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 (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();