//MPI_Info info;
//MPI_File_delete(outAccnosFilename, info);
hasAccnos = false;
- remove(accnosFileName.c_str());
+ m->mothurRemove(accnosFileName);
}
}
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) {
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")); }
}
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;