if(namesFileName != "") { weights = getWeights(); }
else if (countfile != "") {
CountTable ct;
- ct.readTable(countfile);
+ ct.readTable(countfile, false);
weights = ct.getNameMap();
}
int misMatchSize;
in >> misMatchSize; m->gobble(in);
if (misMatchSize > misMatchCounts.size()) { misMatchCounts.resize(misMatchSize, 0); }
- for (int j = 0; j < misMatchCounts.size(); j++) {
+ for (int j = 0; j < misMatchSize; j++) {
in >> tempNum; misMatchCounts[j] += tempNum;
}
m->gobble(in);
if (queryFile.eof()) { break; }
#endif
- if(index % 100 == 0){ m->mothurOut(toString(index)); m->mothurOutEndLine(); }
+ if(index % 100 == 0){ m->mothurOutJustToScreen(toString(index)+"\n"); }
}
queryFile.close();
outChimeraReport.close();
else if(qFileName != "" && aligned == false){ qualFile.close(); }
//report progress
- m->mothurOut(toString(index)); m->mothurOutEndLine();
+ m->mothurOutJustToScreen(toString(index)+"\n");
return index;
}
string sname = ""; nameStream >> sname;
sname = sname.substr(1);
- for (int i = 0; i < sname.length(); i++) {
- if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
- }
+ m->checkName(sname);
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; }
- }
+ m->checkName(sname);
map<string, int>::iterator it = firstSeqNamesReport.find(sname);