};
vector<int> processIDS; //processid
vector<linePair*> lines;
+ bool MPIWroteAccnos;
AlignmentDB* templateDB;
Alignment* alignment;
int driver(linePair*, string, string, string, string);
- void createProcesses(string, string, string, string);
+ int createProcesses(string, string, string, string);
void appendAlignFiles(string, string);
void appendReportFiles(string, string);
- string candidateFileName, templateFileName, distanceFileName, search, align;
+ #ifdef USE_MPI
+ int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<long>&);
+ #endif
+
+ string candidateFileName, templateFileName, distanceFileName, search, align, outputDir;
float match, misMatch, gapOpen, gapExtend, threshold;
int processors, kmerSize;
vector<string> candidateFileNames;