private:
+
+ struct linePair {
+ int start;
+ int numSeqs;
+ linePair(long int i, int j) : start(i), numSeqs(j) {}
+ };
+ vector<int> processIDS; //processid
+ vector<linePair*> lines;
+ int driver(linePair*, string, string, string);
+ void createProcesses(string, string, string);
+ void appendOutputFiles(string, string);
+
bool abort;
- string method, fastafile, templatefile, consfile, quanfile, maskfile;
- bool filter, correction;
- int processors, midpoint, averageLeft, averageRight, window, iters, increment;
+ string method, fastafile, templatefile, consfile, quanfile, maskfile, namefile, outputDir, search;
+ bool filter, correction, svg, printAll, realign;
+ int processors, midpoint, averageLeft, averageRight, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
+ float divR;
Chimera* chimera;