m->mothurConvert(temp, beta);
temp = validParameter.validFile(parameters, "dereplicate", false);
m->mothurConvert(temp, beta);
temp = validParameter.validFile(parameters, "dereplicate", false);
if (ct->hasGroupInfo()) {
cparser = new SequenceCountParser(fastaFileNames[s], *ct);
if (ct->hasGroupInfo()) {
cparser = new SequenceCountParser(fastaFileNames[s], *ct);
if(processors == 1) { numSeqs = driverGroups(outputFileName, accnosFileName, newCountFile, 0, groups.size(), groups);
if (dups) {
if(processors == 1) { numSeqs = driverGroups(outputFileName, accnosFileName, newCountFile, 0, groups.size(), groups);
if (dups) {
if (!m->isBlank(newCountFile)) {
ifstream in2;
m->openInputFile(newCountFile, in2);
if (!m->isBlank(newCountFile)) {
ifstream in2;
m->openInputFile(newCountFile, in2);
vector<string> namesInTable = c.getNamesOfSeqs();
for (int i = 0; i < namesInTable.size(); i++) {
int temp = c.getNumSeqs(namesInTable[i]);
vector<string> namesInTable = c.getNamesOfSeqs();
for (int i = 0; i < namesInTable.size(); i++) {
int temp = c.getNumSeqs(namesInTable[i]);