string sname = ""; nameStream >> sname;
sname = sname.substr(1);
+
+ for (int i = 0; i < sname.length(); i++) {
+ if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
+ }
map<string, int>::iterator it = firstSeqNames.find(sname);
istringstream nameStream(input);
string sname = ""; nameStream >> sname;
+ for (int i = 0; i < sname.length(); i++) {
+ if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
+ }
+
map<string, int>::iterator it = firstSeqNamesReport.find(sname);
if(it != firstSeqNamesReport.end()) { //this is the start of a new chunk