vector<int> nSeqsBreaks;
vector<int> nOTUsBreaks;
- vector<double> flowDataPrI;
- vector<short> flowDataIntI;
- vector<int> lengths;
- vector<string> seqNameVector;
vector<double> singleLookUp;
vector<double> jointLookUp;
+
+ vector<string> seqNameVector;
+ vector<int> lengths;
+ vector<short> flowDataIntI;
+ vector<double> flowDataPrI;
map<string, int> nameMap;
vector<int> otuData;
vector<int> cumNumSeqs;
vector<int> nSeqsPerOTU;
vector<vector<int> > aaP; //tMaster->aanP: each row is a different otu / each col contains the sequence indices
- vector<int> seqNumber; //tMaster->anP: the sequence id number sorted by OTU
vector<vector<int> > aaI; //tMaster->aanI: that are in each otu - can't differentiate between aaP and aaI
+ vector<int> seqNumber; //tMaster->anP: the sequence id number sorted by OTU
vector<int> seqIndex; //tMaster->anI; the index that corresponds to seqNumber
vector<double> dist; //adDist - distance of sequences to centroids
vector<short> change; //did the centroid sequence change? 0 = no; 1 = yes
vector<double> singleTau; //tMaster->adTau: 1-D Tau vector (1xnumSeqs)
vector<short> uniqueFlowgrams;
vector<int> uniqueCount;
- vector<int> uniqueLengths;
vector<int> mapSeqToUnique;
vector<int> mapUniqueToSeq;
+ vector<int> uniqueLengths;
int numSeqs, numUniques, numOTUs, numFlowCells;