Dist* distCalculator;
SequenceDB alignDB;
- string countends, output, fastafile, calc, outputDir;
- int processors;
+ string countends, output, fastafile, calc, outputDir, oldfastafile, column;
+ int processors, numNewFasta;
float cutoff;
map<int, int> processIDS; //end line, processid
vector<linePair*> lines;
//void appendFiles(string, string);
void createProcesses(string);
int driver(/*Dist*, SequenceDB, */int, int, string, float);
+
+ #ifdef USE_MPI
+ int driverMPI(int, int, MPI_File&, float);
+ int driverMPI(int, int, string, long&);
+ #endif
+
int convertMatrix(string);
+ bool sanityCheck();
+ int convertToLowerTriangle(string);
};