added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / mothur.cpp

diff --git a/mothur.cpp b/mothur.cpp
index b551302646c10b813740516eaa65cc46453b4a1d..c9914229c9d41c72da266a46d5f26516e0f60fe4 100644 (file)
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -10,12 +10,13 @@
 #include "mothur.h"
 #include "engine.hpp"
 #include "mothurout.h"
+#include "referencedb.h"
 
 /**************************************************************************************************/
 
 CommandFactory* CommandFactory::_uniqueInstance = 0;
 MothurOut* MothurOut::_uniqueInstance = 0;
-
+ReferenceDB* ReferenceDB::myInstance = 0;
 /***********************************************************************/
 volatile int ctrlc_pressed = 0;
 void ctrlc_handler ( int sig ) {
@@ -227,7 +228,7 @@ int main(int argc, char *argv[]){
                                outNewLog.close();
                                
                                m->appendFiles(logFileName, newlogFileName);
-                               remove(logFileName.c_str());
+                               m->mothurRemove(logFileName);
                        }
                }else{  
                        newlogFileName = outputDir + logFileName;