Merge pull request #22 from thomaskf/bugfix

Fixed the issue regarding the GHOST model with an option -nt AUTO

Author: bqminh

CMakeLists.txt

@@ -116,7 +116,7 @@ find_package(Backtrace)
 # The version number.
 set (iqtree_VERSION_MAJOR 3)
 set (iqtree_VERSION_MINOR 0)
-set (iqtree_VERSION_PATCH ".0")
+set (iqtree_VERSION_PATCH ".1")
 
 option(BUILD_SHARED_LIBS "Build Shared Libraries" OFF)
 

tree/iqtree.cpp

@@ -4686,6 +4686,11 @@ int PhyloTree::testNumThreads() {
 
     cout << "BEST NUMBER OF THREADS: " << bestProc+1 << endl << endl;
     setNumThreads(bestProc+1);
+    
+    // clear the relative treelength arrays if it is GHOST model
+    if (isMixlen()) {
+        ((PhyloTreeMixlen*)this)->clear_relative_treelen();
+    }
 
     return bestProc+1;
 #endif

tree/phylotreemixlen.cpp

@@ -724,6 +724,13 @@ void PhyloTreeMixlen::hessian(const TVector &x, THessian &hessian) {
 }
 #endif
 
+/**
+ * clear the array "relative_treelen"
+ */
+void PhyloTreeMixlen::clear_relative_treelen() {
+    relative_treelen.clear();
+}
+
 // defining log-likelihood derivative function for EM algorithm
 void PhyloTreeMixlen::computeFuncDerv(double value, double &df, double &ddf) {
 

tree/phylotreemixlen.h

@@ -264,6 +264,11 @@ class PhyloTreeMixlen : public IQTree
 
 #endif
 
+    /**
+     * clear the array "relative_treelen"
+     */
+    void clear_relative_treelen();
+
 protected:
 
     /** relative rate, used to initialize branch lengths */