fixed bug with dist.shared subsampling. added mode parameter to dist.shared so...

[mothur.git] / mergefilecommand.cpp

diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
index cb241c6b301396e7c7d0482d98be861a926b8a64..04c92fae9a0d2189cb8f1ed69c9c53572fcfee2e 100644 (file)
--- a/mergefilecommand.cpp
+++ b/mergefilecommand.cpp
@@ -33,7 +33,7 @@ string MergeFileCommand::getHelpString(){
                helpString += "The merge.file command takes a list of files separated by dashes and merges them into one file."; 
                helpString += "The merge.file command parameters are input and output."; 
                helpString += "Example merge.file(input=small.fasta-large.fasta, output=all.fasta).";
-               helpString += "Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputFileName).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputFileName).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -64,7 +64,7 @@ MergeFileCommand::MergeFileCommand(string option)  {
                if(option == "help") {
                        help();
                        abort = true; calledHelp = true;
-               }
+               }else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                else {
                        vector<string> myArray = setParameters();
                        
@@ -140,7 +140,7 @@ int MergeFileCommand::execute(){
                        m->openInputFile(fileNames[i], inputFile);
                        
                        while(!inputFile.eof()){        
-                               if (m->control_pressed) { outputTypes.clear(); inputFile.close(); outputFile.close(); remove(outputFileName.c_str()); return 0;  }
+                               if (m->control_pressed) { outputTypes.clear(); inputFile.close(); outputFile.close(); m->mothurRemove(outputFileName); return 0;  }
                        
                                c = inputFile.get(); 
                                //-1 is eof char
@@ -152,7 +152,7 @@ int MergeFileCommand::execute(){
                
                outputFile.close();
                
-               if (m->control_pressed) { outputTypes.clear();  remove(outputFileName.c_str()); return 0;  }
+               if (m->control_pressed) { outputTypes.clear();  m->mothurRemove(outputFileName); return 0;  }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Name: "); m->mothurOutEndLine();