Fix crash with edge-unlinked (-sp) and -bnni option (reported by Mark…

… Miller)
Cibiv · Feb 6, 2019 · 64d47b5 · 64d47b5
1 parent 692edfd
commit 64d47b5
Show file tree

Hide file tree

Showing 2 changed files with 13 additions and 3 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -513,8 +513,10 @@ if (IQTREE_FLAGS MATCHES "mpi")
 	add_library(mympi utils/TreeCollection.cpp utils/ObjectStream.cpp)
 endif()
 
-if (NOT IQTREE_FLAGS MATCHES "single")
-    if (BINARY32)
+if (NOT IQTREE_FLAGS MATCHES "single")
+    if (APPLE)
+        link_directories(${PROJECT_SOURCE_DIR}/libmac)
+    elseif (BINARY32)
         link_directories(${PROJECT_SOURCE_DIR}/lib32)
     else()
         link_directories(${PROJECT_SOURCE_DIR}/lib)

diff --git a/tree/iqtree.cpp b/tree/iqtree.cpp
@@ -2824,7 +2824,15 @@ void IQTree::refineBootTrees() {
         boot_tree->setNumThreads(num_threads);
 
         // load the current ufboot tree
-        boot_tree->readTreeString(boot_trees[sample]);
+        // 2019-02-06: fix crash with -sp and -bnni
+        boot_tree->PhyloTree::readTreeString(boot_trees[sample]);
+
+        if (boot_tree->isSuperTree() && params->partition_type == BRLEN_OPTIMIZE) {
+            if (((PhyloSuperTree*)boot_tree)->size() > 1) {
+                // re-initialize branch lengths for unlinked model
+                boot_tree->wrapperFixNegativeBranch(true);
+            }
+        }
 
         // TODO: check if this resolves the crash in reorientPartialLh()
         boot_tree->initializeAllPartialLh();