Merge branch 'Sam_main' into main_clone

Author: trongnhanuit

.gitignore

@@ -415,10 +415,11 @@ void cmaple::merge_identicalRACGT_TwoLowers(
     }
 
     if (seq1_region.type == TYPE_R) {
+      auto prev_log_lh = log_lh;
       log_lh += (total_blength_1 + total_blength_2) *
                 (cumulative_rate[end_pos + 1] - cumulative_rate[pos]);
     } else {
-      log_lh += model->diagonal_mut_mat[seq1_region.type] *
+      log_lh += model->getDiagonalMutationMatrixEntry(seq1_region.type, end_pos) *
                 (total_blength_1 + total_blength_2);
     }
   }
@@ -464,11 +465,11 @@ void cmaple::calSiteLhs_identicalRACGT(std::vector<RealNumType>&site_lh_contribu
         * (cumulative_rate[i + 1] - cumulative_rate[i]);
     }
   } else {
-    log_lh += model->diagonal_mut_mat[seq1_region.type] * total_blength;
+    log_lh += model->getDiagonalMutationMatrixEntry(seq1_region.type, pos) * total_blength;
 
     // compute site lh contributions
     site_lh_contributions[static_cast<std::vector<RealNumType>::size_type>(pos)] +=
-        model->diagonal_mut_mat[seq1_region.type] * total_blength;
+        model->getDiagonalMutationMatrixEntry(seq1_region.type, pos) * total_blength;
   }
 }