vector<string> setParameters();
string getCommandName() { return "chimera.check"; }
string getCommandCategory() { return "Sequence Processing"; }
+ string getOutputFileNameTag(string, string);
string getHelpString();
string getCitation() { return "CHIMERA_CHECK version 2.7 written by Niels Larsen (http://wdcm.nig.ac.jp/RDP/docs/chimera_doc.html) \nhttp://www.mothur.org/wiki/Chimera.check"; }
-
+ string getDescription() { return "detect chimeric sequences"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
struct linePair {
- unsigned long int start;
- unsigned long int end;
- linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
+ unsigned long long start;
+ unsigned long long end;
+ linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
};
vector<int> processIDS; //processid
int createProcesses(string, string);
#ifdef USE_MPI
- int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long int>&);
+ int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long long>&);
#endif
- bool abort, svg;
+ bool abort, svg, save;
string fastafile, templatefile, namefile, outputDir;
int processors, increment, ksize, numSeqs, templateSeqsLength;
Chimera* chimera;