+ if (pid == 0) { //you are the root process
+
+ MPIPos = setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
+ numSeqs += num;
+
+ //send file positions to all processes
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+ MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+ }
+
+ //figure out how many sequences you have to do
+ numSeqsPerProcessor = num / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; }
+
+
+ //do your part
+ driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; }
+
+ //wait on chidren
+ for(int i = 1; i < processors; i++) {
+ char buf[4];
+ MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
+ }
+
+ }else { //you are a child process
+ MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
+ MPIPos.resize(num+1);
+ numSeqs += num;
+ MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
+
+ //figure out how many sequences you have to align
+ numSeqsPerProcessor = num / processors;
+ int startIndex = pid * numSeqsPerProcessor;
+ if(pid == (processors - 1)){ numSeqsPerProcessor = num - pid * numSeqsPerProcessor; }
+
+
+ //align your part
+ driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
+
+ if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; }
+
+ char buf[4];
+ strcpy(buf, "done");
+
+ //tell parent you are done.
+ MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
+ }
+
+ MPI_File_close(&outMPI);
+ MPI_File_close(&inMPI);
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+
+#else
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ ifstream inFASTA;
+ int numFastaSeqs;
+ openInputFile(fastafileNames[s], inFASTA);
+ getNumSeqs(inFASTA, numFastaSeqs);
+ inFASTA.close();
+
+ lines.push_back(new linePair(0, numFastaSeqs));
+
+ numSeqs += numFastaSeqs;
+
+ driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
+ }else{
+ setLines(fastafileNames[s]);
+ createProcessesRunFilter(filter, fastafileNames[s]);
+
+ rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str());
+
+ //append fasta files
+ for(int i=1;i<processors;i++){
+ appendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta);
+ remove((fastafileNames[s] + toString(processIDS[i]) + ".temp").c_str());
+ }
+ }
+
+ if (m->control_pressed) { return 1; }
+ #else
+ ifstream inFASTA;
+ int numFastaSeqs;
+ openInputFile(fastafileNames[s], inFASTA);
+ getNumSeqs(inFASTA, numFastaSeqs);
+ inFASTA.close();
+
+ lines.push_back(new linePair(0, numFastaSeqs));
+
+ numSeqs += numFastaSeqs;
+
+ driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
+
+ if (m->control_pressed) { return 1; }
+ #endif
+#endif
+ outputNames.push_back(filteredFasta);
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "filterSequences");
+ exit(1);
+ }
+}
+#ifdef USE_MPI
+/**************************************************************************************/
+int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<long>& MPIPos) {
+ try {
+ string outputString = "";
+ int count = 0;
+ MPI_Status status;
+
+ for(int i=0;i<num;i++){
+
+ if (m->control_pressed) { return 0; }
+
+ //read next sequence
+ int length = MPIPos[start+i+1] - MPIPos[start+i];
+ char* buf4 = new char[length];
+ MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
+
+ string tempBuf = buf4;
+ if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
+ istringstream iss (tempBuf,istringstream::in);
+ delete buf4;