Minor touchups

Author: szhan

python/tests/test_beagle.py

@@ -46,7 +46,7 @@ def convert_to_genetic_map_position(pos):
     """
     Convert genomic site positions (bp) to genetic map positions (cM).
 
-    When a genetic map is not specified, it is assumed that 1 Mbp = 1cM.
+    In BEAGLE 4.1, when a genetic map is not specified, it is assumed that 1 Mbp = 1cM.
 
     This trivial function is meant for documentation.
 
@@ -144,7 +144,7 @@ def get_switch_prob(pos, h, ne=1e6):
 
 def compute_forward_probability_matrix(ref_h, query_h, rho, mu):
     """
-    Implement the forwards algorithm.
+    Implement the forward algorithm.
 
     The forward probablity matrix is of size (m, h),
     where m is the number of genotyped markers
@@ -176,8 +176,10 @@ def compute_forward_probability_matrix(ref_h, query_h, rho, mu):
         # Get site-specific parameters
         shift = rho[i] / h
         scale = (1 - rho[i]) / last_sum
+        # Get allele at genotyped marker i on query haplotype j
         query_a = query_h[i]
         for j in np.arange(h):
+            # Get allele at genotyped marker i on reference haplotype j
             ref_a = ref_h[i, j]
             # Get emission probability
             em_prob = mu[i] if query_a != ref_a else 1.0 - mu[i]
@@ -192,7 +194,7 @@ def compute_forward_probability_matrix(ref_h, query_h, rho, mu):
 
 def compute_backward_probability_matrix(ref_h, query_h, rho, mu):
     """
-    Implement the backwards algorithm.
+    Implement the backward algorithm.
 
     The backward probablity matrix is of size (m, h),
     where m is the number of genotyped markers
@@ -203,7 +205,7 @@ def compute_backward_probability_matrix(ref_h, query_h, rho, mu):
 
     `query_h` is also subsetted to genotyped markers (length m).
 
-    In BEAGLE, the values are kept one site at a time.
+    In BEAGLE 4.1, the values are kept one site at a time.
     Here, we keep the values at all the sites.
 
     :param numpy.ndarray ref_h: Reference haplotypes.