added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / mergefilecommand.cpp

diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
index 04c92fae9a0d2189cb8f1ed69c9c53572fcfee2e..0501859e258f82410fa8360ae86092a0b1ea86f6 100644 (file)
--- a/mergefilecommand.cpp
+++ b/mergefilecommand.cpp
@@ -41,7 +41,6 @@ string MergeFileCommand::getHelpString(){
                exit(1);
        }
 }
-
 //**********************************************************************************************************************
 MergeFileCommand::MergeFileCommand(){  
        try {
@@ -130,29 +129,10 @@ int MergeFileCommand::execute(){
        try {
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
-               ofstream outputFile;
-               m->openOutputFile(outputFileName, outputFile);
-               
-               char c;
-               for(int i=0;i<numInputFiles;i++){
-                       ifstream inputFile; //declaration must be inside for loop of windows throws an error
-                       
-                       m->openInputFile(fileNames[i], inputFile);
-                       
-                       while(!inputFile.eof()){        
-                               if (m->control_pressed) { outputTypes.clear(); inputFile.close(); outputFile.close(); m->mothurRemove(outputFileName); return 0;  }
-                       
-                               c = inputFile.get(); 
-                               //-1 is eof char
-                               if (int(c) != -1) { outputFile << c; }   
-                       }
-                       
-                       inputFile.close();
-               }
-               
-               outputFile.close();
+               m->mothurRemove(outputFileName);
+               for(int i=0;i<numInputFiles;i++){  m->appendFiles(fileNames[i], outputFileName);  }
                
-               if (m->control_pressed) { outputTypes.clear();  m->mothurRemove(outputFileName); return 0;  }
+               if (m->control_pressed) {  m->mothurRemove(outputFileName); return 0;  }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Name: "); m->mothurOutEndLine();