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Add tests when prob_mutation is not specified #106

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Jun 18, 2024
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Add tests when prob_mutation is not specified #106

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10 changes: 7 additions & 3 deletions tests/lsbase.py
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Original file line number Diff line number Diff line change
Expand Up @@ -105,7 +105,7 @@ def get_examples_diploid(self, ts, include_ancestors):
query_miss_most[:, 1:] = core.MISSING
queries = [query_1, query_2, query_miss_last, query_miss_mid, query_miss_most]
# Exclude the arbitrarily chosen queries from the reference panel.
ref_panel = ref_panel[:, 4:]
# ref_panel = ref_panel[:, 4:]
return ref_panel, queries

def get_examples_pars(
Expand Down Expand Up @@ -148,6 +148,7 @@ def get_examples_pars(
np.zeros(m) + 0.01, # Equal recombination and mutation
np.random.rand(m) * 0.2, # Random
1e-5 * (np.random.rand(m) + 0.5) / 2,
None,
]

if include_extreme_rates:
Expand All @@ -162,17 +163,20 @@ def get_examples_pars(
# result in the number of alleles being higher
# than the number of alleles in the reference panel.
num_alleles = core.get_num_alleles(H, query)
prob_mutation = mu
if prob_mutation is None:
prob_mutation = np.zeros(m) + core.estimate_mutation_probability(n)
if ploidy == 1:
e = core.get_emission_matrix_haploid(
mu=mu,
mu=prob_mutation,
num_sites=m,
num_alleles=num_alleles,
scale_mutation_rate=scale_mutation_rate,
)
yield n, m, H, query, e, r, mu
else:
e = core.get_emission_matrix_diploid(
mu=mu,
mu=prob_mutation,
num_sites=m,
num_alleles=num_alleles,
scale_mutation_rate=scale_mutation_rate,
Expand Down
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