if (!dups) {//adjust name if needed
map<string, string>::iterator it = uniqueMap.find(name);
- if (it != uniqueMap.end()) { name = it->second; }
+ if (it != uniqueMap.end()) { currSeq.setName(it->second); }
}
+ name = currSeq.getName();
+
if (name != "") {
//if this name is in the accnos file
if (names.count(name) != 0) {
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
- in >> firstCol;
+ in >> firstCol; m->gobble(in);
in >> secondCol;
string hold = "";
selectedCount += parsedNames.size();
if (m->debug) { sanity["name"].insert(firstCol); }
}else {
+
selectedCount += validSecond.size();
//if the name in the first column is in the set then print it and any other names in second column also in set
//make first name in set you come to first column and then add the remaining names to second column
}else {
+
//you want part of this row
if (validSecond.size() != 0) {