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);
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]);
}
out2.close();
c.printTable(newCountFile);
+ outputNames.push_back(newCountFile); outputTypes["count"].push_back(newCountFile);
}
}
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();
map<string, string>::iterator itUnique;
int total = 0;
- //edit accnos file
- ifstream in2;
- m->openInputFile(accnosFileName, in2);
-
ofstream out2;
m->openOutputFile(accnosFileName+".temp", out2);
set<string> chimerasInFile;
set<string>::iterator itChimeras;
-
- while (!in2.eof()) {
- if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; }
-
- in2 >> name; m->gobble(in2);
-
- //find unique name
- itUnique = uniqueNames.find(name);
-
- if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find " + name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
- else {
- itChimeras = chimerasInFile.find((itUnique->second));
-
- if (itChimeras == chimerasInFile.end()) {
- out2 << itUnique->second << endl;
- chimerasInFile.insert((itUnique->second));
- total++;
- }
- }
- }
- in2.close();
+ if (!m->isBlank(accnosFileName)) {
+ //edit accnos file
+ ifstream in2;
+ m->openInputFile(accnosFileName, in2);
+
+ while (!in2.eof()) {
+ if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; }
+
+ in2 >> name; m->gobble(in2);
+
+ //find unique name
+ itUnique = uniqueNames.find(name);
+
+ if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find " + name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else {
+ itChimeras = chimerasInFile.find((itUnique->second));
+
+ if (itChimeras == chimerasInFile.end()) {
+ out2 << itUnique->second << endl;
+ chimerasInFile.insert((itUnique->second));
+ total++;
+ }
+ }
+ }
+ in2.close();
+ }
out2.close();
m->mothurRemove(accnosFileName);
int totalSeqs = 0;
int numChimeras = 0;
+
ofstream outCountList;
if (hasCount && dups) { m->openOutputFile(countlist, outCountList); }
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(); }