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

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index fc027b9261822880ac0afa1cc99929791a309df4..5c80047681c15640c5926d771536a42ea60a8c9d 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -306,7 +306,7 @@ int SeqErrorCommand::execute(){
                
                printErrorFRFile(errorForward, errorReverse);
                
-               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; }
 
                string errorCountFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.count";
                ofstream errorCountFile;
@@ -321,7 +321,7 @@ int SeqErrorCommand::execute(){
                }
                errorCountFile.close();
                
-               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; }
 
                printSubMatrix();
                                
@@ -478,11 +478,11 @@ int SeqErrorCommand::createProcesses(string filename, string qFileName, string r
                        m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
                        
                        m->appendFiles((summaryFileName + toString(processIDS[i]) + ".temp"), summaryFileName);
-                       remove((summaryFileName + toString(processIDS[i]) + ".temp").c_str());
+                       m->mothurRemove((summaryFileName + toString(processIDS[i]) + ".temp"));
                        m->appendFiles((errorOutputFileName + toString(processIDS[i]) + ".temp"), errorOutputFileName);
-                       remove((errorOutputFileName + toString(processIDS[i]) + ".temp").c_str());
+                       m->mothurRemove((errorOutputFileName + toString(processIDS[i]) + ".temp"));
                        m->appendFiles((chimeraOutputFileName + toString(processIDS[i]) + ".temp"), chimeraOutputFileName);
-                       remove((chimeraOutputFileName + toString(processIDS[i]) + ".temp").c_str());
+                       m->mothurRemove((chimeraOutputFileName + toString(processIDS[i]) + ".temp"));
                        
                        ifstream in;
                        string tempFile =  filename + toString(processIDS[i]) + ".info.temp";
@@ -577,7 +577,7 @@ int SeqErrorCommand::createProcesses(string filename, string qFileName, string r
                        }
                        m->gobble(in);
                        
-                       in.close(); remove(tempFile.c_str());
+                       in.close(); m->mothurRemove(tempFile);
                        
                }
 #endif