chimeraccodecommand.cpp

/*
 *  chimeraccodecommand.cpp
 *  Mothur
 *
 *  Created by westcott on 3/30/10.
 *  Copyright 2010 Schloss Lab. All rights reserved.
 *
 */

#include "chimeraccodecommand.h"
#include "ccode.h"
#include "referencedb.h"
//**********************************************************************************************************************
vector<string> ChimeraCcodeCommand::setParameters(){	
	try {
		CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera-mapinfo-accnos",false,true,true); parameters.push_back(pfasta);
		CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfilter);
		CommandParameter pwindow("window", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pwindow);
		CommandParameter pnumwanted("numwanted", "Number", "", "20", "", "", "","",false,false); parameters.push_back(pnumwanted);
		CommandParameter pmask("mask", "String", "", "", "", "", "","",false,false); parameters.push_back(pmask);
		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
		CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
		
		vector<string> myArray;
		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
		return myArray;
	}
	catch(exception& e) {
		m->errorOut(e, "ChimeraCcodeCommand", "setParameters");
		exit(1);
	}
}
//**********************************************************************************************************************
string ChimeraCcodeCommand::getHelpString(){	
	try {
		string helpString = "";
		helpString += "The chimera.ccode command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
		helpString += "This command was created using the algorithms described in the 'Evaluating putative chimeric sequences from PCR-amplified products' paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.\n";
		helpString += "The chimera.ccode command parameters are fasta, reference, filter, mask, processors, window and numwanted.\n";
		helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required unless you have a valid current fasta file. \n";
		helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
		helpString += "The reference parameter allows you to enter a reference file containing known non-chimeric sequences, and is required. \n";
		helpString += "The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter. \n";
		helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
#ifdef USE_MPI
		helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
#endif
		helpString += "The mask parameter allows you to specify a file containing one sequence you wish to use as a mask for the your sequences. \n";
		helpString += "The window parameter allows you to specify the window size for searching for chimeras. \n";
		helpString += "The numwanted parameter allows you to specify how many sequences you would each query sequence compared with.\n";
		helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
		helpString += "The chimera.ccode command should be in the following format: \n";
		helpString += "chimera.ccode(fasta=yourFastaFile, reference=yourTemplate) \n";
		helpString += "Example: chimera.ccode(fasta=AD.align, reference=core_set_aligned.imputed.fasta) \n";
		helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";	
		return helpString;
	}
	catch(exception& e) {
		m->errorOut(e, "ChimeraCcodeCommand", "getHelpString");
		exit(1);
	}
}
//**********************************************************************************************************************
string ChimeraCcodeCommand::getOutputPattern(string type) {
    try {
        string pattern = "";
        
        if (type == "chimera") {  pattern = "[filename],[tag],ccode.chimeras-[filename],ccode.chimeras"; } 
        else if (type == "accnos") {  pattern = "[filename],[tag],ccode.accnos-[filename],ccode.accnos"; } 
        else if (type == "mapinfo") {  pattern =  "[filename],mapinfo"; }
        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
        
        return pattern;
    }
    catch(exception& e) {
        m->errorOut(e, "ChimeraCcodeCommand", "getOutputPattern");
        exit(1);
    }
}
//**********************************************************************************************************************
ChimeraCcodeCommand::ChimeraCcodeCommand(){	
	try {
		abort = true; calledHelp = true;
		setParameters();
		vector<string> tempOutNames;
		outputTypes["chimera"] = tempOutNames;
		outputTypes["mapinfo"] = tempOutNames;
		outputTypes["accnos"] = tempOutNames;
        
	}
	catch(exception& e) {
		m->errorOut(e, "ChimeraCcodeCommand", "ChimeraCcodeCommand");
		exit(1);
	}
}
//***************************************************************************************************************
ChimeraCcodeCommand::ChimeraCcodeCommand(string option)  {
	try {
		abort = false; calledHelp = false;   
		ReferenceDB* rdb = ReferenceDB::getInstance();
		
		//allow user to run help
		if(option == "help") { help(); abort = true; calledHelp = true; }
		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
		
		else {
			vector<string> myArray = setParameters();
			
			OptionParser parser(option);
			map<string,string> parameters = parser.getParameters();
			
			ValidParameters validParameter("chimera.ccode");
			map<string,string>::iterator it;
			
			//check to make sure all parameters are valid for command
			for (it = parameters.begin(); it != parameters.end(); it++) { 
				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
			}
			
			vector<string> tempOutNames;
			outputTypes["chimera"] = tempOutNames;
			outputTypes["mapinfo"] = tempOutNames;
			outputTypes["accnos"] = tempOutNames;
            
			
			//if the user changes the input directory command factory will send this info to us in the output parameter 
			string inputDir = validParameter.validFile(parameters, "inputdir", false);		
			if (inputDir == "not found"){	inputDir = "";		}
			else {
				string path;
				it = parameters.find("reference");
				//user has given a template file
				if(it != parameters.end()){ 
					path = m->hasPath(it->second);
					//if the user has not given a path then, add inputdir. else leave path alone.
					if (path == "") {	parameters["reference"] = inputDir + it->second;		}
				}
			}

			//check for required parameters
			fastafile = validParameter.validFile(parameters, "fasta", false);
			if (fastafile == "not found") { 				//if there is a current fasta file, use it
				string filename = m->getFastaFile(); 
				if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
				else { 	m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
			}else { 
				m->splitAtDash(fastafile, fastaFileNames);
				
				//go through files and make sure they are good, if not, then disregard them
				for (int i = 0; i < fastaFileNames.size(); i++) {
					
					bool ignore = false;
					if (fastaFileNames[i] == "current") { 
						fastaFileNames[i] = m->getFastaFile(); 
						if (fastaFileNames[i] != "") {  m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
						else { 	
							m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true; 
							//erase from file list
							fastaFileNames.erase(fastaFileNames.begin()+i);
							i--;
						}
					}
					
					if (!ignore) {
					
						if (inputDir != "") {
							string path = m->hasPath(fastaFileNames[i]);
							//if the user has not given a path then, add inputdir. else leave path alone.
							if (path == "") {	fastaFileNames[i] = inputDir + fastaFileNames[i];		}
						}
		
						int ableToOpen;
						ifstream in;
						
						ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
					
						//if you can't open it, try default location
						if (ableToOpen == 1) {
							if (m->getDefaultPath() != "") { //default path is set
								string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
								m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
								ifstream in2;
								ableToOpen = m->openInputFile(tryPath, in2, "noerror");
								in2.close();
								fastaFileNames[i] = tryPath;
							}
						}
						
						//if you can't open it, try default location
						if (ableToOpen == 1) {
							if (m->getOutputDir() != "") { //default path is set
								string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
								m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
								ifstream in2;
								ableToOpen = m->openInputFile(tryPath, in2, "noerror");
								in2.close();
								fastaFileNames[i] = tryPath;
							}
						}
						
						in.close();
						
						if (ableToOpen == 1) { 
							m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); 
							//erase from file list
							fastaFileNames.erase(fastaFileNames.begin()+i);
							i--;
						}else {
							m->setFastaFile(fastaFileNames[i]);
						}
					}
				}
				
				//make sure there is at least one valid file left
				if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
			}
			
			//if the user changes the output directory command factory will send this info to us in the output parameter 
			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = "";	}
			
			maskfile = validParameter.validFile(parameters, "mask", false);
			if (maskfile == "not found") { maskfile = "";  }	
			else if (maskfile != "default")  { 
				if (inputDir != "") {
					string path = m->hasPath(maskfile);
					//if the user has not given a path then, add inputdir. else leave path alone.
					if (path == "") {	maskfile = inputDir + maskfile;		}
				}

				ifstream in;
				int	ableToOpen = m->openInputFile(maskfile, in);
				if (ableToOpen == 1) { abort = true; }
				in.close();
			}
			
			string temp;
			temp = validParameter.validFile(parameters, "filter", false);			if (temp == "not found") { temp = "F"; }
			filter = m->isTrue(temp);
			
			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
			m->setProcessors(temp);
			m->mothurConvert(temp, processors);
			
			temp = validParameter.validFile(parameters, "window", false);			if (temp == "not found") { temp = "0"; }
			m->mothurConvert(temp, window);
			
			temp = validParameter.validFile(parameters, "numwanted", false);		if (temp == "not found") { temp = "20"; }
			m->mothurConvert(temp, numwanted);
			
			temp = validParameter.validFile(parameters, "save", false);			if (temp == "not found"){	temp = "f";				}
			save = m->isTrue(temp); 
			rdb->save = save; 
			if (save) { //clear out old references
				rdb->clearMemory();	
			}
			
			//this has to go after save so that if the user sets save=t and provides no reference we abort
			templatefile = validParameter.validFile(parameters, "reference", true);
			if (templatefile == "not found") { 
				//check for saved reference sequences
				if (rdb->referenceSeqs.size() != 0) {
					templatefile = "saved";
				}else {
					m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required."); 
					m->mothurOutEndLine();
					abort = true; 
				}
			}else if (templatefile == "not open") { abort = true; }	
			else {	if (save) {	rdb->setSavedReference(templatefile);	}	}
			

		}
	}
	catch(exception& e) {
		m->errorOut(e, "ChimeraCcodeCommand", "ChimeraCcodeCommand");
		exit(1);
	}
}
//***************************************************************************************************************
int ChimeraCcodeCommand::execute(){
	try{
		
		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
		
		for (int s = 0; s < fastaFileNames.size(); s++) {
				
			m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
		
			int start = time(NULL);	
			
			//set user options
			if (maskfile == "default") { m->mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); m->mothurOutEndLine();  }

			chimera = new Ccode(fastaFileNames[s], templatefile, filter, maskfile, window, numwanted, outputDir);	
			
			//is your template aligned?
			if (chimera->getUnaligned()) { m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); delete chimera; return 0; }
			templateSeqsLength = chimera->getLength();
			
			if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it
			string outputFileName, accnosFileName;
            map<string, string> variables; 
            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
            string mapInfo = getOutputFileName("mapinfo", variables);
			if (maskfile != "") { variables["[tag]"] = maskfile; }
            outputFileName = getOutputFileName("chimera", variables);
            accnosFileName = getOutputFileName("accnos", variables);
						
			if (m->control_pressed) { delete chimera;  for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	} outputTypes.clear(); return 0;	}
			
		#ifdef USE_MPI
		
				int pid, numSeqsPerProcessor; 
				int tag = 2001;
				vector<unsigned long long> MPIPos;
								
				MPI_Status status; 
				MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
				MPI_Comm_size(MPI_COMM_WORLD, &processors); 

				MPI_File inMPI;
				MPI_File outMPI;
				MPI_File outMPIAccnos;
				
				int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
				int inMode=MPI_MODE_RDONLY; 
				
				char outFilename[1024];
				strcpy(outFilename, outputFileName.c_str());
				
				char outAccnosFilename[1024];
				strcpy(outAccnosFilename, accnosFileName.c_str());
				
				char inFileName[1024];
				strcpy(inFileName, fastaFileNames[s].c_str());

				MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
				MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
				MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);

				if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	} outputTypes.clear();  delete chimera; return 0;  }
			
				if (pid == 0) { //you are the root process 
					string outTemp = "For full window mapping info refer to " + mapInfo + "\n";
					
					//print header
					int length = outTemp.length();
					char* buf2 = new char[length];
					memcpy(buf2, outTemp.c_str(), length);

					MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
					delete buf2;

					MPIPos = m->setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs
					
					//send file positions to all processes
					for(int i = 1; i < processors; i++) { 
						MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
						MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
					}
					
					//figure out how many sequences you have to align
					numSeqsPerProcessor = numSeqs / processors;
					int startIndex =  pid * numSeqsPerProcessor;
					if(pid == (processors - 1)){	numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; 	}
					
				
					//align your part
					driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
					
					if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  m->mothurRemove(outputFileName);  m->mothurRemove(accnosFileName);  for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	} outputTypes.clear();  delete chimera; return 0;  }

				}else{ //you are a child process
					MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
					MPIPos.resize(numSeqs+1);
					MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
					
					//figure out how many sequences you have to align
					numSeqsPerProcessor = numSeqs / processors;
					int startIndex =  pid * numSeqsPerProcessor;
					if(pid == (processors - 1)){	numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; 	}
					
					
					//align your part
					driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
					
					if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	}  outputTypes.clear(); delete chimera; return 0;  }
				}
				
				//close files 
				MPI_File_close(&inMPI);
				MPI_File_close(&outMPI);
				MPI_File_close(&outMPIAccnos);
				
				MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
					
		#else
			ofstream outHeader;
			string tempHeader = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + "ccode.chimeras.tempHeader";
			m->openOutputFile(tempHeader, outHeader);
			
			outHeader << "For full window mapping info refer to " << mapInfo << endl << endl;

			outHeader.close();
			
			
			
			//break up file
			#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);
					
					if (m->control_pressed) { m->mothurRemove(outputFileName); m->mothurRemove(tempHeader); 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];  } outputTypes.clear();  lines.clear(); delete chimera; return 0; }
					
				}else{
					processIDS.resize(0);
					
					numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName); 
				
					rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
					rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str());
						
					//append output files
					for(int i=1;i<processors;i++){
						m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
						m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp"));
					}
					
					//append output files
					for(int i=1;i<processors;i++){
						m->appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
						m->mothurRemove((accnosFileName + toString(processIDS[i]) + ".temp"));
					}
					
					if (m->control_pressed) { 
						m->mothurRemove(outputFileName); 
						m->mothurRemove(accnosFileName);
						for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	} outputTypes.clear();
						for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
						delete chimera;
						return 0;
					}

				}

			#else
				lines.push_back(new linePair(0, 1000));
				numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
				
				if (m->control_pressed) { m->mothurRemove(outputFileName); m->mothurRemove(tempHeader); 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];  } outputTypes.clear();  lines.clear(); delete chimera; return 0; }
				
			#endif
	
			m->appendFiles(outputFileName, tempHeader);
		
			m->mothurRemove(outputFileName);
			rename(tempHeader.c_str(), outputFileName.c_str());
		#endif
		
			delete chimera;
			
			outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
			outputNames.push_back(mapInfo);	outputTypes["mapinfo"].push_back(mapInfo);
			outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
			 
			for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
			
			m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences.");	m->mothurOutEndLine();
		}
		
		
		//set accnos file as new current accnosfile
		string current = "";
		itTypes = outputTypes.find("accnos");
		if (itTypes != outputTypes.end()) {
			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
		}
		
		m->mothurOutEndLine();
		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}	
		m->mothurOutEndLine();
		
		return 0;
		
	}
	catch(exception& e) {
		m->errorOut(e, "ChimeraCcodeCommand", "execute");
		exit(1);
	}
}
//**********************************************************************************************************************

int ChimeraCcodeCommand::driver(linePair* filePos, string outputFName, string filename, string accnos){
	try {
		ofstream out;
		m->openOutputFile(outputFName, out);
		
		ofstream out2;
		m->openOutputFile(accnos, out2);
		
		ifstream inFASTA;
		m->openInputFile(filename, inFASTA);

		inFASTA.seekg(filePos->start);

		bool done = false;
		int count = 0;
	
		while (!done) {
		
			if (m->control_pressed) {	return 1;	}
		
			Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
				
			if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
				
				if (candidateSeq->getAligned().length() != templateSeqsLength) {  
					m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
				}else{
					//find chimeras
					chimera->getChimeras(candidateSeq);
					
					if (m->control_pressed) {	delete candidateSeq; return 1;	}
		
					//print results
					chimera->print(out, out2);
				}
				count++;
			}
			delete candidateSeq;
			
			#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; }
			#endif
			
			//report progress
			if((count) % 100 == 0){	m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n");		}
		}
		//report progress
		if((count) % 100 != 0){	m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n");	}
		
		out.close();
		out2.close();
		inFASTA.close();
				
		return count;
	}
	catch(exception& e) {
		m->errorOut(e, "ChimeraCcodeCommand", "driver");
		exit(1);
	}
}
//**********************************************************************************************************************
#ifdef USE_MPI
int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<unsigned long long>& MPIPos){
	try {
				
		MPI_Status status; 
		int pid;
		MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
		
		for(int i=0;i<num;i++){
		
			if (m->control_pressed) { return 0; }
			
			//read next sequence
			int length = MPIPos[start+i+1] - MPIPos[start+i];
	
			char* buf4 = new char[length];
				
			MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
			
			string tempBuf = buf4;
			if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
			istringstream iss (tempBuf,istringstream::in);
			delete buf4;

			Sequence* candidateSeq = new Sequence(iss);  m->gobble(iss);
				
			if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
				
				if (candidateSeq->getAligned().length() != templateSeqsLength) {  
					m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
				}else{
					//find chimeras
					chimera->getChimeras(candidateSeq);
					
					if (m->control_pressed) {	delete candidateSeq; return 1;	}
		
					//print results
					chimera->print(outMPI, outAccMPI);
				}
			}
			delete candidateSeq;
			
			//report progress
			if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;	m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");		}
		}
		//report progress
		if(num % 100 != 0){		cout << "Processing sequence: " << num << endl;	m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n"); 	}
		
				
		return 0;
	}
	catch(exception& e) {
		m->errorOut(e, "ChimeraCcodeCommand", "driverMPI");
		exit(1);
	}
}
#endif

/**************************************************************************************************/

int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename, string accnos) {
	try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
		int process = 0;
		int num = 0;
		
		//loop through and create all the processes you want
		while (process != processors) {
			int pid = fork();
			
			if (pid > 0) {
				processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
				process++;
			}else if (pid == 0){
				num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp");
				
				//pass numSeqs to parent
				ofstream out;
				string tempFile = outputFileName + toString(getpid()) + ".num.temp";
				m->openOutputFile(tempFile, out);
				out << num << endl;
				out.close();

				exit(0);
			}else { 
				m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
				for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
				exit(0);
			}
		}
		
		//force parent to wait until all the processes are done
		for (int i=0;i<processors;i++) { 
			int temp = processIDS[i];
			wait(&temp);
		}
		
		for (int i = 0; i < processIDS.size(); i++) {
			ifstream in;
			string tempFile =  outputFileName + toString(processIDS[i]) + ".num.temp";
			m->openInputFile(tempFile, in);
			if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
			in.close(); m->mothurRemove(tempFile);
		}
		
		return num;
#endif		
	}
	catch(exception& e) {
		m->errorOut(e, "ChimeraCcodeCommand", "createProcesses");
		exit(1);
	}
}
//**********************************************************************************************************************