X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=chimeracheckcommand.cpp;h=264eb4c4ade8cfa2fd9f56246436b799ecb9d709;hb=2df35fdeea85f574630d75b11fb5b08c39aec31a;hp=ba5e5be5fafaf958c02b2dd2421eac9637f51c41;hpb=fdc1f6eaf544f695fc1511f24bddd7e6069c33ba;p=mothur.git diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp index ba5e5be..264eb4c 100644 --- a/chimeracheckcommand.cpp +++ b/chimeracheckcommand.cpp @@ -8,7 +8,6 @@ */ #include "chimeracheckcommand.h" -#include "chimeracheckrdp.h" //*************************************************************************************************************** @@ -27,7 +26,7 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { OptionParser parser(option); map parameters = parser.getParameters(); - ValidParameters validParameter; + ValidParameters validParameter("chimera.check"); map::iterator it; //check to make sure all parameters are valid for command @@ -39,51 +38,148 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { string inputDir = validParameter.validFile(parameters, "inputdir", false); if (inputDir == "not found"){ inputDir = ""; } else { - string path; - it = parameters.find("fasta"); - //user has given a template file - if(it != parameters.end()){ - path = hasPath(it->second); - //if the user has not given a path then, add inputdir. else leave path alone. - if (path == "") { parameters["fasta"] = inputDir + it->second; } - } - it = parameters.find("template"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + string path = hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["template"] = inputDir + it->second; } } - - it = parameters.find("name"); - //user has given a template file - if(it != parameters.end()){ - path = hasPath(it->second); - //if the user has not given a path then, add inputdir. else leave path alone. - if (path == "") { parameters["name"] = inputDir + it->second; } - } } - //check for required parameters - fastafile = validParameter.validFile(parameters, "fasta", true); - if (fastafile == "not open") { abort = true; } - else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true; } + fastafile = validParameter.validFile(parameters, "fasta", false); + if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true; } + else { + 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++) { + if (inputDir != "") { + string path = 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; + + #ifdef USE_MPI + int pid; + MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running + MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are + + if (pid == 0) { + #endif + + ableToOpen = 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() + getSimpleName(fastaFileNames[i]); + m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); + ableToOpen = openInputFile(tryPath, in, "noerror"); + fastaFileNames[i] = tryPath; + } + } + in.close(); + + #ifdef USE_MPI + for (int j = 1; j < processors; j++) { + MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD); + } + }else{ + MPI_Status status; + MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + } + + #endif + + 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--; + } + } + + //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 = ""; - outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it - } + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; } templatefile = validParameter.validFile(parameters, "template", true); if (templatefile == "not open") { abort = true; } else if (templatefile == "not found") { templatefile = ""; m->mothurOut("template is a required parameter for the chimera.check command."); m->mothurOutEndLine(); abort = true; } - namefile = validParameter.validFile(parameters, "name", true); - if (namefile == "not open") { abort = true; } - else if (namefile == "not found") { namefile = ""; } + namefile = validParameter.validFile(parameters, "name", false); + if (namefile == "not found") { namefile = ""; } + else { + splitAtDash(namefile, nameFileNames); + + //go through files and make sure they are good, if not, then disregard them + for (int i = 0; i < nameFileNames.size(); i++) { + if (inputDir != "") { + string path = hasPath(nameFileNames[i]); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { nameFileNames[i] = inputDir + nameFileNames[i]; } + } + + int ableToOpen; + ifstream in; + + #ifdef USE_MPI + int pid; + MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running + MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are + + if (pid == 0) { + #endif + + ableToOpen = openInputFile(nameFileNames[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() + getSimpleName(nameFileNames[i]); + m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); + ableToOpen = openInputFile(tryPath, in, "noerror"); + nameFileNames[i] = tryPath; + } + } + in.close(); + + #ifdef USE_MPI + for (int j = 1; j < processors; j++) { + MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD); + } + }else{ + MPI_Status status; + MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + } + + #endif + + if (ableToOpen == 1) { + m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); + //erase from file list + nameFileNames.erase(nameFileNames.begin()+i); + i--; + } + + } + + //make sure there is at least one valid file left + if (nameFileNames.size() != 0) { + if (nameFileNames.size() != fastaFileNames.size()) { + m->mothurOut("Different number of valid name files and fasta files, aborting command."); m->mothurOutEndLine(); + abort = true; + } + } + } string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; } convert(temp, processors); @@ -93,6 +189,7 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option) { temp = validParameter.validFile(parameters, "svg", false); if (temp == "not found") { temp = "F"; } svg = isTrue(temp); + if (nameFileNames.size() != 0) { svg = true; } temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "10"; } convert(temp, increment); @@ -112,6 +209,7 @@ void ChimeraCheckCommand::help(){ m->mothurOut("This command was created using the algorythms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n"); m->mothurOut("The chimera.check command parameters are fasta, template, processors, ksize, increment, svg and name.\n"); m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n"); + m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n"); m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n"); m->mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n"); #ifdef USE_MPI @@ -121,6 +219,7 @@ void ChimeraCheckCommand::help(){ m->mothurOut("The ksize parameter allows you to input kmersize, default is 7. \n"); m->mothurOut("The svg parameter allows you to specify whether or not you would like a svg file outputted for each query sequence, default is False.\n"); m->mothurOut("The name parameter allows you to enter a file containing names of sequences you would like .svg files for.\n"); + m->mothurOut("You may enter multiple name files by separating their names with dashes. ie. fasta=abrecovery.svg.names-amzon.svg.names \n"); m->mothurOut("The chimera.check command should be in the following format: \n"); m->mothurOut("chimera.check(fasta=yourFastaFile, template=yourTemplateFile, processors=yourProcessors, ksize=yourKmerSize) \n"); m->mothurOut("Example: chimera.check(fasta=AD.fasta, template=core_set_aligned,imputed.fasta, processors=4, ksize=8) \n"); @@ -143,183 +242,197 @@ int ChimeraCheckCommand::execute(){ if (abort == true) { return 0; } - int start = time(NULL); - - chimera = new ChimeraCheckRDP(fastafile, templatefile, namefile, svg, increment, ksize, outputDir); - - if (m->control_pressed) { delete chimera; return 0; } - - string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "chimeracheck.chimeras"; - - #ifdef USE_MPI - - int pid, end, numSeqsPerProcessor; - int tag = 2001; - vector MPIPos; + for (int i = 0; i < fastaFileNames.size(); i++) { + + m->mothurOut("Checking sequences from " + fastaFileNames[i] + " ..." ); m->mothurOutEndLine(); - 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; - - int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; - int inMode=MPI_MODE_RDONLY; - - char outFilename[outputFileName.length()]; - strcpy(outFilename, outputFileName.c_str()); + int start = time(NULL); - char inFileName[fastafile.length()]; - strcpy(inFileName, fastafile.c_str()); + string thisNameFile = ""; + if (nameFileNames.size() != 0) { thisNameFile = nameFileNames[i]; } + + chimera = new ChimeraCheckRDP(fastaFileNames[i], templatefile, thisNameFile, svg, increment, ksize, outputDir); - 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); + if (m->control_pressed) { delete chimera; return 0; } - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); delete chimera; return 0; } + string outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "chimeracheck.chimeras"; + outputNames.push_back(outputFileName); - if (pid == 0) { //you are the root process - MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs - - //send file positions to all processes - MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //send numSeqs - MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos + #ifdef USE_MPI + + int pid, end, numSeqsPerProcessor; + int tag = 2001; + vector MPIPos; - //figure out how many sequences you have to align - numSeqsPerProcessor = numSeqs / processors; - if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; } - int startIndex = pid * numSeqsPerProcessor; + 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; + + int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; + int inMode=MPI_MODE_RDONLY; + + char outFilename[1024]; + strcpy(outFilename, outputFileName.c_str()); - //align your part - driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos); + char inFileName[1024]; + strcpy(inFileName, fastaFileNames[i].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); - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); remove(outputFileName.c_str()); delete chimera; return 0; } + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } + + if (pid == 0) { //you are the root process + MPIPos = setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs + + //send file positions to all processes + for(int j = 1; j < processors; j++) { + MPI_Send(&numSeqs, 1, MPI_INT, j, tag, MPI_COMM_WORLD); + MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, j, 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; } + - //wait on chidren - for(int i = 1; i < processors; i++) { + //align your part + driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos); + + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } + + //wait on chidren + for(int j = 1; j < processors; j++) { + char buf[4]; + MPI_Recv(buf, 4, MPI_CHAR, j, tag, MPI_COMM_WORLD, &status); + } + }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, MPIPos); + + if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } delete chimera; return 0; } + + //tell parent you are done. char buf[4]; - MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); + strcpy(buf, "done"); + MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD); } - }else{ //you are a child process - MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs - MPIPos.resize(numSeqs+1); - MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions - - //figure out how many sequences you have to align - numSeqsPerProcessor = numSeqs / processors; - if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; } - int startIndex = pid * numSeqsPerProcessor; - - //align your part - driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos); - - if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); delete chimera; return 0; } - //tell parent you are done. - char buf[4]; - strcpy(buf, "done"); - MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD); - } + //close files + MPI_File_close(&inMPI); + MPI_File_close(&outMPI); + MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case + #else - //close files - MPI_File_close(&inMPI); - MPI_File_close(&outMPI); - #else - - //break up file - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - if(processors == 1){ - ifstream inFASTA; - openInputFile(fastafile, inFASTA); - numSeqs=count(istreambuf_iterator(inFASTA),istreambuf_iterator(), '>'); - inFASTA.close(); - - lines.push_back(new linePair(0, numSeqs)); - - driver(lines[0], outputFileName, fastafile); - - if (m->control_pressed) { - remove(outputFileName.c_str()); - for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); - delete chimera; - return 0; - } - - }else{ - vector positions; - processIDS.resize(0); - - ifstream inFASTA; - openInputFile(fastafile, inFASTA); - - string input; - while(!inFASTA.eof()){ - input = getline(inFASTA); - if (input.length() != 0) { - if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); } + //break up file + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + if(processors == 1){ + ifstream inFASTA; + openInputFile(fastaFileNames[i], inFASTA); + getNumSeqs(inFASTA, numSeqs); + inFASTA.close(); + + lines.push_back(new linePair(0, numSeqs)); + + driver(lines[0], outputFileName, fastaFileNames[i]); + + if (m->control_pressed) { + for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } + for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear(); + delete chimera; + return 0; } - } - inFASTA.close(); - - numSeqs = positions.size(); - - int numSeqsPerProcessor = numSeqs / processors; - - for (int i = 0; i < processors; i++) { - long int startPos = positions[ i * numSeqsPerProcessor ]; - if(i == processors - 1){ - numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor; + + }else{ + vector positions; + processIDS.resize(0); + + ifstream inFASTA; + openInputFile(fastaFileNames[i], inFASTA); + + string input; + while(!inFASTA.eof()){ + input = getline(inFASTA); + if (input.length() != 0) { + if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); } + } } - lines.push_back(new linePair(startPos, numSeqsPerProcessor)); - } - + inFASTA.close(); + + numSeqs = positions.size(); + + int numSeqsPerProcessor = numSeqs / processors; + + for (int j = 0; j < processors; j++) { + unsigned long int startPos = positions[ j * numSeqsPerProcessor ]; + if(j == processors - 1){ + numSeqsPerProcessor = numSeqs - j * numSeqsPerProcessor; + } + lines.push_back(new linePair(startPos, numSeqsPerProcessor)); + } + + + createProcesses(outputFileName, fastaFileNames[i]); - createProcesses(outputFileName, fastafile); - - rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str()); + rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str()); + + //append output files + for(int j=1;jcontrol_pressed) { + for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } + for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear(); + delete chimera; + return 0; + } } + + #else + ifstream inFASTA; + openInputFile(fastaFileNames[i], inFASTA); + getNumSeqs(inFASTA, numSeqs); + inFASTA.close(); + lines.push_back(new linePair(0, numSeqs)); + + driver(lines[0], outputFileName, fastaFileNames[i]); if (m->control_pressed) { - remove(outputFileName.c_str()); - for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); - delete chimera; - return 0; + for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear(); + for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } + delete chimera; + return 0; } - } - - #else - ifstream inFASTA; - openInputFile(candidateFileNames[s], inFASTA); - numSeqs=count(istreambuf_iterator(inFASTA),istreambuf_iterator(), '>'); - inFASTA.close(); - lines.push_back(new linePair(0, numSeqs)); + #endif + #endif + delete chimera; + for (int j = 0; j < lines.size(); j++) { delete lines[j]; } lines.clear(); - driver(lines[0], outputFileName, fastafile); - - if (m->control_pressed) { - remove(outputFileName.c_str()); - for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); - delete chimera; - return 0; - } - #endif - #endif - delete chimera; - for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear(); - - m->mothurOutEndLine(); m->mothurOut("This method does not determine if a sequence is chimeric, but allows you to make that determination based on the IS values."); m->mothurOutEndLine(); + m->mothurOutEndLine(); m->mothurOut("This method does not determine if a sequence is chimeric, but allows you to make that determination based on the IS values."); m->mothurOutEndLine(); + m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine(); + + } m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); - m->mothurOut(outputFileName); m->mothurOutEndLine(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } m->mothurOutEndLine(); - m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); - + return 0; } @@ -377,7 +490,7 @@ int ChimeraCheckCommand::driver(linePair* line, string outputFName, string filen } //********************************************************************************************************************** #ifdef USE_MPI -int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector& MPIPos){ +int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector& MPIPos){ try { MPI_File outAccMPI; MPI_Status status; @@ -391,12 +504,13 @@ int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File //read next sequence int length = MPIPos[start+i+1] - MPIPos[start+i]; - char buf4[length]; + 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); gobble(iss);