if(namesFileName != "") { weights = getWeights(); }
else if (countfile != "") {
CountTable ct;
- ct.readTable(countfile);
+ ct.readTable(countfile, false);
weights = ct.getNameMap();
}
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;
}