else {
//valid paramters for this command
- string Array[] = {"fasta","name", "group", "alignreport", "accnos", "list","taxonomy","outputdir","inputdir"};
+ string Array[] = {"fasta","name", "group", "alignreport", "accnos", "dups", "list","taxonomy","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
in.close();
out.close();
- if (wroteSomething == false) {
- m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();
- remove(outputFileName.c_str());
- }else { outputNames.push_back(outputFileName); }
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName);
return 0;
in.close();
out.close();
- if (wroteSomething == false) {
- m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();
- remove(outputFileName.c_str());
- }else { outputNames.push_back(outputFileName); }
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName);
return 0;
in.close();
out.close();
- if (wroteSomething == false) {
- m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();
- remove(outputFileName.c_str());
- }else { outputNames.push_back(outputFileName); }
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName);
return 0;
in.close();
out.close();
- if (wroteSomething == false) {
- m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();
- remove(outputFileName.c_str());
- }else { outputNames.push_back(outputFileName); }
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName);
return 0;
in.close();
out.close();
- if (wroteSomething == false) {
- m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();
- remove(outputFileName.c_str());
- }else { outputNames.push_back(outputFileName); }
-
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName);
+
return 0;
}
in.close();
out.close();
- if (wroteSomething == false) {
- m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();
- remove(outputFileName.c_str());
- }else { outputNames.push_back(outputFileName); }
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName);
return 0;