Fixes bug with phylotree levels

Makefile

@@ -27,7 +27,7 @@ ifeq  ($(strip $(OPTIMIZE)),yes)
     CXXFLAGS += -O3
 endif
 
-CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION} -O3
+CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
 
 ifeq  ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
 else

makefile-internal

@@ -1,7 +1,7 @@
 64BIT_VERSION ?= yes
-USEREADLINE ?= yes
-USEBOOST ?= yes
-RELEASE_DATE = "\"2/2/2017\""
+USEREADLINE ?= no
+USEBOOST ?= no
+RELEASE_DATE = "\"2/7/2017\""
 VERSION = "\"1.39.1\""
 
 # Optimize to level 3:
@@ -10,12 +10,12 @@ VERSION = "\"1.39.1\""
 
 ifeq  ($(strip $(64BIT_VERSION)),yes)
     #if you are a mac user use the following line
-    TARGET_ARCH += -arch x86_64
+    #TARGET_ARCH += -arch x86_64
 
     #if you using cygwin to build Windows the following line
-    #CXX = x86_64-w64-mingw32-g++
-    #CC = x86_64-w64-mingw32-g++
-    #TARGET_ARCH += -m64 -static
+    CXX = x86_64-w64-mingw32-g++
+    CC = x86_64-w64-mingw32-g++
+    TARGET_ARCH += -m64 -static
 
     #if you are a linux user use the following line - specific processor builds in future??
     #CXXFLAGS += -mtune=generic

source/classifier/phylotree.cpp

@@ -18,6 +18,7 @@ PhyloTree::PhyloTree(){
 		numSeqs = 0;
 		tree.push_back(TaxNode("Root"));
 		tree[0].heirarchyID = "0";
+        tree[0].level = 0;
 		maxLevel = 0;
 		calcTotals = true;
 		addSeqToTree("unknown", "unknown;");
@@ -78,6 +79,7 @@ PhyloTree::PhyloTree(string tfile){
 		numSeqs = 0;
 		tree.push_back(TaxNode("Root"));
 		tree[0].heirarchyID = "0";
+        tree[0].level = 0;
 		maxLevel = 0;
 		calcTotals = true;
 		string name, tax;
@@ -219,6 +221,7 @@ int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
 				tree.push_back(TaxNode(taxon));
 				numNodes++;
 				tree[currentNode].children[taxon] = numNodes-1;
+                tree[currentNode].level = level;
 				tree[numNodes-1].parent = currentNode;
 				
 				currentNode = tree[currentNode].children[taxon];
@@ -296,7 +299,7 @@ void PhyloTree::assignHeirarchyIDs(int index){
                 
 			tree[it->second].heirarchyID = tree[index].heirarchyID + '.' + toString(counter);
 			counter++;
-			tree[it->second].level = tree[index].level + 1;
+			//tree[it->second].level = tree[index].level + 1;
 						
 			//save maxLevel for binning the unclassified seqs
 			if (tree[it->second].level > maxLevel) { maxLevel = tree[it->second].level; }