};
vector<int> processIDS; //processid
vector<linePair*> lines;
+ bool MPIWroteAccnos;
AlignmentDB* templateDB;
Alignment* alignment;
void appendAlignFiles(string, string);
void appendReportFiles(string, string);
+ #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;