diff --git a/python/tests/beagle_numba.py b/python/tests/beagle_numba.py index b85c448beb..65ebb55a7e 100644 --- a/python/tests/beagle_numba.py +++ b/python/tests/beagle_numba.py @@ -362,7 +362,7 @@ def get_map_alleles(allele_prob): return (imputed_alleles, max_allele_prob) -def run_beagle( +def run_interpolation_beagle( ref_h, query_h, pos, @@ -371,7 +371,8 @@ def run_beagle( genetic_map=None, ): """ - Run a simplified version of the BEAGLE algorithm based on Equation 1 of BB2016. + Perform a simplified procedure of interpolation-style imputation + based on Equation 1 of BB2016. Reference haplotypes and query haplotype are of size (m + x, h) and (m + x). @@ -380,7 +381,7 @@ def run_beagle( This produces imputed alleles and their interpolated probabilities at the ungenotyped markers of the query haplotype. - The default values of `error_rate` and `ne` are taken from BEAGLE 4.1, not 5.4. + The default values of `ne` and `error_rate` are taken from BEAGLE 4.1, not 5.4. In BEAGLE 5.4, the default value of `ne` is 1e5 and `error_rate` is data-dependent. :param numpy.ndarray ref_h: Reference haplotypes. @@ -437,8 +438,8 @@ def run_tsimpute( genetic_map=None, ): """ - Run the BEAGLE 4.1 algorithm except that the forward and backward probability - matrices are computed from a tree sequence. + Perform interpolation-style imputation, except that the forward and backward + probability matrices are computed from a tree sequence. TODO: Put this function elsewhere. TODO: Set default precision. What should it be?