added count.seqs command and made some modifcations to the uchime code to allow it...

[mothur.git] / systemcommand.cpp

diff --git a/systemcommand.cpp b/systemcommand.cpp
index e5aeb3e8b73dfb59008f6ddccaa3b0703b25e696..5ace75e3a2d152f27e6483aab2ad4a697f952c79 100644 (file)
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -91,20 +91,23 @@ int SystemCommand::execute(){
                
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
-               //system(command.c_str());
-               FILE *lsofFile_p = popen(command.c_str(), "r");
+               command += " > ./commandScreen.output 2>&1";
+               system(command.c_str());
                
-               if (!lsofFile_p) { return 0; }
+               ifstream in;
+               string filename = "./commandScreen.output";
+               m->openInputFile(filename, in);
                
-               char buffer[1024];
-               while ( fgets(buffer, 1024, lsofFile_p) != NULL ) {
-                       string temp = buffer;
-                       m->mothurOut(temp); 
+               string output = "";
+               while(char c = in.get()){
+                       if(in.eof())            {       break;                  }
+                       else                            {       output += c;    }
                }
-               m->mothurOutEndLine();
-               
-               pclose(lsofFile_p);
+               in.close();
                
+               m->mothurOut(output); m->mothurOutEndLine();
+               remove(filename.c_str());
+                               
                return 0;               
        }