added comment about negative index

theano/scan_module/scan.py

@@ -857,6 +857,10 @@ def scan(fn,
                             tensor.shape_padleft(input.variable), 0),
                         actual_n_steps))
                 sit_sot_inner_outputs.append(input.update)
+                # Not that pos is not a negative index. The sign of pos is used
+                # as a flag to indicate if this output should be part of the
+                # update rules or part of the standard outputs of scan. Its
+                # absolute value (-1 in case is negative) represents an index
                 sit_sot_rightOrder.append(-1 - len(sit_sot_shared))
                 sit_sot_shared.append(input.variable)
                 givens[input.variable] = new_var
@@ -1058,7 +1062,11 @@ def scan(fn,
         if pos >= 0:
             scan_out_list[pos] = _scan_out_list[idx]
         else:
-            update_map[sit_sot_shared[abs(pos)-1]] = _scan_out_list[idx][-1]
+            # Not that pos is not a negative index. The sign of pos is used
+            # as a flag to indicate if this output should be part of the
+            # update rules or part of the standard outputs of scan. Its
+            # absolute value (-1 in case is negative) represents an index
+            update_map[sit_sot_shared[abs(pos) - 1]] = _scan_out_list[idx][-1]
     scan_out_list = [x for x in scan_out_list if x is not None]
     if len(scan_out_list) == 1:
         scan_out_list = scan_out_list[0]