paralellized seq.error and dist.shared added some error checks to libshuff and dist...

[mothur.git] / binsequencecommand.cpp

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index d1764acec4602f5d90783f7a0abf35195b63149d..c4ef741f80c22bc784df4e6916f4a214fb2feacd 100644 (file)
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -41,7 +41,7 @@ string BinSeqCommand::getHelpString(){
                helpString += "The default value for label is all lines in your inputfile.\n";
                helpString += "The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name.\n";
                helpString += "If you provide a groupfile, then it also appends the sequences group to the name.\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) {
@@ -71,6 +71,7 @@ BinSeqCommand::BinSeqCommand(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();
@@ -281,10 +282,6 @@ int BinSeqCommand::execute(){
                
                if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str());         }  return 0; }  
                
-               delete input;  
-               delete fasta; 
-               if (groupfile != "") {  delete groupMap;   } 
-               
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }