major change to the tree class to use the count table class instead of tree map....

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index fe0685bea19678213fa0ddb8ccfade9ad08c4b12..19ffc899d60ac778ac4eedbeb2034a62b5e04bd7 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -1931,7 +1931,7 @@ void ShhherCommand::writeClusters(vector<int> otuCounts){
 
 int ShhherCommand::execute(){
        try {
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                getSingleLookUp();      if (m->control_pressed) { return 0; }
                getJointLookUp();       if (m->control_pressed) { return 0; }