public:
AlignCommand(string);
+ AlignCommand();
~AlignCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
private:
struct linePair {
- int start;
- int numSeqs;
- linePair(long int i, int j) : start(i), numSeqs(j) {}
+ unsigned long int start;
+ unsigned long int end;
+ linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
};
vector<int> processIDS; //processid
vector<linePair*> lines;
bool MPIWroteAccnos;
+ map<string, vector<string> > outputTypes;
AlignmentDB* templateDB;
Alignment* alignment;
void appendReportFiles(string, string);
#ifdef USE_MPI
- int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<long>&);
+ int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
#endif
string candidateFileName, templateFileName, distanceFileName, search, align, outputDir;
float match, misMatch, gapOpen, gapExtend, threshold;
int processors, kmerSize;
vector<string> candidateFileNames;
+ vector<string> outputNames;
bool abort, flip;
};