temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
m->mothurConvert(temp, iters);
- output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "lt"; }
+ output = validParameter.validFile(parameters, "output", false);
+ if(output == "not found"){ output = "lt"; }
+ else { createPhylip = true; }
if ((output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are lt and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
temp = validParameter.validFile(parameters, "subsample", false); if (temp == "not found") { temp = "F"; }
variables["[calc]"] = sumCalculators[i]->getName();
variables["[distance]"] = thisLookup[0]->getLabel();
variables["[outputtag]"] = output;
+ variables["[tag2]"] = "";
string distFileName = getOutputFileName("phylip",variables);
outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
ofstream outDist;
for (int i = 0; i < calcDists.size(); i++) { calcDists[i].clear(); }
}
- if (iters != 1) {
+ if (iters != 0) {
//we need to find the average distance and standard deviation for each groups distance
vector< vector<seqDist> > calcAverages; calcAverages.resize(sumCalculators.size());