rewrote metastats command in c++, added mothurRemove function to handle ~ error....

[mothur.git] / getsharedotucommand.cpp

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index 046460d0f1d11f345c14ddd99b687fddbafa8ec9..02461365b505bdea22cc977594fc1341ca7bac46 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -266,7 +266,7 @@ int GetSharedOTUCommand::execute(){
                        
                        if (m->control_pressed) { 
                                if (lastlist != NULL) {         delete lastlist;        }
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }  outputTypes.clear();
+                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); }  outputTypes.clear();
                                delete groupMap; return 0;
                        }
                        
@@ -329,7 +329,7 @@ int GetSharedOTUCommand::execute(){
                
                if (lastlist != NULL) {         delete lastlist;        }
                
-               if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str()); }  delete groupMap; return 0; } 
+               if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]); }  delete groupMap; return 0; } 
                
                //set fasta file as new current fastafile
                string current = "";
@@ -381,7 +381,7 @@ int GetSharedOTUCommand::process(ListVector* shared) {
                                
                //go through each bin, find out if shared
                for (int i = 0; i < shared->getNumBins(); i++) {
-                       if (m->control_pressed) { outNames.close(); remove(outputFileNames.c_str()); return 0; }
+                       if (m->control_pressed) { outNames.close(); m->mothurRemove(outputFileNames); return 0; }
                        
                        bool uniqueOTU = true;
                        
@@ -459,7 +459,7 @@ int GetSharedOTUCommand::process(ListVector* shared) {
                outNames.close();
                
                if (!wroteSomething) {
-                       remove(outputFileNames.c_str());
+                       m->mothurRemove(outputFileNames);
                        string outputString = "\t" + toString(num) + " - No otus shared by groups";
                        
                        string groupString = "";