#include "mothur.h"
#include "command.hpp"
-#include "chimera.h"
-
/***********************************************************/
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, 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;
-
-
};
/***********************************************************/