Investigate `get_ancestral_haplotypes` in `lsbase.py`

astheeggeggs / lshmm

code to run Li and Stephens

MIT License

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Closed szhan closed 2 weeks ago

szhan commented 3 weeks ago

The function isn't generating the expected number of ancestral haplotypes, so it should be examined.

szhan commented 2 weeks ago

We should remove ancestral haplotypes containing only NONCOPY values before returning the genotype matrix. See #86.

szhan commented 2 weeks ago

It seems fine now. At least in the haplotypes simulated during testing, the number of copiable entries per site is not exceeding the maximum.