fixed unifrac bug with multiple processors if numComps was less than processors....

[mothur.git] / unifracweightedcommand.cpp

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index bee10cb4e9954f56960c96e7efe8904958d67c97..1fa1a2833c1fa7604a9e2cbb07bf255ace9dcd94 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -24,8 +24,7 @@ vector<string> UnifracWeightedCommand::getValidParameters(){
 //**********************************************************************************************************************
 UnifracWeightedCommand::UnifracWeightedCommand(){      
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["weighted"] = tempOutNames;
                outputTypes["wsummary"] = tempOutNames;
@@ -65,11 +64,11 @@ vector<string> UnifracWeightedCommand::getRequiredFiles(){
 UnifracWeightedCommand::UnifracWeightedCommand(string option) {
        try {
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                Groups.clear();
                        
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -181,13 +180,15 @@ void UnifracWeightedCommand::help(){
 int UnifracWeightedCommand::execute() {
        try {
        
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                int start = time(NULL);
                
                //get weighted for users tree
                userData.resize(numComp,0);  //data[0] = weightedscore AB, data[1] = weightedscore AC...
                randomData.resize(numComp,0); //data[0] = weightedscore AB, data[1] = weightedscore AC...
+               
+               if (numComp < processors) { processors = numComp; }
                                
                //get weighted scores for users trees
                for (int i = 0; i < T.size(); i++) {
@@ -262,7 +263,7 @@ int UnifracWeightedCommand::execute() {
                                        if (m->control_pressed) { delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str());  } return 0; }
                                        
                                        //report progress
-                                       m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();          
+//                                     m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();          
                                }
                                lines.clear();