changed how we count sequences in a fastafile to allow for '>' in sequence names

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 435cd301a53c42b0e00765d588c681f98da5dfed..004cfb0c9e1124cd5ad78c542c6df3815bd4541d 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -261,8 +261,10 @@ int ChimeraSlayerCommand::execute(){
                                MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
                                
                                //send file positions to all processes
-                               MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
-                               MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos        
+                               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 align
                                numSeqsPerProcessor = numSeqs / processors;
@@ -281,16 +283,15 @@ int ChimeraSlayerCommand::execute(){
                                        if (tempResult != 0) { MPIWroteAccnos = true; }
                                }
                        }else{ //you are a child process
-                               MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
+                               MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
                                MPIPos.resize(numSeqs+1);
-                               MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+                               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;      }
                                
-                               
                                //align your part
                                driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
                                
@@ -303,6 +304,7 @@ int ChimeraSlayerCommand::execute(){
                        MPI_File_close(&inMPI);
                        MPI_File_close(&outMPI);
                        MPI_File_close(&outMPIAccnos);
+                       MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
                        
                        //delete accnos file if blank
                        if (pid == 0) {
@@ -327,7 +329,7 @@ int ChimeraSlayerCommand::execute(){
                        if(processors == 1){
                                ifstream inFASTA;
                                openInputFile(fastafile, inFASTA);
-                               numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                               getNumSeqs(inFASTA, numSeqs);
                                inFASTA.close();
                                
                                lines.push_back(new linePair(0, numSeqs));
@@ -374,7 +376,6 @@ int ChimeraSlayerCommand::execute(){
                                        lines.push_back(new linePair(startPos, numSeqsPerProcessor));
                                }
                                
-                               
                                createProcesses(outputFileName, fastafile, accnosFileName); 
                        
                                rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
@@ -416,7 +417,7 @@ int ChimeraSlayerCommand::execute(){
                #else
                        ifstream inFASTA;
                        openInputFile(fastafile, inFASTA);
-                       numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                       getNumSeqs(inFASTA, numSeqs);
                        inFASTA.close();
                        lines.push_back(new linePair(0, numSeqs));