#include "mothur.h"
#include "command.hpp"
+#include "sequenceparser.h"
/***********************************************************/
void help() { m->mothurOut(getHelpString()); }
private:
+ struct linePair {
+ int start;
+ int end;
+ linePair(int i, int j) : start(i), end(j) {}
+ };
+
vector<int> processIDS; //processid
- int driver(string, string, string, string);
- int createProcesses(string, string, string, string);
+ int driver(string, string, string, string, int&);
+ int createProcesses(string, string, string, string, int&);
bool abort, useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract;
- string fastafile, templatefile, outputDir, namefile, abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract;
+ string fastafile, groupfile, templatefile, outputDir, namefile, abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract;
int processors;
vector<string> outputNames;
vector<string> fastaFileNames;
vector<string> nameFileNames;
+ vector<string> groupFileNames;
+ string getNamesFile(string&);
+ int readFasta(string, map<string, string>&);
+ int printFile(vector<seqPriorityNode>&, string);
+ int deconvoluteResults(SequenceParser&, string, string, string);
+ int driverGroups(SequenceParser&, string, string, string, string, int, int, vector<string>);
+ int createProcessesGroups(SequenceParser&, string, string, string, string, vector<string>);
+
+
};
/***********************************************************/