Refine docs and rename function

szhan · Jan 15, 2024 · c6015f4 · c6015f4
1 parent 172574b
commit c6015f4
Showing 1 changed file with 6 additions and 5 deletions.
diff --git 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?