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astheeggeggs / lshmm

code to run Li and Stephens
MIT License
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Refactor functions to simulate test data #126

Closed szhan closed 1 week ago

szhan commented 1 week ago

The functions get_ts_simple_n* should be refactored so that the number of samples simulated is parametrized. Instead of using msprime.simulate, the functions msprime.sim_ancestry and msprime.sim_mutations should be used throughout.

szhan commented 1 week ago

Also, some minor refactoring.

szhan commented 1 week ago

Also, reduce the size of the ref. panels to at most 30 to keep CI tests somewhat tolerably low.