int abort;
- string outputDir, flowFileName, flowFilesFileName, lookupFileName, compositeFASTAFileName;
+ string outputDir, flowFileName, flowFilesFileName, lookupFileName, compositeFASTAFileName, compositeNamesFileName;
int processors, maxIters;
float cutoff, sigma, minDelta;
vector<int> mapSeqToUnique;
vector<int> mapUniqueToSeq;
vector<int> uniqueLengths;
-
+
+ vector<string> outputNames;
+
int numSeqs, numUniques, numOTUs, numFlowCells;
void getSingleLookUp();