 4 months ago

By default, prob_mutation is set to None when calling set_emission_probabilities. When this happens (e.g. when no estimate is available), prob_mutation is defined as proposed in Li & Stephens (2003) (probably Watterson's estimator). Using this estimator is not covered in the tests.

szhan commented 3 months ago

This #103 needs to be done first.