Fix copyTree for a taxa_set to work with rooted tree properly (reported by Suha Naser)

Author: bqminh

tree/constrainttree.cpp

@@ -103,6 +103,12 @@ void ConstraintTree::initFromTree() {
 
 void ConstraintTree::readConstraint(MTree &src_tree) {
     copyTree(&src_tree);
+    // convert all rooted constraint tree to unrooted
+    if (rooted) {
+        if (verbose_mode >= VB_MED)
+            cout << "Converting rooted constraint tree to unrooted" << endl;
+        convertToUnrooted();
+    }
     initFromTree();
 }
 

tree/mtree.cpp

@@ -142,6 +142,7 @@ void MTree::copyTree(MTree *tree) {
 }
 
 void MTree::copyTree(MTree *tree, string &taxa_set) {
+    rooted = tree->rooted;
     if (rooted) {
         ASSERT(tree->rooted);
         taxa_set.push_back(1);