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Check that the number of haplotypes meets a minimum #108

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Jun 18, 2024
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Check that the number of haplotypes meets a minimum #108

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3 changes: 3 additions & 0 deletions lshmm/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -409,6 +409,9 @@ def get_index_in_emission_matrix_diploid(ref_genotype, query_genotype):
# Miscellaneous functions.
def estimate_mutation_probability(num_haps):
"""Return the mutation probability as defined by A2 and A3 in Li & Stephens (2003)."""
if num_haps < 3:
err_msg = "Number of haplotypes must be at least 3."
raise ValueError(err_msg)
theta_tilde = 1 / np.sum([1 / k for k in range(1, num_haps - 1)])
prob_mutation = 0.5 * (theta_tilde / (num_haps + theta_tilde))
return prob_mutation
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