if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport or list."); m->mothurOutEndLine(); abort = true; }
- int okay = 2;
- if (outputDir != "") { okay++; }
- if (usedDups != "") { okay++; }
+ //int okay = 2;
+ //if (outputDir != "") { okay++; }
+ //if (usedDups != "") { okay++; }
if ((usedDups != "") && (namefile == "")) { m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine(); abort = true; }
- if (parameters.size() > okay) { m->mothurOut("You may only enter one of the following: fasta, name, group, alignreport, or list."); m->mothurOutEndLine(); abort = true; }
+ //if (parameters.size() > okay) { m->mothurOut("You may only enter one of the following: fasta, name, group, alignreport, or list."); m->mothurOutEndLine(); abort = true; }
}
}
//read through the correct file and output lines you want to keep
if (fastafile != "") { readFasta(); }
- else if (namefile != "") { readName(); }
- else if (groupfile != "") { readGroup(); }
- else if (alignfile != "") { readAlign(); }
- else if (listfile != "") { readList(); }
+ if (namefile != "") { readName(); }
+ if (groupfile != "") { readGroup(); }
+ if (alignfile != "") { readAlign(); }
+ if (listfile != "") { readList(); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
wroteSomething = true;
currSeq.printSequence(out);
- }else { names.erase(name); }
+ }//else { names.erase(name); }
}
gobble(in);
}
if (names.count(name) == 0) {
wroteSomething = true;
out << name << '\t' << group << endl;
- }else { names.erase(name); }
+ }//else { names.erase(name); }
gobble(in);
}
out << endl;
}else {//still read just don't do anything with it
- names.erase(name);
+ //names.erase(name);
//read rest
for (int i = 0; i < 15; i++) {