vector<string> setParameters();
string getCommandName() { return "chimera.ccode"; }
string getCommandCategory() { return "Sequence Processing"; }
+
string getHelpString();
- string getCitation() { return "Evaluating putative chimeric sequences from PCR-amplified products' paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez. http://www.mothur.org/wiki/Chimera.ccode"; }
+ string getOutputPattern(string);
+ string getCitation() { return "Gonzalez JM, Zimmermann J, Saiz-Jimenez C (2005). Evaluating putative chimeric sequences from PCR-amplified products. Bioinformatics 21: 333-7. \nhttp://www.mothur.org/wiki/Chimera.ccode"; }
+ 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
vector<linePair*> lines;
int createProcesses(string, string, string);
#ifdef USE_MPI
- int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
+ int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&);
#endif
- bool abort, filter;
+ bool abort, filter, save;
string fastafile, templatefile, outputDir, maskfile;
int processors, window, numwanted, numSeqs, templateSeqsLength;
Chimera* chimera;