trim.flows mod

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 0ab12ab81e21e64e53b876ce8b1be4d43bbd9399..ce4b8950c3f1946054c7b24c82445a9ea1bc1cec 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -86,7 +86,7 @@ string GetOTURepCommand::getHelpString(){
                helpString += "The groups parameter allows you to indicate that you want representative sequences for each group specified for each OTU, group name should be separated by dashes. ex. groups=A-B-C.\n";
                helpString += "The get.oturep command outputs a .fastarep and .rep.names file for each distance you specify, selecting one OTU representative for each bin.\n";
                helpString += "If you provide a groupfile, then it also appends the names of the groups present in that bin.\n";
-               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -117,6 +117,7 @@ GetOTURepCommand::GetOTURepCommand(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();
                        
@@ -645,7 +646,7 @@ string GetOTURepCommand::findRep(vector<string> names) {
        try{
                // if only 1 sequence in bin or processing the "unique" label, then 
                // the first sequence of the OTU is the representative one
-               if ((names.size() == 1) || (list->getLabel() == "unique")) {
+               if ((names.size() == 1)) {
                        return names[0];
                }else{
                        vector<int> seqIndex(names.size());