made a small mod to the alignment parameters in trim.seqs

[mothur.git] / chimeraccodecommand.cpp

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index cc046ea3dcd44c5443434d84493025791ab2910e..280fd8f0acf60c045f732ac07172476c7f9ab29e 100644 (file)
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -233,8 +233,10 @@ int ChimeraCcodeCommand::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;
@@ -253,9 +255,9 @@ int ChimeraCcodeCommand::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;
@@ -276,6 +278,8 @@ int ChimeraCcodeCommand::execute(){
                        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) {
                                if (!MPIWroteAccnos) { 
@@ -300,7 +304,7 @@ int ChimeraCcodeCommand::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));
@@ -389,7 +393,7 @@ int ChimeraCcodeCommand::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));