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szhan committed Jan 24, 2024
1 parent 744285e commit 6931412
Showing 1 changed file with 3 additions and 3 deletions.
6 changes: 3 additions & 3 deletions python/tests/beagle_numba.py
Original file line number Diff line number Diff line change
Expand Up @@ -131,15 +131,15 @@ def get_mutation_rates(pos, error_rate):
"""
Set mutation rates at genotyped positions.
Mutation rates should be dominated by the genotyping error rate.
Mutation rates should be dominated by the allele error rate.
In BEAGLE 4.1/5.4, the default value is set to 0.0001 and capped at 0.50.
In IMPUTE5, the default value is also set to 0.0001.
When using `_tskit.LsHmm`, this is `mu`.
:param numpy.ndarray pos: Physical positions (bp).
:param float error_rate: Genotyping error rate.
:param float error_rate: Allele error rate.
:return: Per-site mutation rates.
:rtype: numpy.ndarray
"""
Expand Down Expand Up @@ -415,7 +415,7 @@ def run_interpolation_beagle(
:param numpy.ndarray query_h: One query haplotype.
:param numpy.ndarray pos: Physical positions of all the markers (bp).
:param int ne: Effective population size.
:param float error_rate: Genotyping error rate.
:param float error_rate: Allele error rate.
:param GeneticMap genetic_map: Genetic map.
:return: Imputed alleles and their interpolated probabilities.
:rtype: tuple(numpy.ndarray, numpy.ndarray)
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