class SeqSummaryCommand : public Command {
public:
SeqSummaryCommand(string);
+ SeqSummaryCommand();
~SeqSummaryCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
bool abort;
string fastafile, outputDir;
int processors;
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
struct linePair {
- int start;
- int num;
- linePair(long int i, long int j) : start(i), num(j) {}
+ unsigned long int start;
+ unsigned long int end;
+ linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
};
+
vector<linePair*> lines;
vector<int> processIDS;
int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string);
int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string, linePair*);
- int setLines(string);
#ifdef USE_MPI
- int MPICreateSummary(int, int, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, MPI_File&, MPI_File&, vector<long>&);
+ int MPICreateSummary(int, int, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, MPI_File&, MPI_File&, vector<unsigned long int>&);
#endif