temp = validParameter.validFile(parameters, "oligos", true);
if (temp == "not found") { oligoFileName = ""; }
else if(temp == "not open") { abort = true; }
- else { oligoFileName = temp; }
+ else { oligoFileName = temp; m->setOligosFile(oligoFileName); }
temp = validParameter.validFile(parameters, "fasta", false); if (temp == "not found"){ fasta = 0; }
else if(m->isTrue(temp)) { fasta = 1; }
}
if(size < 10){
- remove(barcodePrimerComboFileNames[i][j].c_str());
+ m->mothurRemove(barcodePrimerComboFileNames[i][j]);
}
else{
output << barcodePrimerComboFileNames[i][j] << endl;
m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
m->appendFiles((trimFlowFileName + toString(processIDS[i]) + ".temp"), trimFlowFileName);
- remove((trimFlowFileName + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((trimFlowFileName + toString(processIDS[i]) + ".temp"));
// m->mothurOut("\tDone with trim.flow file"); m->mothurOutEndLine();
m->appendFiles((scrapFlowFileName + toString(processIDS[i]) + ".temp"), scrapFlowFileName);
- remove((scrapFlowFileName + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((scrapFlowFileName + toString(processIDS[i]) + ".temp"));
// m->mothurOut("\tDone with scrap.flow file"); m->mothurOutEndLine();
if(fasta){
m->appendFiles((fastaFileName + toString(processIDS[i]) + ".temp"), fastaFileName);
- remove((fastaFileName + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((fastaFileName + toString(processIDS[i]) + ".temp"));
// m->mothurOut("\tDone with flow.fasta file"); m->mothurOutEndLine();
}
if(allFiles){
for (int j = 0; j < barcodePrimerComboFileNames.size(); j++) {
for (int k = 0; k < barcodePrimerComboFileNames[0].size(); k++) {
m->appendFiles((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"), barcodePrimerComboFileNames[j][k]);
- remove((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"));
}
}
}