added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / chimerapintailcommand.cpp

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index 33ac69a37a33e6cb3b6e2993850ae7611f5f5a74..c5c678e78a344eed06ea0308c0df6178e7f22a51 100644 (file)
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -69,6 +69,27 @@ string ChimeraPintailCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string ChimeraPintailCommand::getOutputFileNameTag(string type, string inputName=""){  
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "chimera") {  outputFileName =  "pintail.chimeras"; }
+            else if (type == "accnos") {  outputFileName =  "pintail.accnos"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChimeraPintailCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 ChimeraPintailCommand::ChimeraPintailCommand(){        
        try {
                abort = true; calledHelp = true;
@@ -225,13 +246,13 @@ 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); 
@@ -397,11 +418,11 @@ int ChimeraPintailCommand::execute(){
                        if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it
                        string outputFileName, accnosFileName;
                        if (maskfile != "") {
-                               outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + ".pintail.chimeras";
-                               accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + ".pintail.accnos";
+                               outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + getOutputFileNameTag("chimera");
+                               accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + getOutputFileNameTag("accnos");
                        }else {
-                               outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "pintail.chimeras";
-                               accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "pintail.accnos";
+                               outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("chimera");
+                               accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("accnos");
                        }
                        
                        if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) {        m->mothurRemove(outputNames[j]);        }  return 0;    }
@@ -416,7 +437,7 @@ 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 +507,15 @@ 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)
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+                               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 +553,7 @@ 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; }
@@ -609,8 +632,8 @@ int ChimeraPintailCommand::driver(linePair* filePos, string outputFName, string
                        }
                        delete candidateSeq;
                        
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                               unsigned long int pos = inFASTA.tellg();
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+                               unsigned long long pos = inFASTA.tellg();
                                if ((pos == -1) || (pos >= filePos->end)) { break; }
                        #else
                                if (inFASTA.eof()) { break; }
@@ -635,7 +658,7 @@ 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; 
@@ -695,7 +718,7 @@ int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fi
 
 int ChimeraPintailCommand::createProcesses(string outputFileName, string filename, string accnos) {
        try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                int process = 0;
                int num = 0;