trim.seqs fix

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index b2b4de0559feff2074fb6269b6e18a8dafb9d6e4..066a9c51f26b764f14fa3f9490e094748ad3e7b6 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -250,9 +250,6 @@ int ShhherCommand::execute(){
                int tag = 1976;
                MPI_Status status; 
 
-               double begClock = clock();
-               unsigned long int begTime = time(NULL);
-               
                if(pid == 0){
 
                        for(int i=1;i<ncpus;i++){
@@ -288,9 +285,10 @@ int ShhherCommand::execute(){
                        }
                        
                        for(int i=0;i<numFiles;i++){
-                               flowFileName = flowFileVector[i];
+                               double begClock = clock();
+                               unsigned long int begTime = time(NULL);
 
-                               
+                               flowFileName = flowFileVector[i];
                                
                                m->mothurOut("\n>>>>>\tProcessing " + flowFileName + " (file " + toString(i+1) + " of " + toString(numFiles) + ")\t<<<<<\n");
                                m->mothurOut("Reading flowgrams...\n");
@@ -370,7 +368,7 @@ int ShhherCommand::execute(){
                                                MPI_Send(&nSeqsPerOTU[0], numOTUs, MPI_INT, i, tag, MPI_COMM_WORLD);
                                                MPI_Send(&cumNumSeqs[0], numOTUs, MPI_INT, i, tag, MPI_COMM_WORLD);
                                        }
-                               
+                                       
                                        calcCentroidsDriver(0, numOTUsOnCPU);
                                        
                                        for(int i=1;i<ncpus;i++){
@@ -489,7 +487,6 @@ int ShhherCommand::execute(){
                }
                else{
                        int abort = 1;
-                       bool live = 1;
 
                        MPI_Recv(&abort, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
                        if(abort){      return 0;       }
@@ -499,6 +496,8 @@ int ShhherCommand::execute(){
 
                        for(int i=0;i<numFiles;i++){
                                //Now into the pyrodist part
+                               bool live = 1;
+
                                char fileName[1024];
                                MPI_Recv(&fileName, 1024, MPI_CHAR, 0, tag, MPI_COMM_WORLD, &status);
                                MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
@@ -554,12 +553,12 @@ int ShhherCommand::execute(){
                                int total;
 
                                while(live){
-
+                                       
                                        MPI_Recv(&total, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
                                        singleTau.assign(total, 0.0000);
                                        seqNumber.assign(total, 0);
                                        seqIndex.assign(total, 0);
-                                       
+
                                        MPI_Recv(&change[0], numOTUs, MPI_SHORT, 0, tag, MPI_COMM_WORLD, &status);
                                        MPI_Recv(&centroids[0], numOTUs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
                                        MPI_Recv(&singleTau[0], total, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
@@ -567,13 +566,12 @@ int ShhherCommand::execute(){
                                        MPI_Recv(&seqIndex[0], total, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
                                        MPI_Recv(&nSeqsPerOTU[0], total, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
                                        MPI_Recv(&cumNumSeqs[0], numOTUs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
-                                       
+
                                        calcCentroidsDriver(startOTU, endOTU);
 
                                        MPI_Send(&centroids[0], numOTUs, MPI_INT, 0, tag, MPI_COMM_WORLD);
                                        MPI_Send(&change[0], numOTUs, MPI_SHORT, 0, tag, MPI_COMM_WORLD);
 
-                                       
                                        MPI_Recv(&centroids[0], numOTUs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
                                        MPI_Recv(&weight[0], numOTUs, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
                                        MPI_Recv(&change[0], numOTUs, MPI_SHORT, 0, tag, MPI_COMM_WORLD, &status);
@@ -592,8 +590,8 @@ int ShhherCommand::execute(){
                                }
                        }
                }               
-
                MPI_Barrier(MPI_COMM_WORLD);
+
                return 0;
 
        }
@@ -704,10 +702,6 @@ int ShhherCommand::execute(){
                        double begClock = clock();
                        unsigned long int begTime = time(NULL);
 
-                       
-                       cout << numOTUs << endl;
-                       
-                       
                        m->mothurOut("\nDenoising flowgrams...\n");
                        m->mothurOut("iter\tmaxDelta\tnLL\t\tcycletime\n");
                        
@@ -1282,12 +1276,6 @@ void ShhherCommand::getOTUData(string listFileName){
                
                listFile.close();       
                
-               for(int i=0;i<seqNumber.size();i++){
-                       cout << seqNumber[i] << ' ';
-               }
-               cout << endl;
-               
-               
        }
        catch(exception& e) {
                m->errorOut(e, "ShhherCommand", "getOTUData");
@@ -1308,8 +1296,6 @@ void ShhherCommand::initPyroCluster(){
                nSeqsBreaks.assign(processors+1, 0);
                nOTUsBreaks.assign(processors+1, 0);
 
-               cout << numSeqs << '\t' << numOTUs << '\t' << processors << endl;
-               
                nSeqsBreaks[0] = 0;
                for(int i=0;i<processors;i++){
                        nSeqsBreaks[i+1] = nSeqsBreaks[i] + (int)((double) numSeqs / (double) processors);
@@ -1408,10 +1394,7 @@ void ShhherCommand::calcCentroidsDriver(int start, int finish){
        
        try{
                
-//             for(int i=0;i<seqNumber.size();i++){
-//                     cout << seqNumber[i] << ' ';
-//             }cout << endl;
-               
+       
                for(int i=start;i<finish;i++){
                        
                        double count = 0;