added pcr.seqs command. fixed bug in rarefacftion.single that caused parsing error...

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 78bd73b45bfa6e5bc1337eb81cd783d9a6f1ec82..f22975ec56ed288026ca4681a223cad66b206137 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -67,6 +67,13 @@ ShhherCommand::ShhherCommand(){
 
 ShhherCommand::ShhherCommand(string option) {
        try {
+        
+#ifdef USE_MPI
+               MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+               MPI_Comm_size(MPI_COMM_WORLD, &ncpus);
+        
+               if(pid == 0){
+#endif
                abort = false; calledHelp = false;   
                
                //allow user to run help
@@ -314,6 +321,9 @@ ShhherCommand::ShhherCommand(string option) {
                        }
                        
                }
+#ifdef USE_MPI
+               }                               
+#endif
        }
        catch(exception& e) {
                m->errorOut(e, "ShhherCommand", "ShhherCommand");
@@ -328,9 +338,7 @@ int ShhherCommand::execute(){
                
                int tag = 1976;
                MPI_Status status; 
-               MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-               MPI_Comm_size(MPI_COMM_WORLD, &ncpus);
-        
+                       
                if(pid == 0){
 
                        for(int i=1;i<ncpus;i++){
@@ -344,6 +352,22 @@ int ShhherCommand::execute(){
                        getSingleLookUp();      if (m->control_pressed) { return 0; }
                        getJointLookUp();       if (m->control_pressed) { return 0; }
                        
+            vector<string> flowFileVector;
+                       if(flowFilesFileName != "not found"){
+                               string fName;
+                
+                               ifstream flowFilesFile;
+                               m->openInputFile(flowFilesFileName, flowFilesFile);
+                               while(flowFilesFile){
+                                       fName = m->getline(flowFilesFile);
+                                       flowFileVector.push_back(fName);
+                                       m->gobble(flowFilesFile);
+                               }
+                       }
+                       else{
+                               flowFileVector.push_back(flowFileName);
+                       }
+            
                        int numFiles = flowFileVector.size();
 
                        for(int i=1;i<ncpus;i++){
@@ -3042,11 +3066,13 @@ void ShhherCommand::writeQualities(int numOTUs, int numFlowCells, string filenam
                        
                        if(otuCounts[i] > 0){
                                qualityFile << '>' << seqNameVector[mapUniqueToSeq[i]] << endl;
-                               
+                       
                                int j=4;        //need to get past the first four bases
                                while(qualities[i][j] != -1){
-                                       qualityFile << qualities[i][j] << ' ';
-                                       j++;
+                    //cout << i << '\t' << j << '\t' << qualities[i][j] << endl;
+                    qualityFile << qualities[i][j] << ' ';
+                    j++;
+                    
                                }
                                qualityFile << endl;
                        }