if (namefile != "") { m->readNames(namefile, nameMap, true); }
if (groupfile != "") { groupMap = new GroupMap(groupfile); groupMap->readMap(); groups = groupMap->getNamesOfGroups(); }
else { groupMap = NULL; }
- if (countfile != "") { ct = new CountTable(); ct->readTable(countfile); if (ct->hasGroupInfo()) { groups = ct->getNamesOfGroups(); } }
+ if (countfile != "") { ct = new CountTable(); ct->readTable(countfile, true); if (ct->hasGroupInfo()) { groups = ct->getNamesOfGroups(); } }
else { ct = NULL; }
//read taxonomy file and save in map for easy access in building bin trees
//add this bins taxonomy to summary
if (basis == "sequence") {
for(int j = 0; j < names.size(); j++) {
- int numReps = 1;
- if (countfile != "") { numReps = ct->getNumSeqs(names[j]); }
- for(int k = 0; k < numReps; k++) { taxaSum->addSeqToTree(names[j], noConfidenceConTax); }
+ //int numReps = 1;
+ //if (countfile != "") { numReps = ct->getNumSeqs(names[j]); }
+ //for(int k = 0; k < numReps; k++) { taxaSum->addSeqToTree(names[j], noConfidenceConTax); }
+ taxaSum->addSeqToTree(names[j], noConfidenceConTax);
}
}else { //otu
map<string, bool> containsGroup;