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

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index e3db3dda8db657d23e671cc704e90f78833cfca2..a32ec4df279b2fa1158ec5e818ce03545de4ed0c 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -436,7 +436,7 @@ int AlignCommand::execute(){
                                                //MPI_Info info;
                                                //MPI_File_delete(outAccnosFilename, info);
                                                hasAccnos = false;      
-                                               remove(accnosFileName.c_str()); 
+                                               m->mothurRemove(accnosFileName); 
                                        }
                                }
                                
@@ -456,10 +456,10 @@ int AlignCommand::execute(){
                        numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
        #endif
                        
-                       if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear();  return 0; }
+                       if (m->control_pressed) { m->mothurRemove(accnosFileName); m->mothurRemove(alignFileName); m->mothurRemove(reportFileName); outputTypes.clear();  return 0; }
                        
                        //delete accnos file if its blank else report to user
-                       if (m->isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
+                       if (m->isBlank(accnosFileName)) {  m->mothurRemove(accnosFileName);  hasAccnos = false; }
                        else { 
                                m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
                                if (!flip) {
@@ -849,24 +849,24 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
                
                vector<string> nonBlankAccnosFiles;
                if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
-               else { remove(accnosFName.c_str()); } //remove so other files can be renamed to it
+               else { m->mothurRemove(accnosFName); } //remove so other files can be renamed to it
                        
                for (int i = 0; i < processIDS.size(); i++) {
                        ifstream in;
                        string tempFile =  alignFileName + toString(processIDS[i]) + ".num.temp";
                        m->openInputFile(tempFile, in);
                        if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
-                       in.close(); remove(tempFile.c_str());
+                       in.close(); m->mothurRemove(tempFile);
                        
                        appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
-                       remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
+                       m->mothurRemove((alignFileName + toString(processIDS[i]) + ".temp"));
                        
                        appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
-                       remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
+                       m->mothurRemove((reportFileName + toString(processIDS[i]) + ".temp"));
                        
                        if (!(m->isBlank(accnosFName + toString(processIDS[i]) + ".temp"))) {
                                nonBlankAccnosFiles.push_back(accnosFName + toString(processIDS[i]) + ".temp");
-                       }else { remove((accnosFName + toString(processIDS[i]) + ".temp").c_str());  }
+                       }else { m->mothurRemove((accnosFName + toString(processIDS[i]) + ".temp"));  }
                        
                }
                
@@ -876,7 +876,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
                        
                        for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
                                appendAlignFiles(nonBlankAccnosFiles[h], accnosFName);
-                               remove(nonBlankAccnosFiles[h].c_str());
+                               m->mothurRemove(nonBlankAccnosFiles[h]);
                        }
                }else { //recreate the accnosfile if needed
                        ofstream out;