fixed trim.seqs group counts by adding back in the primer group

[mothur.git] / mergegroupscommand.cpp

diff --git a/mergegroupscommand.cpp b/mergegroupscommand.cpp
index 4738389010cda4ecc598da27e4bd52b1205a8218..60b9c85481a2d455d53ab4b13a3bd46cfaf5a389 100644 (file)
--- a/mergegroupscommand.cpp
+++ b/mergegroupscommand.cpp
@@ -25,8 +25,7 @@ vector<string> MergeGroupsCommand::getValidParameters(){
 //**********************************************************************************************************************
 MergeGroupsCommand::MergeGroupsCommand(){      
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["shared"] = tempOutNames;
        }
@@ -64,12 +63,12 @@ vector<string> MergeGroupsCommand::getRequiredFiles(){
 MergeGroupsCommand::MergeGroupsCommand(string option) {
        try {
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                allLines = 1;
                labels.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
@@ -180,7 +179,7 @@ MergeGroupsCommand::~MergeGroupsCommand(){}
 int MergeGroupsCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                if (outputDir == "") {  outputDir += m->hasPath(sharedfile);  }
                string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "merge" +  m->getExtension(sharedfile);
@@ -274,6 +273,14 @@ int MergeGroupsCommand::execute(){
                
                if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0;}
                
+               
+               //set shared file as new current sharedfile
+               string current = "";
+               itTypes = outputTypes.find("shared");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
+               }
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }