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

[mothur.git] / getotuscommand.cpp

diff --git a/getotuscommand.cpp b/getotuscommand.cpp
index d29773ca340cf1119f04c312f897a0e5f2d7d4e8..b94b42a8a37038d188bf19a430a7ee8951f2f86c 100644 (file)
--- a/getotuscommand.cpp
+++ b/getotuscommand.cpp
@@ -195,7 +195,7 @@ int GetOtusCommand::execute(){
                //read through the list file keeping any otus that contain any sequence from the groups selected
                readListGroup();
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0; }
                                
                if (outputNames.size() != 0) {
                        m->mothurOutEndLine();
@@ -258,7 +258,7 @@ int GetOtusCommand::readListGroup(){
                //as long as you are not at the end of the file or done wih the lines you want
                while((list != NULL) && (userLabels.size() != 0)) {
                        
-                       if (m->control_pressed) {  delete list; delete input; out.close();  outGroup.close(); remove(outputFileName.c_str());  remove(outputGroupFileName.c_str());return 0;  }
+                       if (m->control_pressed) {  delete list; delete input; out.close();  outGroup.close(); m->mothurRemove(outputFileName);  m->mothurRemove(outputGroupFileName);return 0;  }
                        
                        if(labels.count(list->getLabel()) == 1){
                                processList(list, groupMap, out, outGroup, wroteSomething);
@@ -292,7 +292,7 @@ int GetOtusCommand::readListGroup(){
                }
                
                
-               if (m->control_pressed) {  if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); remove(outputFileName.c_str());  remove(outputGroupFileName.c_str()); return 0;  }
+               if (m->control_pressed) {  if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); m->mothurRemove(outputFileName);  m->mothurRemove(outputGroupFileName); return 0;  }
                
                //output error messages about any remaining user labels
                set<string>::iterator it;