ListVector oldList;
vector<seqDist> overlapMatrix;
- string blastfile, method, namefile, overlapFile, distFile;
+ string blastfile, method, namefile, overlapFile, distFile, outputDir;
ofstream sabundFile, rabundFile, listFile;
- float cutoff, penalty;
+ double cutoff;
+ float penalty;
int precision, length, precisionLength;
- bool abort, minWanted, hclusterWanted, merge;
+ bool abort, minWanted, hclusterWanted, merge, hard;
void printData(ListVector*);
ListVector* mergeOPFs(map<string, int>, float);