int error;
if (hasCount) {
CountTable ct;
- ct.readTable(nameFile);
+ ct.readTable(nameFile, true);
for(map<string, string>::iterator it = seqs.begin(); it != seqs.end(); it++) {
int num = ct.getNumSeqs(it->first);
if (num == 0) { error = 1; }
if(processors == 1) { totalSeqs = driverGroups(outputFileName, newFasta, accnosFileName, alnsFileName, newCountFile, 0, groups.size(), groups);
if (hasCount && dups) {
- CountTable c; c.readTable(nameFile);
+ CountTable c; c.readTable(nameFile, true);
if (!m->isBlank(newCountFile)) {
ifstream in2;
m->openInputFile(newCountFile, in2);
if (hasCount) {
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(nameFile); }
+ if (hasCount && dups) { newCount.readTable(nameFile, true); }
//sanity check
if (groups.size() < processors) { processors = groups.size(); }