added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / chimerapintailcommand.cpp

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index 33ac69a37a33e6cb3b6e2993850ae7611f5f5a74..3eb6589a83beebf79f8cf812ce519b35d0bcc37e 100644 (file)
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -225,13 +225,13 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "0"; }
-                       convert(temp, window);
+                       m->mothurConvert(temp, window);
                        
                        temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "25"; }
-                       convert(temp, increment);
+                       m->mothurConvert(temp, increment);
                        
                        temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
                        save = m->isTrue(temp); 
@@ -416,7 +416,7 @@ int ChimeraPintailCommand::execute(){
                #ifdef USE_MPI
                        int pid, numSeqsPerProcessor; 
                                int tag = 2001;
-                               vector<unsigned long int> MPIPos;
+                               vector<unsigned long long> MPIPos;
                                
                                MPI_Status status; 
                                MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
@@ -486,14 +486,15 @@ int ChimeraPintailCommand::execute(){
                                MPI_File_close(&outMPIAccnos);
                                MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
                #else
-                       vector<unsigned long int> positions = m->divideFile(fastaFileNames[s], processors);
-                               
-                       for (int i = 0; i < (positions.size()-1); i++) {
-                               lines.push_back(new linePair(positions[i], positions[(i+1)]));
-                       }       
-                       
+                                               
                        //break up file
                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                               vector<unsigned long long> positions = m->divideFile(fastaFileNames[s], processors);
+                       
+                               for (int i = 0; i < (positions.size()-1); i++) {
+                                       lines.push_back(new linePair(positions[i], positions[(i+1)]));
+                               }       
+                       
                                if(processors == 1){
                
                                        numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
@@ -531,6 +532,7 @@ int ChimeraPintailCommand::execute(){
                                }
 
                        #else
+                               lines.push_back(new linePair(0, 1000));
                                numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
                                
                                if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]);        } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear(); delete chimera; return 0; }
@@ -610,7 +612,7 @@ int ChimeraPintailCommand::driver(linePair* filePos, string outputFName, string
                        delete candidateSeq;
                        
                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                               unsigned long int pos = inFASTA.tellg();
+                               unsigned long long pos = inFASTA.tellg();
                                if ((pos == -1) || (pos >= filePos->end)) { break; }
                        #else
                                if (inFASTA.eof()) { break; }
@@ -635,7 +637,7 @@ int ChimeraPintailCommand::driver(linePair* filePos, string outputFName, string
 }
 //**********************************************************************************************************************
 #ifdef USE_MPI
-int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<unsigned long int>& MPIPos){
+int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<unsigned long long>& MPIPos){
        try {
                                
                MPI_Status status;