SequenceCountParser* cparser;
if (pDataArray->hasCount) {
CountTable* ct = new CountTable();
- ct->readTable(pDataArray->namefile);
+ ct->readTable(pDataArray->namefile, true);
cparser = new SequenceCountParser(pDataArray->fastafile, *ct);
delete ct;
}else {
chimeraFile << j << '\t' << sequences[j].seqName << "\t0\t0\tNull\t0\t0\t0\tNull\tNull\t0.0\t0.0\t0.0\t0\t0\t0\t0.0\t0.0\tgood" << endl;
}
//report progress
- if((j+1) % 100 == 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(j+1) + "\n"); }
+ if((j+1) % 100 == 0){ pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(j+1) + "\n"); }
}
- if((numSeqs) % 100 != 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(numSeqs) + "\n"); }
+ if((numSeqs) % 100 != 0){ pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(numSeqs) + "\n"); }
chimeraFile.close();
accnosFile.close();
if (pDataArray->hasCount) {
while (!in.eof()) {
in >> name; pDataArray->m->gobble(in);
- outCountList << name << '\t' << groups[u] << endl;
+ outCountList << name << '\t' << pDataArray->groups[u] << endl;
}
in.close();
}else {
- map<string, string> thisnamemap = parser->getNameMap(groups[u]);
+ map<string, string> thisnamemap = parser->getNameMap(pDataArray->groups[u]);
map<string, string>::iterator itN;
ofstream out;
pDataArray->m->openOutputFile(accnosFileName+".temp", out);