X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerapintailcommand.cpp;h=3eb6589a83beebf79f8cf812ce519b35d0bcc37e;hb=0ca63a8165baa0afa459e644ebe140ba496d5ba0;hp=01a905f40d4c69514230ad033367cc02982cd3db;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index 01a905f..3eb6589 100644
--- 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); 
@@ -392,7 +392,6 @@ int ChimeraPintailCommand::execute(){
 					}
 				}
 			}
-			
 			chimera = new Pintail(fastaFileNames[s], templatefile, filter, processors, maskfile, consfile, quanfile, window, increment, outputDir);
 			
 			if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it
@@ -417,7 +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
@@ -487,14 +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);
@@ -532,6 +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; }
@@ -611,7 +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; }
@@ -636,7 +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;