\r
public:\r
FilterSeqsCommand(string);\r
+ FilterSeqsCommand();\r
~FilterSeqsCommand() {};\r
+ vector<string> getRequiredParameters();\r
+ vector<string> getValidParameters();\r
+ vector<string> getRequiredFiles();\r
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }\r
int execute(); \r
void help();\r
\r
private:\r
struct linePair {\r
- int start;\r
- int num;\r
- linePair(long int i, long int j) : start(i), num(j) {}\r
+ unsigned long int start;\r
+ unsigned long int end;\r
+ linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}\r
};\r
+\r
vector<linePair*> lines;\r
vector<int> processIDS;\r
\r
int alignmentLength, processors;\r
vector<int> bufferSizes;\r
vector<string> outputNames;\r
+ map<string, vector<string> > outputTypes;\r
\r
char trump;\r
bool abort;\r
int driverRunFilter(string, string, string, linePair*);\r
int driverCreateFilter(Filters& F, string filename, linePair* line);\r
#ifdef USE_MPI\r
- int driverMPIRun(int, int, MPI_File&, MPI_File&, vector<long>&);\r
- int MPICreateFilter(int, int, Filters&, MPI_File&, vector<long>&); \r
+ int driverMPIRun(int, int, MPI_File&, MPI_File&, vector<unsigned long int>&);\r
+ int MPICreateFilter(int, int, Filters&, MPI_File&, vector<unsigned long int>&); \r
#endif\r
- int setLines(string);\r
- \r
\r
};\r
\r