X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.cpp;h=95604fc4ff4f738dc780de23b01ab65d4f473fe7;hb=e150b0b0664caec517485ee6d69dcdade6dcae77;hp=624aab439855f60d9072889ae2cd80b33dae320e;hpb=191ae1be0679d5cf4eda950b3b1bf26fb7dd503d;p=mothur.git diff --git a/aligncommand.cpp b/aligncommand.cpp index 624aab4..95604fc 100644 --- a/aligncommand.cpp +++ b/aligncommand.cpp @@ -25,47 +25,67 @@ #include "nast.hpp" #include "nastreport.hpp" - -//********************************************************************************************************************** -vector AlignCommand::getValidParameters(){ - try { - string AlignArray[] = {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors","flip","threshold","outputdir","inputdir"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "AlignCommand", "getValidParameters"); - exit(1); - } -} //********************************************************************************************************************** -vector AlignCommand::getRequiredParameters(){ +vector AlignCommand::setParameters(){ try { - string AlignArray[] = {"template","candidate"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate); + CommandParameter pcandidate("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pcandidate); + CommandParameter psearch("search", "Multiple", "kmer-blast-suffix", "kmer", "", "", "",false,false); parameters.push_back(psearch); + CommandParameter pksize("ksize", "Number", "", "8", "", "", "",false,false); parameters.push_back(pksize); + CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch); + CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign); + CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch); + CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen); + CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); + CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip); + CommandParameter pthreshold("threshold", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(pthreshold); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } return myArray; } catch(exception& e) { - m->errorOut(e, "AlignCommand", "getRequiredParameters"); + m->errorOut(e, "AlignCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -vector AlignCommand::getRequiredFiles(){ +string AlignCommand::getHelpString(){ try { - vector myArray; - return myArray; + string helpString = ""; + helpString += "The align.seqs command reads a file containing sequences and creates an alignment file and a report file."; + helpString += "The align.seqs command parameters are reference, fasta, search, ksize, align, match, mismatch, gapopen, gapextend and processors."; + helpString += "The reference and fasta parameters are required. You may leave fasta blank if you have a valid fasta file. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta."; + helpString += "The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is kmer."; + helpString += "The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman."; + helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8."; + helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0."; + helpString += "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0."; + helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0."; + helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0."; + helpString += "The flip parameter is used to specify whether or not you want mothur to try the reverse complement if a sequence falls below the threshold. The default is false."; + helpString += "The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. The default threshold is 0.50, meaning 50% of the bases are removed in the alignment."; + helpString += "If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported."; + helpString += "The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed."; + helpString += "The align.seqs command should be in the following format:"; + helpString += "align.seqs(reference=yourTemplateFile, fasta=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty)"; + helpString += "Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)"; + helpString += "Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile)."; + return helpString; } catch(exception& e) { - m->errorOut(e, "AlignCommand", "getRequiredFiles"); + m->errorOut(e, "AlignCommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** AlignCommand::AlignCommand(){ try { - abort = true; - //initialize outputTypes + abort = true; calledHelp = true; + setParameters(); vector tempOutNames; outputTypes["fasta"] = tempOutNames; outputTypes["alignreport"] = tempOutNames; @@ -79,16 +99,14 @@ AlignCommand::AlignCommand(){ //********************************************************************************************************************** AlignCommand::AlignCommand(string option) { try { - abort = false; + abort = false; calledHelp = false; //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true;} + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - - //valid paramters for this command - string AlignArray[] = {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors","flip","threshold","outputdir","inputdir"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -118,78 +136,96 @@ AlignCommand::AlignCommand(string option) { else { string path; - it = parameters.find("template"); + 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["template"] = inputDir + it->second; } + if (path == "") { parameters["reference"] = inputDir + it->second; } } } //check for required parameters - templateFileName = validParameter.validFile(parameters, "template", true); + templateFileName = validParameter.validFile(parameters, "reference", true); if (templateFileName == "not found") { - m->mothurOut("template is a required parameter for the align.seqs command."); + m->mothurOut("reference is a required parameter for the align.seqs command."); m->mothurOutEndLine(); abort = true; }else if (templateFileName == "not open") { abort = true; } - candidateFileName = validParameter.validFile(parameters, "candidate", false); - if (candidateFileName == "not found") { m->mothurOut("candidate is a required parameter for the align.seqs command."); m->mothurOutEndLine(); abort = true; } - else { + candidateFileName = validParameter.validFile(parameters, "fasta", false); + if (candidateFileName == "not found") { + //if there is a current fasta file, use it + string filename = m->getFastaFile(); + if (filename != "") { candidateFileNames.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 candidate parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { m->splitAtDash(candidateFileName, candidateFileNames); //go through files and make sure they are good, if not, then disregard them for (int i = 0; i < candidateFileNames.size(); i++) { //candidateFileNames[i] = m->getFullPathName(candidateFileNames[i]); - if (inputDir != "") { - string path = m->hasPath(candidateFileNames[i]); - //if the user has not given a path then, add inputdir. else leave path alone. - if (path == "") { candidateFileNames[i] = inputDir + candidateFileNames[i]; } - } - - int ableToOpen; - ifstream in; - ableToOpen = m->openInputFile(candidateFileNames[i], in, "noerror"); - in.close(); - - //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(candidateFileNames[i]); - m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); - ifstream in2; - ableToOpen = m->openInputFile(tryPath, in2, "noerror"); - in2.close(); - candidateFileNames[i] = tryPath; + bool ignore = false; + if (candidateFileNames[i] == "current") { + candidateFileNames[i] = m->getFastaFile(); + if (candidateFileNames[i] != "") { m->mothurOut("Using " + candidateFileNames[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 + candidateFileNames.erase(candidateFileNames.begin()+i); + i--; } } - //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(candidateFileNames[i]); - m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine(); - ifstream in2; - ableToOpen = m->openInputFile(tryPath, in2, "noerror"); - in2.close(); - candidateFileNames[i] = tryPath; - } - } + if (!ignore) { - + if (inputDir != "") { + string path = m->hasPath(candidateFileNames[i]); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { candidateFileNames[i] = inputDir + candidateFileNames[i]; } + } + + int ableToOpen; + ifstream in; + ableToOpen = m->openInputFile(candidateFileNames[i], in, "noerror"); + in.close(); + + //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(candidateFileNames[i]); + m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + candidateFileNames[i] = tryPath; + } + } + + //if you can't open it, try output location + if (ableToOpen == 1) { + if (m->getOutputDir() != "") { //default path is set + string tryPath = m->getOutputDir() + m->getSimpleName(candidateFileNames[i]); + m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + candidateFileNames[i] = tryPath; + } + } + + - if (ableToOpen == 1) { - m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); - //erase from file list - candidateFileNames.erase(candidateFileNames.begin()+i); - i--; + if (ableToOpen == 1) { + m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); + //erase from file list + candidateFileNames.erase(candidateFileNames.begin()+i); + i--; + } } - } //make sure there is at least one valid file left @@ -214,7 +250,8 @@ AlignCommand::AlignCommand(string option) { temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; } convert(temp, gapExtend); - temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; } + temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } + m->setProcessors(temp); convert(temp, processors); temp = validParameter.validFile(parameters, "flip", false); if (temp == "not found"){ temp = "f"; } @@ -224,8 +261,11 @@ AlignCommand::AlignCommand(string option) { convert(temp, threshold); search = validParameter.validFile(parameters, "search", false); if (search == "not found"){ search = "kmer"; } + if ((search != "suffix") && (search != "kmer") && (search != "blast")) { m->mothurOut("invalid search option: choices are kmer, suffix or blast."); m->mothurOutEndLine(); abort=true; } align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; } + if ((align != "needleman") && (align != "gotoh") && (align != "blast") && (align != "noalign")) { m->mothurOut("invalid align option: choices are needleman, gotoh, blast or noalign."); m->mothurOutEndLine(); abort=true; } + } } @@ -235,7 +275,6 @@ AlignCommand::AlignCommand(string option) { } } //********************************************************************************************************************** - AlignCommand::~AlignCommand(){ if (abort == false) { @@ -244,42 +283,11 @@ AlignCommand::~AlignCommand(){ delete alignment; } } - -//********************************************************************************************************************** - -void AlignCommand::help(){ - try { - m->mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n"); - m->mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen, gapextend and processors.\n"); - m->mothurOut("The template and candidate parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n"); - m->mothurOut("The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is kmer.\n"); - m->mothurOut("The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n"); - m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n"); - m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n"); - m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n"); - m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n"); - m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n"); - m->mothurOut("The flip parameter is used to specify whether or not you want mothur to try the reverse complement if a sequence falls below the threshold. The default is false.\n"); - m->mothurOut("The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. The default threshold is 0.50, meaning 50% of the bases are removed in the alignment.\n"); - m->mothurOut("If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.\n"); - m->mothurOut("The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed.\n"); - m->mothurOut("The align.seqs command should be in the following format: \n"); - m->mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n"); - m->mothurOut("Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "AlignCommand", "help"); - exit(1); - } -} - - //********************************************************************************************************************** int AlignCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch); int longestBase = templateDB->getLongestBase(); @@ -310,7 +318,7 @@ int AlignCommand::execute(){ int start = time(NULL); #ifdef USE_MPI - int pid, end, numSeqsPerProcessor; + int pid, numSeqsPerProcessor; int tag = 2001; vector MPIPos; MPIWroteAccnos = false; @@ -423,62 +431,12 @@ int AlignCommand::execute(){ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) if(processors == 1){ numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); - - if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear(); return 0; } - - //delete accnos file if its blank else report to user - if (m->isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; } - else { - m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + "."); - if (!flip) { - m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well."); - }else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); } - m->mothurOutEndLine(); - } }else{ - processIDS.resize(0); - numFastaSeqs = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); - - rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str()); - rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str()); - - //append alignment and report files - for(int i=1;i nonBlankAccnosFiles; - //delete blank accnos files generated with multiple processes - for(int i=0;iisBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) { - nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp"); - }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str()); } - } - - //append accnos files - if (nonBlankAccnosFiles.size() != 0) { - rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str()); - - for (int h=1; h < nonBlankAccnosFiles.size(); h++) { - appendAlignFiles(nonBlankAccnosFiles[h], accnosFileName); - remove(nonBlankAccnosFiles[h].c_str()); - } - m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + "."); - if (!flip) { - m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well."); - }else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); } - m->mothurOutEndLine(); - }else{ hasAccnos = false; } - - if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear(); return 0; } } #else numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); + #endif if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear(); return 0; } @@ -491,8 +449,6 @@ int AlignCommand::execute(){ }else{ m->mothurOut(" If the reverse compliment proved to be better it was reported."); } m->mothurOutEndLine(); } - - #endif #endif @@ -516,6 +472,12 @@ int AlignCommand::execute(){ m->mothurOutEndLine(); } + //set align file as new current fastafile + string currentFasta = ""; + itTypes = outputTypes.find("fasta"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); } + } m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); @@ -555,7 +517,8 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam if (m->control_pressed) { return 0; } Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA); - + report.setCandidate(candidateSeq); + int origNumBases = candidateSeq->getNumBases(); string originalUnaligned = candidateSeq->getUnaligned(); int numBasesNeeded = origNumBases * threshold; @@ -618,7 +581,6 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam accnosFile << candidateSeq->getName() << wasBetter << endl; } - report.setCandidate(candidateSeq); report.setTemplate(templateSeq); report.setSearchParameters(search, searchScore); report.setAlignmentParameters(align, alignment); @@ -706,7 +668,8 @@ int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& align istringstream iss (tempBuf,istringstream::in); Sequence* candidateSeq = new Sequence(iss); - + report.setCandidate(candidateSeq); + int origNumBases = candidateSeq->getNumBases(); string originalUnaligned = candidateSeq->getUnaligned(); int numBasesNeeded = origNumBases * threshold; @@ -777,7 +740,6 @@ int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& align MPIWroteAccnos = true; } - report.setCandidate(candidateSeq); report.setTemplate(templateSeq); report.setSearchParameters(search, searchScore); report.setAlignmentParameters(align, alignment); @@ -828,7 +790,8 @@ int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& align int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) { try { #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - int process = 0; + processIDS.resize(0); + int process = 1; int num = 0; // processIDS.resize(0); @@ -850,21 +813,57 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s out.close(); exit(0); - }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); 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); + } } + //do my part + num = driver(lines[0], alignFileName, reportFileName, accnosFName, filename); + //force parent to wait until all the processes are done - for (int i=0;i nonBlankAccnosFiles; + if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); } + else { remove(accnosFName.c_str()); } //remove so other files can be renamed to it + for (int i = 0; i < processIDS.size(); i++) { ifstream in; string tempFile = alignFileName + toString(processIDS[i]) + ".num.temp"; m->openInputFile(tempFile, in); if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; } in.close(); remove(tempFile.c_str()); + + appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName); + remove((alignFileName + toString(processIDS[i]) + ".temp").c_str()); + + appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName); + remove((reportFileName + toString(processIDS[i]) + ".temp").c_str()); + + if (!(m->isBlank(accnosFName + toString(processIDS[i]) + ".temp"))) { + nonBlankAccnosFiles.push_back(accnosFName + toString(processIDS[i]) + ".temp"); + }else { remove((accnosFName + toString(processIDS[i]) + ".temp").c_str()); } + + } + + //append accnos files + if (nonBlankAccnosFiles.size() != 0) { + rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str()); + + for (int h=1; h < nonBlankAccnosFiles.size(); h++) { + appendAlignFiles(nonBlankAccnosFiles[h], accnosFName); + remove(nonBlankAccnosFiles[h].c_str()); + } + }else { //recreate the accnosfile if needed + ofstream out; + m->openOutputFile(accnosFName, out); + out.close(); } return num;