added some debug stuff to chimera.uchime. optimized phylo.diversity to improve raref...

[mothur.git] / chimerauchimecommand.cpp

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 026e91b01f188ce180c3b645de8451138efe0e02..e28775f016c4e992d2d8f2d23904c93c6e3f74ef 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -12,7 +12,7 @@
 //#include "uc.h"
 #include "sequence.hpp"
 #include "referencedb.h"
-
+#include "systemcommand.h"
 
 //**********************************************************************************************************************
 vector<string> ChimeraUchimeCommand::setParameters(){  
@@ -463,10 +463,20 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
                        string uchimeCommand;
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        uchimeCommand = path + "uchime";        //      format the database, -o option gives us the ability
+            if (m->debug) { 
+                m->mothurOut("[DEBUG]: Uchime location using \"which uchime\" = "); 
+                Command* newCommand = new SystemCommand("which uchime"); m->mothurOutEndLine();
+                newCommand->execute();
+                delete newCommand;
+                m->mothurOut("[DEBUG]: Mothur's location using \"which mothur\" = "); 
+                newCommand = new SystemCommand("which mothur"); m->mothurOutEndLine();
+                newCommand->execute();
+                delete newCommand;
+            }
 #else
                        uchimeCommand = path + "uchime.exe";
 #endif
-                       
+        
                        //test to make sure uchime exists
                        ifstream in;
                        uchimeCommand = m->getFullPathName(uchimeCommand);