m->mothurConvert(temp, beta);
temp = validParameter.validFile(parameters, "dereplicate", false);
- if (temp == "not found") {
- if (groupfile != "") { temp = "false"; }
- else { temp = "true"; }
- }
+ if (temp == "not found") { temp = "false"; }
dups = m->isTrue(temp);
}
}
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]);
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
}
+
+ itTypes = outputTypes.find("count");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+ }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
}
//report progress
- if((i+1) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(i+1) + "\n"); }
+ if((i+1) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(i+1) + "\n"); }
}
- if((numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(numSeqs) + "\n"); }
+ if((numSeqs) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(numSeqs) + "\n"); }
chimeraFile.close();
accnosFile.close();
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(); }