Merge pull request #17 from thomaskf/bugfix

Urgent bug fix for the issues #15 and #16

Author: bqminh

main/phyloanalysis.cpp

@@ -904,7 +904,7 @@ void reportTree(ofstream &out, Params &params, PhyloTree &tree, double tree_lh,
     out << "Bayesian information criterion (BIC) score: " << BIC_score << endl;
 
     // mAIC report
-    if (tree.isSuperTree() && params.partition_type != TOPO_UNLINKED) {
+    if (tree.isSuperTree() && params.partition_type != TOPO_UNLINKED && !params.contain_nonrev) {
         // compute mAIC/mBIC/mAICc if it is a partition model
         int ntrees; //mix_df;
         double mix_lh;

main/phylotesting.cpp

@@ -3295,13 +3295,13 @@ int64_t CandidateModelSet::getNextModel() {
             }
         }
     }
-    }
     if (next_model != current_model) {
         current_model = next_model;
         at(next_model).setFlag(MF_RUNNING);
-        return next_model;
     } else
-        return -1;
+        next_model = -1;
+    }
+    return next_model;
 }
 
 CandidateModel CandidateModelSet::evaluateAll(Params &params, PhyloTree* in_tree, ModelCheckpoint &model_info,

tree/phylokernelnew.h

@@ -2272,6 +2272,10 @@ void PhyloTree::computeLikelihoodDervGenericSIMD(PhyloNeighbor *dad_branch, Phyl
     size_t orig_nptn = aln->size();
     size_t max_orig_nptn = roundUpToMultiple(orig_nptn, VectorClass::size());
     size_t nptn = max_orig_nptn + model_factory->unobserved_ptns.size();
+
+    size_t g_matrix_nptn = max_orig_nptn + max(get_safe_upper_limit(model->num_states),
+                                                                          get_safe_upper_limit(
+                                                                                  model_factory->unobserved_ptns.size()));
     ASCType ASC_type = model_factory->getASC();
     bool ASC_Holder = (ASC_type == ASC_VARIANT_MISSING || ASC_type == ASC_INFORMATIVE_MISSING);
     bool ASC_Lewis = (ASC_type == ASC_VARIANT || ASC_type == ASC_INFORMATIVE);
@@ -2464,7 +2468,7 @@ void PhyloTree::computeLikelihoodDervGenericSIMD(PhyloNeighbor *dad_branch, Phyl
             }
         } else {
             // to access g-matrix elements to store derivatives
-            size_t g_index = branch_id * nptn;
+            size_t g_index = branch_id * g_matrix_nptn;
             // normal joint branch length model
             for (size_t ptn = ptn_lower; ptn < ptn_upper; ptn+=VectorClass::size()) {
                 VectorClass lh_ptn;

utils/tools.cpp

@@ -5912,9 +5912,9 @@ void parseArg(int argc, char *argv[], Params &params) {
                 err += "\" option.";
                 throw err;
             } else {
-//                if (params.user_file == NULL)
-//                    params.user_file = argv[cnt];
-//                else
+                if (params.user_file == NULL)
+                    params.user_file = argv[cnt];
+                else
                     params.out_file = argv[cnt];
             }
         }