if (hasCount) {
CountTable* ct = new CountTable();
- ct->readTable(nameFile);
+ ct->readTable(nameFile, true);
if (ct->hasGroupInfo()) {
cparser = new SequenceCountParser(fastaFileNames[s], *ct);
if(processors == 1) { numSeqs = driverGroups(outputFileName, accnosFileName, newCountFile, 0, groups.size(), groups);
if (dups) {
- CountTable c; c.readTable(nameFile);
+ CountTable c; c.readTable(nameFile, true);
if (!m->isBlank(newCountFile)) {
ifstream in2;
m->openInputFile(newCountFile, in2);
numChimeras = deconvoluteResults(uniqueNames, outputFileName, accnosFileName);
}else {
set<string> doNotRemove;
- CountTable c; c.readTable(newCountFile);
+ CountTable c; c.readTable(newCountFile, true);
vector<string> namesInTable = c.getNamesOfSeqs();
for (int i = 0; i < namesInTable.size(); i++) {
int temp = c.getNumSeqs(namesInTable[i]);
int num = 0;
CountTable newCount;
- if (hasCount && dups) { newCount.readTable(name); }
+ if (hasCount && dups) { newCount.readTable(name, true); }
//sanity check
if (groups.size() < processors) { processors = groups.size(); }