added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / chimeracheckcommand.cpp

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 2b88eb5736bfd37364461facb043b0db76aa3cfc..9f53b1753903a44b469f0766a261894cb3177476 100644 (file)
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -281,7 +281,7 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
 
                        string 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, "save", false);                     if (temp == "not found"){       temp = "f";                             }
                        save = m->isTrue(temp); 
@@ -306,14 +306,14 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
                        
                        
                        temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
-                       convert(temp, ksize);
+                       m->mothurConvert(temp, ksize);
                        
                        temp = validParameter.validFile(parameters, "svg", false);                              if (temp == "not found") { temp = "F"; }
                        svg = m->isTrue(temp);
                        if (nameFileNames.size() != 0) { svg = true; }
                        
                        temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "10"; }
-                       convert(temp, increment);                       
+                       m->mothurConvert(temp, increment);                      
                }
        }
        catch(exception& e) {
@@ -349,7 +349,7 @@ int ChimeraCheckCommand::execute(){
                
                                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
@@ -424,14 +424,16 @@ int ChimeraCheckCommand::execute(){
                                MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
                #else
                        
-                       vector<unsigned long int> positions = m->divideFile(fastaFileNames[i], processors);
-                               
-                       for (int s = 0; s < (positions.size()-1); s++) {
-                               lines.push_back(new linePair(positions[s], positions[(s+1)]));
-                       }       
+                       
                        
                        //break up file
                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                               vector<unsigned long long> positions = m->divideFile(fastaFileNames[i], processors);
+                       
+                               for (int s = 0; s < (positions.size()-1); s++) {
+                                       lines.push_back(new linePair(positions[s], positions[(s+1)]));
+                               }       
+                       
                                if(processors == 1){
                                        numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]);
                                        
@@ -459,6 +461,7 @@ int ChimeraCheckCommand::execute(){
                                }
 
                        #else
+                               lines.push_back(new linePair(0, 1000));
                                numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]);
                                
                                if (m->control_pressed) { for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear(); for (int j = 0; j < outputNames.size(); j++) {  m->mothurRemove(outputNames[j]);        } outputTypes.clear(); delete chimera; return 0; }
@@ -520,7 +523,7 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi
                        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; }
@@ -544,7 +547,7 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi
 }
 //**********************************************************************************************************************
 #ifdef USE_MPI
-int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos){
+int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long long>& MPIPos){
        try {
                MPI_File outAccMPI;
                MPI_Status status;