+ MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
+ MPI_File_open(MPI_COMM_WORLD, sumFileName, outMode, MPI_INFO_NULL, &outMPI);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; }
+
+ if (pid == 0) { //you are the root process
+ //print header
+ string outputString = "seqname\tstart\tend\tnbases\tambigs\tpolymer\n";
+ int length = outputString.length();
+ char* buf2 = new char[length];
+ memcpy(buf2, outputString.c_str(), length);
+
+ MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &statusOut);
+ delete buf2;
+
+ MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
+
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+ MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+ }
+
+ //figure out how many sequences you have to do
+ numSeqsPerProcessor = numSeqs / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
+
+ //do your part
+ MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
+
+ }else { //i am the child process
+
+ MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+ MPIPos.resize(numSeqs+1);
+ MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
+
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = numSeqs / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
+
+ //do your part
+ MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
+ }
+
+ MPI_File_close(&inMPI);
+ MPI_File_close(&outMPI);
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+
+ if (pid == 0) {
+ //get the info from the child processes
+ for(int i = 1; i < processors; i++) {
+ int size;
+ MPI_Recv(&size, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);