if (m->debug) { m->mothurOut("[DEBUG]: distName.size() = " + toString(distName.size()) + ".\n"); }
//output a merged distance file
- if (splitmethod == "fasta") { createMergedDistanceFile(distName); }
-
+ //if (splitmethod == "fasta") { createMergedDistanceFile(distName); }
if (m->control_pressed) { return 0; }
if (itLabel->first == -1) { thisLabel = "unique"; }
else { thisLabel = toString(itLabel->first, length-1); }
- outList << thisLabel << '\t' << itLabel->second << '\t';
+ //outList << thisLabel << '\t' << itLabel->second << '\t';
RAbundVector* rabund = NULL;
+ ListVector completeList;
+ completeList.setLabel(thisLabel);
+
if (countfile == "") {
rabund = new RAbundVector();
rabund->setLabel(thisLabel);
//add in singletons
if (listSingle != NULL) {
for (int j = 0; j < listSingle->getNumBins(); j++) {
- outList << listSingle->get(j) << '\t';
+ //outList << listSingle->get(j) << '\t';
+ completeList.push_back(listSingle->get(j));
if (countfile == "") { rabund->push_back(m->getNumNames(listSingle->get(j))); }
}
}
if (list == NULL) { m->mothurOut("Error merging listvectors in file " + listNames[k]); m->mothurOutEndLine(); }
else {
for (int j = 0; j < list->getNumBins(); j++) {
- outList << list->get(j) << '\t';
+ //outList << list->get(j) << '\t';
+ completeList.push_back(list->get(j));
if (countfile == "") { rabund->push_back(m->getNumNames(list->get(j))); }
}
delete list;
sabund.print(outSabund);
rabund->print(outRabund);
}
- outList << endl;
+ //outList << endl;
+ completeList.print(outList);
if (rabund != NULL) { delete rabund; }
}
if ((processToAssign-1) == 1) { m->mothurOut(distName[i].begin()->first + "\n"); }
}
- //not lets reverse the order of ever other process, so we balance big files running with little ones
+ //now lets reverse the order of ever other process, so we balance big files running with little ones
for (int i = 0; i < processors; i++) {
//cout << i << endl;
int remainder = ((i+1) % processors);
cluster->readPhylipFile(thisDistFile, nameMap);
}else if (countfile != "") {
ct = new CountTable();
- ct->readTable(thisNamefile);
+ ct->readTable(thisNamefile, false);
cluster->readPhylipFile(thisDistFile, ct);
}
tag = cluster->getTag();
read->read(nameMap);
}else if (countfile != "") {
ct = new CountTable();
- ct->readTable(thisNamefile);
+ ct->readTable(thisNamefile, false);
read->read(ct);
}else { read->read(nameMap); }