added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / mothur.cpp

diff --git a/mothur.cpp b/mothur.cpp
index ab4fea0e09482b3c8c988ade3e244fa4c8504750..d4177e3368be8d836374e935b9e884d6ff26c5f4 100644 (file)
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -99,14 +99,10 @@ int main(int argc, char *argv[]){
                        mothur = new InteractEngine(argv[0]);   
                }
                
-               //used to intercept the terminate signal, so instead of terminating mothur it will end a command
-               //void (*prev_fn)(int);
-               //prev_fn = signal(SIGTERM, mothur->terminateCommand(0));
-               
-               //if (prev_fn==SIG_IGN) signal (SIGTERM,SIG_IGN);
-
-               
                while(bail == 0)                {       bail = mothur->getInput();                      }
+               
+               string outputDir = mothur->getOutputDir();
+               logFileName = outputDir + logFileName;
        
                delete mothur;