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astheeggeggs / lshmm

code to run Li and Stephens
MIT License
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Add tests when prob_mutation is not specified #106

Closed szhan closed 2 weeks ago

szhan commented 2 weeks ago

Fix #70

szhan commented 2 weeks ago

When using estimate_mutation_probability, a pathological case happened when the number of ref. haplotypes is 2 when running test_ts_simple_n6, because four haplotypes (which are then used as queries) are excluded from the simulated ref. panel. See #108

szhan commented 2 weeks ago

A temporary workaround is to not exclude the haplotypes chosen as queries from the ref. panel used downstream. The proper way is to rework get_examples* so that no haplotypes are excluded from the simulated ref. panel but the query haplotypes are randomly mutated copies of some of the haplotypes in the ref. panel. This will be addressed in a separate issue.