X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqerrorcommand.cpp;h=5ec6cf2d1cc4778399d289ea2280c882f936b944;hb=79a7d3273749b08d4f9f8dfe350c964ff0c4351e;hp=5efb1ce78c659577c520defc124c48e60b848dc8;hpb=75962c819c16814e5c2340d99af1aa62e564dc20;p=mothur.git diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp index 5efb1ce..5ec6cf2 100644 --- a/seqerrorcommand.cpp +++ b/seqerrorcommand.cpp @@ -13,6 +13,7 @@ #include "refchimeratest.h" #include "filterseqscommand.h" + //********************************************************************************************************************** vector SeqErrorCommand::setParameters(){ try { @@ -24,7 +25,7 @@ vector SeqErrorCommand::setParameters(){ CommandParameter pignorechimeras("ignorechimeras", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pignorechimeras); CommandParameter pthreshold("threshold", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pthreshold); CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); - CommandParameter pfilter("filter", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pfilter); + CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave); CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); @@ -42,6 +43,15 @@ string SeqErrorCommand::getHelpString(){ try { string helpString = ""; helpString += "The seq.error command reads a query alignment file and a reference alignment file and creates .....\n"; + helpString += "The fasta parameter...\n"; + helpString += "The reference parameter...\n"; + helpString += "The qfile parameter...\n"; + helpString += "The report parameter...\n"; + helpString += "The name parameter...\n"; + helpString += "The ignorechimeras parameter...\n"; + helpString += "The threshold parameter...\n"; + helpString += "The processors parameter...\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 += "Example seq.error(...).\n"; helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n"; helpString += "For more details please check out the wiki http://www.mothur.org/wiki/seq.error .\n"; @@ -53,19 +63,52 @@ string SeqErrorCommand::getHelpString(){ } } //********************************************************************************************************************** +string SeqErrorCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::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 == "errorsummary") { outputFileName = "error.summary"; } + else if (type == "errorseq") { outputFileName = "error.seq"; } + else if (type == "errorquality") { outputFileName = "error.quality"; } + else if (type == "errorqualforward") { outputFileName = "error.qual.forward"; } + else if (type == "errorqualreverse") { outputFileName = "error.qual.reverse"; } + else if (type == "errorforward") { outputFileName = "error.seq.forward"; } + else if (type == "errorreverse") { outputFileName = "error.seq.reverse"; } + else if (type == "errorcount") { outputFileName = "error.count"; } + else if (type == "errormatrix") { outputFileName = "error.matrix"; } + else if (type == "errorchimera") { outputFileName = "error.chimera"; } + else if (type == "errorref-query") { outputFileName = "error.ref-query"; } + 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, "SeqErrorCommand", "getOutputFileNameTag"); + exit(1); + } +} +//********************************************************************************************************************** SeqErrorCommand::SeqErrorCommand(){ try { abort = true; calledHelp = true; + setParameters(); vector tempOutNames; - outputTypes["error.summary"] = tempOutNames; - outputTypes["error.seq"] = tempOutNames; - outputTypes["error.quality"] = tempOutNames; - outputTypes["error.qual.forward"] = tempOutNames; - outputTypes["error.qual.reverse"] = tempOutNames; - outputTypes["error.forward"] = tempOutNames; - outputTypes["error.reverse"] = tempOutNames; - outputTypes["error.count"] = tempOutNames; - outputTypes["error.matrix"] = tempOutNames; + outputTypes["errorsummary"] = tempOutNames; + outputTypes["errorseq"] = tempOutNames; + outputTypes["errorquality"] = tempOutNames; + outputTypes["errorqualforward"] = tempOutNames; + outputTypes["errorqualreverse"] = tempOutNames; + outputTypes["errorforward"] = tempOutNames; + outputTypes["errorreverse"] = tempOutNames; + outputTypes["errorcount"] = tempOutNames; + outputTypes["errormatrix"] = tempOutNames; + outputTypes["errorchimera"] = tempOutNames; + outputTypes["errorref-query"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "SeqErrorCommand", "SeqErrorCommand"); @@ -78,6 +121,7 @@ SeqErrorCommand::SeqErrorCommand(string option) { try { abort = false; calledHelp = false; + rdb = ReferenceDB::getInstance(); //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } @@ -100,15 +144,17 @@ SeqErrorCommand::SeqErrorCommand(string option) { //initialize outputTypes vector tempOutNames; - outputTypes["error.summary"] = tempOutNames; - outputTypes["error.seq"] = tempOutNames; - outputTypes["error.quality"] = tempOutNames; - outputTypes["error.qual.forward"] = tempOutNames; - outputTypes["error.qual.reverse"] = tempOutNames; - outputTypes["error.forward"] = tempOutNames; - outputTypes["error.reverse"] = tempOutNames; - outputTypes["error.count"] = tempOutNames; - outputTypes["error.matrix"] = tempOutNames; + outputTypes["errorsummary"] = tempOutNames; + outputTypes["errorseq"] = tempOutNames; + outputTypes["errorquality"] = tempOutNames; + outputTypes["errorqualforward"] = tempOutNames; + outputTypes["errorqualreverse"] = tempOutNames; + outputTypes["errorforward"] = tempOutNames; + outputTypes["errorreverse"] = tempOutNames; + outputTypes["errorcount"] = tempOutNames; + outputTypes["errormatrix"] = tempOutNames; + outputTypes["errorchimera"] = tempOutNames; + outputTypes["errorref-query"] = tempOutNames; //if the user changes the input directory command factory will send this info to us in the output parameter @@ -164,22 +210,24 @@ SeqErrorCommand::SeqErrorCommand(string option) { if (queryFileName != "") { m->mothurOut("Using " + queryFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); } else { m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; } } - else if (queryFileName == "not open") { abort = true; } + else if (queryFileName == "not open") { queryFileName = ""; abort = true; } + else { m->setFastaFile(queryFileName); } referenceFileName = validParameter.validFile(parameters, "reference", true); if (referenceFileName == "not found") { m->mothurOut("reference is a required parameter for the seq.error command."); m->mothurOutEndLine(); abort = true; } else if (referenceFileName == "not open") { abort = true; } - //check for optional parameters namesFileName = validParameter.validFile(parameters, "name", true); if(namesFileName == "not found"){ namesFileName = ""; } else if (namesFileName == "not open") { namesFileName = ""; abort = true; } + else { m->setNameFile(namesFileName); } qualFileName = validParameter.validFile(parameters, "qfile", true); if(qualFileName == "not found"){ qualFileName = ""; } else if (qualFileName == "not open") { qualFileName = ""; abort = true; } - + else { m->setQualFile(qualFileName); } + reportFileName = validParameter.validFile(parameters, "report", true); if(reportFileName == "not found"){ reportFileName = ""; } else if (reportFileName == "not open") { reportFileName = ""; abort = true; } @@ -199,20 +247,44 @@ SeqErrorCommand::SeqErrorCommand(string option) { //check for optional parameter and set defaults // ...at some point should added some additional type checking... temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found") { temp = "1.00"; } - convert(temp, threshold); + m->mothurConvert(temp, threshold); + + 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 + referenceFileName = validParameter.validFile(parameters, "reference", true); + if (referenceFileName == "not found") { + //check for saved reference sequences + if (rdb->referenceSeqs.size() != 0) { + referenceFileName = "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 (referenceFileName == "not open") { abort = true; } + else { if (save) { rdb->setSavedReference(referenceFileName); } } + temp = validParameter.validFile(parameters, "ignorechimeras", false); if (temp == "not found") { temp = "T"; } ignoreChimeras = m->isTrue(temp); - temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "T"; } - filter = m->isTrue(temp); - temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } m->setProcessors(temp); - convert(temp, processors); + m->mothurConvert(temp, processors); substitutionMatrix.resize(6); for(int i=0;i<6;i++){ substitutionMatrix[i].resize(6,0); } + + if ((namesFileName == "") && (queryFileName != "")){ + vector files; files.push_back(queryFileName); + parser.getNameFile(files); + } } } catch(exception& e) { @@ -230,42 +302,24 @@ int SeqErrorCommand::execute(){ maxLength = 2000; totalBases = 0; totalMatches = 0; - - //run vertical filter on query and reference files. - if (filter) { - string inputString = "fasta=" + queryFileName + "-" + referenceFileName; - m->mothurOut("/******************************************/"); m->mothurOutEndLine(); - m->mothurOut("Running command: filter.seqs(" + inputString + ") to improve processing time."); m->mothurOutEndLine(); - - Command* filterCommand = new FilterSeqsCommand(inputString); - filterCommand->execute(); - - map > filenames = filterCommand->getOutputFiles(); - - delete filterCommand; - - m->mothurOut("/******************************************/"); m->mothurOutEndLine(); - - queryFileName = filenames["fasta"][0]; - referenceFileName = filenames["fasta"][1]; - } - string errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary"; - outputNames.push_back(errorSummaryFileName); outputTypes["error.summary"].push_back(errorSummaryFileName); + string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(queryFileName)); + string errorSummaryFileName = fileNameRoot + getOutputFileNameTag("errorsummary"); + outputNames.push_back(errorSummaryFileName); outputTypes["errorsummary"].push_back(errorSummaryFileName); - string errorSeqFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq"; - outputNames.push_back(errorSeqFileName); outputTypes["error.seq"].push_back(errorSeqFileName); + string errorSeqFileName = fileNameRoot + getOutputFileNameTag("errorseq"); + outputNames.push_back(errorSeqFileName); outputTypes["errorseq"].push_back(errorSeqFileName); - string errorChimeraFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.chimera"; - outputNames.push_back(errorChimeraFileName); outputTypes["error.chimera"].push_back(errorChimeraFileName); + string errorChimeraFileName = fileNameRoot + getOutputFileNameTag("errorchimera"); + outputNames.push_back(errorChimeraFileName); outputTypes["errorchimera"].push_back(errorChimeraFileName); getReferences(); //read in reference sequences - make sure there's no ambiguous bases if(namesFileName != ""){ weights = getWeights(); } - vector fastaFilePos; - vector qFilePos; - vector reportFilePos; + vector fastaFilePos; + vector qFilePos; + vector reportFilePos; setLines(queryFileName, qualFileName, reportFileName, fastaFilePos, qFilePos, reportFilePos); @@ -279,7 +333,7 @@ int SeqErrorCommand::execute(){ if(qualFileName == "") { qLines = lines; rLines = lines; } //fills with duds int numSeqs = 0; -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) if(processors == 1){ numSeqs = driver(queryFileName, qualFileName, reportFileName, errorSummaryFileName, errorSeqFileName, errorChimeraFileName, lines[0], qLines[0], rLines[0]); }else{ @@ -296,12 +350,12 @@ int SeqErrorCommand::execute(){ printErrorFRFile(errorForward, errorReverse); - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } - string errorCountFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.count"; + string errorCountFileName = fileNameRoot + getOutputFileNameTag("errorcount"); ofstream errorCountFile; m->openOutputFile(errorCountFileName, errorCountFile); - outputNames.push_back(errorCountFileName); outputTypes["error.count"].push_back(errorCountFileName); + outputNames.push_back(errorCountFileName); outputTypes["errorcount"].push_back(errorCountFileName); m->mothurOut("Overall error rate:\t" + toString((double)(totalBases - totalMatches) / (double)totalBases) + "\n"); m->mothurOut("Errors\tSequences\n"); errorCountFile << "Errors\tSequences\n"; @@ -311,14 +365,14 @@ int SeqErrorCommand::execute(){ } errorCountFile.close(); - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } printSubMatrix(); - string megAlignmentFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.ref-query"; + string megAlignmentFileName = fileNameRoot + getOutputFileNameTag("errorref-query"); ofstream megAlignmentFile; m->openOutputFile(megAlignmentFileName, megAlignmentFile); - outputNames.push_back(megAlignmentFileName); outputTypes["error.ref-query"].push_back(megAlignmentFileName); + outputNames.push_back(megAlignmentFileName); outputTypes["errorref-query"].push_back(megAlignmentFileName); for(int i=0;i >::iterator it; int num = 0; -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) //loop through and create all the processes you want while (process != processors) { @@ -468,11 +522,11 @@ int SeqErrorCommand::createProcesses(string filename, string qFileName, string r m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine(); m->appendFiles((summaryFileName + toString(processIDS[i]) + ".temp"), summaryFileName); - remove((summaryFileName + toString(processIDS[i]) + ".temp").c_str()); + m->mothurRemove((summaryFileName + toString(processIDS[i]) + ".temp")); m->appendFiles((errorOutputFileName + toString(processIDS[i]) + ".temp"), errorOutputFileName); - remove((errorOutputFileName + toString(processIDS[i]) + ".temp").c_str()); + m->mothurRemove((errorOutputFileName + toString(processIDS[i]) + ".temp")); m->appendFiles((chimeraOutputFileName + toString(processIDS[i]) + ".temp"), chimeraOutputFileName); - remove((chimeraOutputFileName + toString(processIDS[i]) + ".temp").c_str()); + m->mothurRemove((chimeraOutputFileName + toString(processIDS[i]) + ".temp")); ifstream in; string tempFile = filename + toString(processIDS[i]) + ".info.temp"; @@ -567,7 +621,7 @@ int SeqErrorCommand::createProcesses(string filename, string qFileName, string r } m->gobble(in); - in.close(); remove(tempFile.c_str()); + in.close(); m->mothurRemove(tempFile); } #endif @@ -663,7 +717,8 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName, if(numParentSeqs > 1 && ignoreChimeras == 1) { ignoreSeq = 1; } else { ignoreSeq = 0; } - Compare minCompare = getErrors(query, referenceSeqs[closestRefIndex]); + Compare minCompare; + getErrors(query, referenceSeqs[closestRefIndex], minCompare); if(namesFileName != ""){ it = weights.find(query.getName()); @@ -678,8 +733,10 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName, for(int i=0;i= line.end)) { break; } #else if (queryFile.eof()) { break; } #endif - if(index % 100 == 0){ m->mothurOut(toString(index) + '\n'); } + if(index % 100 == 0){ m->mothurOut(toString(index)); m->mothurOutEndLine(); } } queryFile.close(); if(qFileName != "" && rFileName != ""){ reportFile.close(); qualFile.close(); } @@ -729,7 +790,7 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName, errorSeqFile.close(); //report progress - if(index % 100 != 0){ m->mothurOut(toString(index) + '\n'); } + if(index % 100 != 0){ m->mothurOut(toString(index)); m->mothurOutEndLine(); } return index; } @@ -742,41 +803,75 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName, void SeqErrorCommand::getReferences(){ try { - - ifstream referenceFile; - m->openInputFile(referenceFileName, referenceFile); - int numAmbigSeqs = 0; int maxStartPos = 0; int minEndPos = 100000; - while(referenceFile){ - Sequence currentSeq(referenceFile); - int numAmbigs = currentSeq.getAmbigBases(); - if(numAmbigs > 0){ numAmbigSeqs++; } - -// int startPos = currentSeq.getStartPos(); -// if(startPos > maxStartPos) { maxStartPos = startPos; } -// -// int endPos = currentSeq.getEndPos(); -// if(endPos < minEndPos) { minEndPos = endPos; } - referenceSeqs.push_back(currentSeq); + if (referenceFileName == "saved") { + int start = time(NULL); + m->mothurOutEndLine(); m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory."); m->mothurOutEndLine(); + + for (int i = 0; i < rdb->referenceSeqs.size(); i++) { + int numAmbigs = rdb->referenceSeqs[i].getAmbigBases(); + if(numAmbigs > 0){ numAmbigSeqs++; } + + // int startPos = rdb->referenceSeqs[i].getStartPos(); + // if(startPos > maxStartPos) { maxStartPos = startPos; } + // + // int endPos = rdb->referenceSeqs[i].getEndPos(); + // if(endPos < minEndPos) { minEndPos = endPos; } + if (rdb->referenceSeqs[i].getNumBases() == 0) { + m->mothurOut("[WARNING]: " + rdb->referenceSeqs[i].getName() + " is blank, ignoring.");m->mothurOutEndLine(); + }else { + referenceSeqs.push_back(rdb->referenceSeqs[i]); + } - m->gobble(referenceFile); + } + referenceFileName = rdb->getSavedReference(); + + m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(referenceSeqs.size()) + " sequences.");m->mothurOutEndLine(); + + }else { + int start = time(NULL); + + ifstream referenceFile; + m->openInputFile(referenceFileName, referenceFile); + + while(referenceFile){ + Sequence currentSeq(referenceFile); + int numAmbigs = currentSeq.getAmbigBases(); + if(numAmbigs > 0){ numAmbigSeqs++; } + + // int startPos = currentSeq.getStartPos(); + // if(startPos > maxStartPos) { maxStartPos = startPos; } + // + // int endPos = currentSeq.getEndPos(); + // if(endPos < minEndPos) { minEndPos = endPos; } + if (currentSeq.getNumBases() == 0) { + m->mothurOut("[WARNING]: " + currentSeq.getName() + " is blank, ignoring.");m->mothurOutEndLine(); + }else { + referenceSeqs.push_back(currentSeq); + if (rdb->save) { rdb->referenceSeqs.push_back(currentSeq); } + } + + m->gobble(referenceFile); + } + referenceFile.close(); + + m->mothurOut("It took " + toString(time(NULL) - start) + " to read " + toString(referenceSeqs.size()) + " sequences.");m->mothurOutEndLine(); } - referenceFile.close(); + numRefs = referenceSeqs.size(); - for(int i=0;imothurOut("Warning: " + toString(numAmbigSeqs) + " reference sequences have ambiguous bases, these bases will be ignored\n"); - } + } } catch(exception& e) { @@ -787,7 +882,7 @@ void SeqErrorCommand::getReferences(){ //*************************************************************************************************************** -Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){ +int SeqErrorCommand::getErrors(Sequence query, Sequence reference, Compare& errors){ try { if(query.getAlignLength() != reference.getAlignLength()){ m->mothurOut("Warning: " + toString(query.getName()) + " and " + toString(reference.getName()) + " are different lengths\n"); @@ -798,56 +893,68 @@ Compare SeqErrorCommand::getErrors(Sequence query, Sequence reference){ string r = reference.getAligned(); int started = 0; - Compare errors; + //Compare errors; for(int i=0;ierrorOut(e, "SeqErrorCommand", "getErrors"); @@ -979,10 +1087,11 @@ void SeqErrorCommand::printErrorData(Compare error, int numParentSeqs, ofstream& void SeqErrorCommand::printSubMatrix(){ try { - string subMatrixFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.matrix"; + string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(queryFileName)); + string subMatrixFileName = fileNameRoot + getOutputFileNameTag("errormatrix"); ofstream subMatrixFile; m->openOutputFile(subMatrixFileName, subMatrixFile); - outputNames.push_back(subMatrixFileName); outputTypes["error.matrix"].push_back(subMatrixFileName); + outputNames.push_back(subMatrixFileName); outputTypes["errormatrix"].push_back(subMatrixFileName); vector bases(6); bases[0] = "A"; bases[1] = "T"; @@ -1025,10 +1134,11 @@ void SeqErrorCommand::printSubMatrix(){ void SeqErrorCommand::printErrorFRFile(map > errorForward, map > errorReverse){ try{ - string errorForwardFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq.forward"; + string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(queryFileName)); + string errorForwardFileName = fileNameRoot + getOutputFileNameTag("errorforward"); ofstream errorForwardFile; m->openOutputFile(errorForwardFileName, errorForwardFile); - outputNames.push_back(errorForwardFileName); outputTypes["error.forward"].push_back(errorForwardFileName); + outputNames.push_back(errorForwardFileName); outputTypes["errorforward"].push_back(errorForwardFileName); errorForwardFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl; for(int i=0;i > errorForward, map } errorForwardFile.close(); - string errorReverseFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.seq.reverse"; + string errorReverseFileName = fileNameRoot + getOutputFileNameTag("errorreverse"); ofstream errorReverseFile; m->openOutputFile(errorReverseFileName, errorReverseFile); - outputNames.push_back(errorReverseFileName); outputTypes["error.reverse"].push_back(errorReverseFileName); + outputNames.push_back(errorReverseFileName); outputTypes["errorreverse"].push_back(errorReverseFileName); errorReverseFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl; for(int i=0;i > errorForward, map void SeqErrorCommand::printErrorQuality(map > qScoreErrorMap){ try{ - - string errorQualityFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.quality"; + string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(queryFileName)); + string errorQualityFileName = fileNameRoot + getOutputFileNameTag("errorquality"); ofstream errorQualityFile; m->openOutputFile(errorQualityFileName, errorQualityFile); - outputNames.push_back(errorQualityFileName); outputTypes["error.quality"].push_back(errorQualityFileName); + outputNames.push_back(errorQualityFileName); outputTypes["errorquality"].push_back(errorQualityFileName); errorQualityFile << "qscore\tmatches\tsubstitutions\tinsertions\tambiguous" << endl; for(int i=0;i<41;i++){ @@ -1105,11 +1215,11 @@ void SeqErrorCommand::printQualityFR(vector > qualForwardMap, vector } } } - - string qualityForwardFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.qual.forward"; + string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(queryFileName)); + string qualityForwardFileName = fileNameRoot + getOutputFileNameTag("errorqualforward"); ofstream qualityForwardFile; m->openOutputFile(qualityForwardFileName, qualityForwardFile); - outputNames.push_back(qualityForwardFileName); outputTypes["error.qual.forward"].push_back(qualityForwardFileName); + outputNames.push_back(qualityForwardFileName); outputTypes["errorqualforward"].push_back(qualityForwardFileName); for(int i=0;i > qualForwardMap, vector qualityForwardFile.close(); - string qualityReverseFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.qual.reverse"; + string qualityReverseFileName = fileNameRoot + getOutputFileNameTag("errorqualreverse"); ofstream qualityReverseFile; m->openOutputFile(qualityReverseFileName, qualityReverseFile); - outputNames.push_back(qualityReverseFileName); outputTypes["error.qual.reverse"].push_back(qualityReverseFileName); + outputNames.push_back(qualityReverseFileName); outputTypes["errorqualreverse"].push_back(qualityReverseFileName); for(int i=0;i > qualForwardMap, vector } /**************************************************************************************************/ -int SeqErrorCommand::setLines(string filename, string qfilename, string rfilename, vector& fastaFilePos, vector& qfileFilePos, vector& rfileFilePos) { +int SeqErrorCommand::setLines(string filename, string qfilename, string rfilename, vector& fastaFilePos, vector& qfileFilePos, vector& rfileFilePos) { try { -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) //set file positions for fasta file fastaFilePos = m->divideFile(filename, processors); @@ -1190,7 +1300,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam map::iterator it = firstSeqNames.find(sname); if(it != firstSeqNames.end()) { //this is the start of a new chunk - unsigned long int pos = inQual.tellg(); + unsigned long long pos = inQual.tellg(); qfileFilePos.push_back(pos - input.length() - 1); firstSeqNames.erase(it); } @@ -1211,7 +1321,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam //get last file position of qfile FILE * pFile; - unsigned long int size; + unsigned long long size; //get num bytes in file pFile = fopen (qfilename.c_str(),"rb"); @@ -1249,7 +1359,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam map::iterator it = firstSeqNamesReport.find(sname); if(it != firstSeqNamesReport.end()) { //this is the start of a new chunk - unsigned long int pos = inR.tellg(); + unsigned long long pos = inR.tellg(); rfileFilePos.push_back(pos - input.length() - 1); firstSeqNamesReport.erase(it); } @@ -1270,7 +1380,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam //get last file position of qfile FILE * rFile; - unsigned long int sizeR; + unsigned long long sizeR; //get num bytes in file rFile = fopen (rfilename.c_str(),"rb"); @@ -1290,7 +1400,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam fastaFilePos.push_back(0); qfileFilePos.push_back(0); //get last file position of fastafile FILE * pFile; - unsigned long int size; + unsigned long long size; //get num bytes in file pFile = fopen (filename.c_str(),"rb");