- vector< vector<data_struct> > chimeraResults;
- vector<string> chimeraFlags;
-
- string fastafile, templateFile;
+ vector<data_struct> chimeraResults;
+ string chimeraFlags, searchMethod, fastafile;
+ bool realign;
+ int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
+ float divR;
+
+ void printBlock(data_struct, string, ostream&);
+ string getBlock(data_struct, string);