Program: 50230
Project: 50230
Buggy source:
public void buildTaxonomyTree(String name){
  IndexHits<Node> hits=nodeIndex.get("String_Node_Str",name);
  Node firstNode=hits.getSingle();
  hits.close();
  if (firstNode == null) {
    System.out.println("String_Node_Str");
    return;
  }
  TraversalDescription CHILDOF_TRAVERSAL=Traversal.description().relationships(RelTypes.CHILDOF,Direction.INCOMING);
  System.out.println(firstNode.getProperty("String_Node_Str"));
  JadeNode root=new JadeNode();
  root.setName(((String)firstNode.getProperty("String_Node_Str")).replace("String_Node_Str","String_Node_Str"));
  HashMap<Node,JadeNode> nodes=new HashMap<Node,JadeNode>();
  nodes.put(firstNode,root);
  int count=0;
  for (  Relationship friendrel : CHILDOF_TRAVERSAL.traverse(firstNode).relationships()) {
    count+=1;
    if (nodes.containsKey(friendrel.getStartNode()) == false) {
      JadeNode node=new JadeNode();
      node.setName(((String)friendrel.getStartNode().getProperty("String_Node_Str")).replace("String_Node_Str","String_Node_Str").replace("String_Node_Str","String_Node_Str").replace("String_Node_Str","String_Node_Str").replace("String_Node_Str","String_Node_Str").replace("String_Node_Str","String_Node_Str"));
      nodes.put(friendrel.getStartNode(),node);
    }
    if (nodes.containsKey(friendrel.getEndNode()) == false) {
      JadeNode node=new JadeNode();
      node.setName(((String)friendrel.getEndNode().getProperty("String_Node_Str")).replace("String_Node_Str","String_Node_Str").replace("String_Node_Str","String_Node_Str").replace("String_Node_Str","String_Node_Str").replace("String_Node_Str","String_Node_Str").replace("String_Node_Str","String_Node_Str"));
      nodes.put(friendrel.getEndNode(),node);
    }
    nodes.get(friendrel.getEndNode()).addChild(nodes.get(friendrel.getStartNode()));
    if (count % 100000 == 0)     System.out.println(count);
  }
  JadeTree tree=new JadeTree(root);
  PrintWriter outFile;
  try {
    outFile=new PrintWriter(new FileWriter("String_Node_Str"));
    outFile.write(tree.getRoot().getNewick(false));
    outFile.write("String_Node_Str");
    outFile.close();
  }
 catch (  IOException e) {
    e.printStackTrace();
  }
}

Fixed version (ground truth):
public void buildTaxonomyTree(String name){
  IndexHits<Node> hits=nodeIndex.get("String_Node_Str",name);
  Node firstNode=hits.getSingle();
  hits.close();
  if (firstNode == null) {
    System.out.println("String_Node_Str");
    return;
  }
  TraversalDescription CHILDOF_TRAVERSAL=Traversal.description().relationships(RelTypes.TAXCHILDOF,Direction.INCOMING);
  System.out.println(firstNode.getProperty("String_Node_Str"));
  JadeNode root=new JadeNode();
  root.setName(((String)firstNode.getProperty("String_Node_Str")).replace("String_Node_Str","String_Node_Str"));
  HashMap<Node,JadeNode> nodes=new HashMap<Node,JadeNode>();
  nodes.put(firstNode,root);
  int count=0;
  for (  Relationship friendrel : CHILDOF_TRAVERSAL.traverse(firstNode).relationships()) {
    count+=1;
    if (nodes.containsKey(friendrel.getStartNode()) == false) {
      JadeNode node=new JadeNode();
      node.setName(((String)friendrel.getStartNode().getProperty("String_Node_Str")).replace("String_Node_Str","String_Node_Str").replace("String_Node_Str","String_Node_Str").replace("String_Node_Str","String_Node_Str").replace("String_Node_Str","String_Node_Str").replace("String_Node_Str","String_Node_Str"));
      nodes.put(friendrel.getStartNode(),node);
    }
    if (nodes.containsKey(friendrel.getEndNode()) == false) {
      JadeNode node=new JadeNode();
      node.setName(((String)friendrel.getEndNode().getProperty("String_Node_Str")).replace("String_Node_Str","String_Node_Str").replace("String_Node_Str","String_Node_Str").replace("String_Node_Str","String_Node_Str").replace("String_Node_Str","String_Node_Str").replace("String_Node_Str","String_Node_Str"));
      nodes.put(friendrel.getEndNode(),node);
    }
    nodes.get(friendrel.getEndNode()).addChild(nodes.get(friendrel.getStartNode()));
    if (count % 100000 == 0)     System.out.println(count);
  }
  JadeTree tree=new JadeTree(root);
  PrintWriter outFile;
  try {
    outFile=new PrintWriter(new FileWriter("String_Node_Str"));
    outFile.write(tree.getRoot().getNewick(false));
    outFile.write("String_Node_Str");
    outFile.close();
  }
 catch (  IOException e) {
    e.printStackTrace();
  }
}