vector<int> processIDS; //processid
vector<linePair*> lines;
- int driver(linePair*, string, string);
- void createProcesses(string, string);
+ int driver(linePair*, string, string, string);
+ void createProcesses(string, string, string);
void appendOutputFiles(string, string);
bool abort;
- string method, fastafile, templatefile, consfile, quanfile, maskfile, namefile, outputDir;
- bool filter, correction, svg, printAll;
- int processors, midpoint, averageLeft, averageRight, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs;
+ 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;