string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
- string listFileName = fileroot+ tag + "." + getOutputFileNameTag("list");
+ string listFileName = fileroot+ tag + ".";
+ if (countfile != "") { listFileName += "unique_"; }
+ listFileName += getOutputFileNameTag("list");
if (countfile == "") {
m->openOutputFile(sabundFileName, sabundFile);
if (!hclusterWanted) {
//get distmatrix and overlap
- SparseMatrix* distMatrix = read->getDistMatrix();
+ SparseDistanceMatrix* distMatrix = read->getDistMatrix();
overlapMatrix = read->getOverlapMatrix(); //already sorted by read
delete read;