fix: return all matching donors instead of excluding one, and report the actual mismatch number

Author: Regev32

grma/__init__.py

@@ -1,2 +1,2 @@
 from grma.donorsgraph.build_donors_graph import BuildMatchingGraph
-from grma.match import matching, find_matches
+from grma.match.match import matching, find_matches

grma/match/donors_matching.py

@@ -627,7 +627,13 @@ def __append_matching_donor(
         add_donors["Match_Between_Most_Commons_DRB"].append(compare_commons[4])
 
         add_donors["Matching_Probability"].append(match_prob)
-        add_donors["Number_Of_Mismatches"].append(mm_number)
+        
+        actual_mismatches = 0
+        for match_score in compare_commons:
+            if match_score != 2:
+                actual_mismatches += (2 - match_score)
+
+        add_donors["Number_Of_Mismatches"].append(actual_mismatches)
 
         # compute GvH / HvG counts
         pat = self.patients[patient]

grma/match/graph_wrapper.py

@@ -112,7 +112,7 @@ def neighbors(
     def neighbors_2nd(self, node):
         node_num = self._map_node_to_number[node]
         r0, r1 = self._graph.neighbors_2nd(node_num)
-        return r0[:-1], r1
+        return r0, r1
 
     def node_value_from_id(self, node_id: int) -> NODES_TYPES:
         """convert lol ID to node value"""

grma/match/lol_graph.pyx

@@ -177,8 +177,8 @@ cdef class LolGraph:
                 neighbors_id[pointer] = self._neighbors_list[j]
                 pointer += 1
 
-        neighbors_value = np.zeros((num_of_neighbors_2nd - 1, 10), dtype=np.uint16)
-        for i in range(len(neighbors_id) - 1):
+        neighbors_value = np.zeros((num_of_neighbors_2nd, 10), dtype=np.uint16)
+        for i in range(len(neighbors_id)):
             neighbor_id = neighbors_id[i]
             arr = self.arr_node_value_from_id(neighbor_id)
             for j in range(10):