added normalize.shared command

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index d98a4cfc9f5bd27847f342434a7fda7ad817741a..c3080d9ed8785e0b62ecb1e03f27583425beb5d9 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -220,10 +220,10 @@ int ScreenSeqsCommand::execute(){
                                numSeqsPerProcessor = numFastaSeqs / processors;
                                int startIndex =  pid * numSeqsPerProcessor;
                                if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
-                               
+                       cout << pid << '\t' << numSeqsPerProcessor << '\t' <<   startIndex << endl;
                                //align your part
                                driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
-
+                       cout << pid << " done" << endl;
                                if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos);  return 0; }
 
                                for (int i = 1; i < processors; i++) {
@@ -253,10 +253,10 @@ int ScreenSeqsCommand::execute(){
                                numSeqsPerProcessor = numFastaSeqs / processors;
                                int startIndex =  pid * numSeqsPerProcessor;
                                if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
-                               
+               cout << pid << '\t' << numSeqsPerProcessor << '\t' <<   startIndex << endl;             
                                //align your part
                                driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
-
+cout << pid << " done" << endl;
                                if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos); return 0; }
                                
                                //send bad list 
@@ -421,7 +421,7 @@ int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
                outputNames.push_back(goodNameFile); 
                
                ofstream goodNameOut;   m->openOutputFile(goodNameFile, goodNameOut);
-               
+       
                while(!inputNames.eof()){
                        if (m->control_pressed) { goodNameOut.close();  inputNames.close(); remove(goodNameFile.c_str());  return 0; }
 
@@ -449,7 +449,7 @@ int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
                }
                inputNames.close();
                goodNameOut.close();
-               
+       
                //we were unable to remove some of the bad sequences
                if (badSeqNames.size() != 0) {
                        for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {