Reformat

szhan · Jun 24, 2024 · 1009d83 · 1009d83
1 parent 54556c5
commit 1009d83
Showing 1 changed file with 15 additions and 5 deletions.
diff --git a/python/tests/test_haplotype_matching.py b/python/tests/test_haplotype_matching.py
@@ -336,7 +336,9 @@ def update_probabilities(self, site, haplotype_state):
                 match = haplotype_state == allelic_state[v]
                 is_query_missing = haplotype_state == MISSING
                 # Note that the node u is used only by Viterbi
-                st.value = self.compute_next_probability(site.id, st.value, match, is_query_missing, u)
+                st.value = self.compute_next_probability(
+                    site.id, st.value, match, is_query_missing, u
+                )
 
         # Unset the states
         allelic_state[tree.root] = -1
@@ -403,7 +405,9 @@ def run(self, h):
     def compute_normalisation_factor(self):
         raise NotImplementedError()
 
-    def compute_next_probability(self, site_id, p_last, is_match, is_query_missing, node):
+    def compute_next_probability(
+        self, site_id, p_last, is_match, is_query_missing, node
+    ):
         raise NotImplementedError()
 
 
@@ -434,7 +438,9 @@ def compute_normalisation_factor(self):
             s += self.N[j] * st.value
         return s
 
-    def compute_next_probability(self, site_id, p_last, is_match, is_query_missing, node):
+    def compute_next_probability(
+        self, site_id, p_last, is_match, is_query_missing, node
+    ):
         rho = self.rho[site_id]
         n = self.ts.num_samples
         if is_query_missing:
@@ -450,7 +456,9 @@ class BackwardAlgorithm(ForwardAlgorithm):
     The Li and Stephens backward algorithm.
     """
 
-    def compute_next_probability(self, site_id, p_next, is_match, is_query_missing, node):
+    def compute_next_probability(
+        self, site_id, p_next, is_match, is_query_missing, node
+    ):
         if is_query_missing:
             p_e = 1.0
         else:
@@ -520,7 +528,9 @@ def compute_normalisation_factor(self):
             )
         return max_st.value
 
-    def compute_next_probability(self, site_id, p_last, is_match, is_query_missing, node):
+    def compute_next_probability(
+        self, site_id, p_last, is_match, is_query_missing, node
+    ):
         rho = self.rho[site_id]
         n = self.ts.num_samples