added headers to shared and relabund files

[mothur.git] / mergegroupscommand.cpp

diff --git a/mergegroupscommand.cpp b/mergegroupscommand.cpp
index cb990e467f49afddfd56a2106ee7c47c12d0bd7e..f62bb0ca8bcf0e0cd5b63ca080208af0b1a5d00d 100644 (file)
--- a/mergegroupscommand.cpp
+++ b/mergegroupscommand.cpp
@@ -73,6 +73,7 @@ MergeGroupsCommand::MergeGroupsCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -191,6 +192,8 @@ int MergeGroupsCommand::execute(){
                        if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
                                
                                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+                               
+                               if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
                                process(lookup, out);
                                
                                processedLabels.insert(lookup[0]->getLabel());
@@ -204,6 +207,7 @@ int MergeGroupsCommand::execute(){
                                lookup = input.getSharedRAbundVectors(lastLabel);
                                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
                                
+                               if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
                                process(lookup, out);
                                
                                processedLabels.insert(lookup[0]->getLabel());
@@ -245,6 +249,7 @@ int MergeGroupsCommand::execute(){
                        
                        m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
                        
+                       if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
                        process(lookup, out);
                        
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }