Minor edits in docs

szhan · Jan 13, 2024 · ff5cfa1 · ff5cfa1
1 parent 509a606
commit ff5cfa1
Showing 1 changed file with 8 additions and 8 deletions.
diff --git a/python/tests/beagle_numba.py b/python/tests/beagle_numba.py
@@ -22,7 +22,7 @@ def convert_to_genetic_map_position(pos, genetic_map_pos=None, genetic_map_cm=No
 
     If a genetic map is specified, then the genetic map positions are
     either taken straight from it or interpolated from it. The genetic map
-    needs to contain physical positions and corresponding genetic positions.
+    needs to contain physical positions and corresponding genetic map positions.
     See `PlinkGenMap.java` in the BEAGLE 4.1 source code for details.
 
     :param numpy.ndarray pos: Physical positions (bp).
@@ -63,8 +63,8 @@ def get_weights(genotyped_pos, ungenotyped_pos, genotyped_cm, ungenotyped_cm):
     lambda_m,x = [g(m + 1) - g(x)] / [g(m + 1) - g(m)],
     where g(i) = genetic map position of marker i.
 
-    :param numpy.ndarray genotyped_pos: Site positions of genotyped markers.
-    :param numpy.ndarray ungenotyped_pos: Site positions of ungenotyped markers.
+    :param numpy.ndarray genotyped_pos: Physical positions of genotyped markers.
+    :param numpy.ndarray ungenotyped_pos: Physical positions of ungenotyped markers.
     :param numpy.ndarray genotyped_cm: Genetic map positions of genotyped markers.
     :param numpy.ndarray ungenotyped_cm: Genetic map positions of ungenotyped markers.
     :return: Weights and marker interval start indices.
@@ -106,7 +106,7 @@ def get_mismatch_prob(pos, miscall_rate):
     In BEAGLE, the mismatch probability is dominated by the allelic miscall rate.
     By default, it is set to 0.0001 and capped at 0.50.
 
-    :param numpy.ndarray pos: Site positions.
+    :param numpy.ndarray pos: Physical positions.
     :param float miscall_rate: Allelic miscall rate.
     :return: Mismatch probabilities.
     :rtype: numpy.ndarray
@@ -289,8 +289,8 @@ def interpolate_allele_prob(
 
     :param numpy.ndarray sm: HMM state probability matrix at genotyped markers.
     :param numpy.ndarray ref_h: Reference haplotypes subsetted to imputed markers.
-    :param numpy.ndarray genotyped_pos: Site positions at genotyped markers.
-    :param numpy.ndarray ungenotyped_pos: Site positions at ungenotyped markers.
+    :param numpy.ndarray genotyped_pos: Physical positions at genotyped markers.
+    :param numpy.ndarray ungenotyped_pos: Physical positions at ungenotyped markers.
     :param numpy.ndarray genotyped_cm: Genetic map positions at genotyped markers.
     :param numpy.ndarray ungenotyped_cm: Genetic map positions at ungenotyped markers.
     :return: Interpolated allele probabilities.
@@ -355,7 +355,7 @@ def run_beagle(
 
     :param numpy.ndarray ref_h: Reference haplotypes.
     :param numpy.ndarray query_h: One query haplotype.
-    :param numpy.ndarray pos: Site positions of all the markers.
+    :param numpy.ndarray pos: Physical positions of all the markers.
     :param float miscall_rate: Allelic miscall rate.
     :param int ne: Effective population size.
     :param numpy.ndarray genetic_map_pos: Physical positions of genetic map.
@@ -425,7 +425,7 @@ def run_tsimpute(
 
     :param numpy.ndarray ref_ts: Tree sequence containing reference haplotypes.
     :param numpy.ndarray query_h: One query haplotype.
-    :param numpy.ndarray pos: Site positions of all the markers.
+    :param numpy.ndarray pos: Physical positions of all the markers.
     :param numpy.ndarray mu: Mutation rate.
     :param numpy.ndarray rho: Recombination rate.
     :param int precision: Precision when running LS HMM (default = 22).