if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
Sequence currSeq(in);
+
+ if (!dups) {//adjust name if needed
+ map<string, string>::iterator it = uniqueMap.find(currSeq.getName());
+ if (it != uniqueMap.end()) { currSeq.setName(it->second); }
+ }
+
name = currSeq.getName();
if (name != "") {
if (names.count(name) == 0) {
wroteSomething = true;
- currSeq.printSequence(out);
+ currSeq.printSequence(out);
}else { removedCount++; }
}
m->gobble(in);
m->gobble(in);
+ if (!dups) {//adjust name if needed
+ map<string, string>::iterator it = uniqueMap.find(saveName);
+ if (it != uniqueMap.end()) { name = ">" + it->second; saveName = it->second; }
+ }
+
if (names.count(saveName) == 0) {
wroteSomething = true;
wroteSomething = true;
out << validSecond[0] << '\t';
+ //we are changing the unique name in the fasta file
+ uniqueMap[firstCol] = validSecond[0];
//you know you have at least one valid second since first column is valid
for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
in >> name; //read from first column
in >> tax; //read from second column
+ if (!dups) {//adjust name if needed
+ map<string, string>::iterator it = uniqueMap.find(name);
+ if (it != uniqueMap.end()) { name = it->second; }
+ }
+
//if this name is in the accnos file
if (names.count(name) == 0) {
wroteSomething = true;
+
out << name << '\t' << tax << endl;
}else { removedCount++; }
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
in >> name; //read from first column
+
+ if (!dups) {//adjust name if needed
+ map<string, string>::iterator it = uniqueMap.find(name);
+ if (it != uniqueMap.end()) { name = it->second; }
+ }
//if this name is in the accnos file
if (names.count(name) == 0) {