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, true); if (ct->hasGroupInfo()) { groups = ct->getNamesOfGroups(); } }
+ if (countfile != "") { ct = new CountTable(); ct->readTable(countfile, true, false); if (ct->hasGroupInfo()) { groups = ct->getNamesOfGroups(); } }
else { ct = NULL; }
//read taxonomy file and save in map for easy access in building bin trees
PhyloSummary* taxaSum;
if (countfile != "") {
- if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, ct); }
- else { taxaSum = new PhyloSummary(ct); }
+ if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, ct,false); }
+ else { taxaSum = new PhyloSummary(ct,false); }
}else {
- if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, groupMap); }
- else { taxaSum = new PhyloSummary(groupMap); }
+ if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, groupMap,false); }
+ else { taxaSum = new PhyloSummary(groupMap,false); }
}
vector<ofstream*> outSums;
PhyloSummary* taxaSumt;
if (countfile != "") {
- if (refTaxonomy != "") { taxaSumt = new PhyloSummary(refTaxonomy, ct); }
- else { taxaSumt = new PhyloSummary(ct); }
+ if (refTaxonomy != "") { taxaSumt = new PhyloSummary(refTaxonomy, ct, false); }
+ else { taxaSumt = new PhyloSummary(ct, false); }
}else {
- if (refTaxonomy != "") { taxaSumt = new PhyloSummary(refTaxonomy, groupMap); }
- else { taxaSumt = new PhyloSummary(groupMap); }
+ if (refTaxonomy != "") { taxaSumt = new PhyloSummary(refTaxonomy, groupMap,false); }
+ else { taxaSumt = new PhyloSummary(groupMap,false); }
}
taxaSums.push_back(taxaSumt);
}
//for each bin in the list vector
string snumBins = toString(processList->getNumBins());
+ vector<string> binLabels = processList->getLabels();
for (int i = 0; i < processList->getNumBins(); i++) {
if (m->control_pressed) { break; }
names = findConsensusTaxonomy(thisNames, size, conTax);
if (m->control_pressed) { break; }
-
- //output to new names file
- string binLabel = "Otu";
- string sbinNumber = toString(i+1);
- if (sbinNumber.length() < snumBins.length()) {
- int diff = snumBins.length() - sbinNumber.length();
- for (int h = 0; h < diff; h++) { binLabel += "0"; }
- }
- binLabel += sbinNumber;
- out << binLabel << '\t' << size << '\t' << conTax << endl;
+ out << binLabels[i] << '\t' << size << '\t' << conTax << endl;
string noConfidenceConTax = conTax;
m->removeConfidences(noConfidenceConTax);
if (m->control_pressed) { break; }
- //output to new names file
- string binLabel = "Otu";
- string sbinNumber = toString(i+1);
- if (sbinNumber.length() < snumBins.length()) {
- int diff = snumBins.length() - sbinNumber.length();
- for (int h = 0; h < diff; h++) { binLabel += "0"; }
- }
- binLabel += sbinNumber;
- (*outs[groupIndex[itParsed->first]]) << binLabel << '\t' << size << '\t' << conTax << endl;
+ (*outs[groupIndex[itParsed->first]]) << binLabels[i] << '\t' << size << '\t' << conTax << endl;
string noConfidenceConTax = conTax;
m->removeConfidences(noConfidenceConTax);