seqerrorcommand.cpp

   1 /*
   2  *  seqerrorcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 7/15/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "seqerrorcommand.h"
  11 #include "reportfile.h"
  12 #include "qualityscores.h"
  13 #include "refchimeratest.h"
  14 #include "filterseqscommand.h"
  15
  16
  17 //**********************************************************************************************************************
  18 vector<string> SeqErrorCommand::setParameters(){
  19         try {
  20                 CommandParameter pquery("fasta", "InputTypes", "", "", "none", "none", "none","errorType",false,true,true); parameters.push_back(pquery);
  21                 CommandParameter preference("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(preference);
  22                 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "QualReport","",false,false); parameters.push_back(pqfile);
  23                 CommandParameter preport("report", "InputTypes", "", "", "none", "none", "QualReport","",false,false); parameters.push_back(preport);
  24                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pname);
  25                 CommandParameter pignorechimeras("ignorechimeras", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pignorechimeras);
  26                 CommandParameter pthreshold("threshold", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pthreshold);
  27                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
  28                 CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
  29                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  30                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  31
  32                 vector<string> myArray;
  33                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  34                 return myArray;
  35         }
  36         catch(exception& e) {
  37                 m->errorOut(e, "SeqErrorCommand", "setParameters");
  38                 exit(1);
  39         }
  40 }
  41 //**********************************************************************************************************************
  42 string SeqErrorCommand::getHelpString(){
  43         try {
  44                 string helpString = "";
  45                 helpString += "The seq.error command reads a query alignment file and a reference alignment file and creates .....\n";
  46                 helpString += "The fasta parameter...\n";
  47                 helpString += "The reference parameter...\n";
  48                 helpString += "The qfile parameter...\n";
  49                 helpString += "The report parameter...\n";
  50                 helpString += "The name parameter...\n";
  51                 helpString += "The ignorechimeras parameter...\n";
  52                 helpString += "The threshold parameter...\n";
  53                 helpString += "The processors parameter...\n";
  54                 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.";
  55                 helpString += "Example seq.error(...).\n";
  56                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  57                 helpString += "For more details please check out the wiki http://www.mothur.org/wiki/seq.error .\n";
  58                 return helpString;
  59         }
  60         catch(exception& e) {
  61                 m->errorOut(e, "SeqErrorCommand", "getHelpString");
  62                 exit(1);
  63         }
  64 }
  65 //**********************************************************************************************************************
  66 string SeqErrorCommand::getOutputPattern(string type) {
  67     try {
  68         string pattern = "";
  69
  70         if (type == "errorsummary")            {   pattern = "[filename],error.summary";   }
  71         else if (type == "errorseq")            {   pattern = "[filename],error.seq";   }
  72         else if (type == "errorquality")            {   pattern = "[filename],error.quality";   }
  73         else if (type == "errorqualforward")            {   pattern = "[filename],error.qual.forward";   }
  74         else if (type == "errorqualreverse")            {   pattern = "[filename],error.qual.reverse";   }
  75         else if (type == "errorforward")            {   pattern = "[filename],error.seq.forward";   }
  76         else if (type == "errorreverse")            {   pattern = "[filename],error.seq.reverse";   }
  77         else if (type == "errorcount")            {   pattern = "[filename],error.count";   }
  78         else if (type == "errormatrix")            {   pattern = "[filename],error.matrix";   }
  79         else if (type == "errorchimera")            {   pattern = "[filename],error.chimera";   }
  80         else if (type == "errorref-query")            {   pattern = "[filename],error.ref-query";   }
  81         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  82
  83         return pattern;
  84     }
  85     catch(exception& e) {
  86         m->errorOut(e, "SeqErrorCommand", "getOutputPattern");
  87         exit(1);
  88     }
  89 }
  90 //**********************************************************************************************************************
  91 SeqErrorCommand::SeqErrorCommand(){
  92         try {
  93                 abort = true; calledHelp = true;
  94                 setParameters();
  95                 vector<string> tempOutNames;
  96                 outputTypes["errorsummary"] = tempOutNames;
  97                 outputTypes["errorseq"] = tempOutNames;
  98                 outputTypes["errorquality"] = tempOutNames;
  99                 outputTypes["errorqualforward"] = tempOutNames;
 100                 outputTypes["errorqualreverse"] = tempOutNames;
 101                 outputTypes["errorforward"] = tempOutNames;
 102                 outputTypes["errorreverse"] = tempOutNames;
 103                 outputTypes["errorcount"] = tempOutNames;
 104                 outputTypes["errormatrix"] = tempOutNames;
 105         outputTypes["errorchimera"] = tempOutNames;
 106         outputTypes["errorref-query"] = tempOutNames;
 107         }
 108         catch(exception& e) {
 109                 m->errorOut(e, "SeqErrorCommand", "SeqErrorCommand");
 110                 exit(1);
 111         }
 112 }
 113 //***************************************************************************************************************
 114
 115 SeqErrorCommand::SeqErrorCommand(string option)  {
 116         try {
 117
 118                 abort = false; calledHelp = false;
 119                 rdb = ReferenceDB::getInstance();
 120
 121                 //allow user to run help
 122                 if(option == "help") { help(); abort = true; calledHelp = true; }
 123                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 124
 125                 else {
 126                         string temp;
 127                         vector<string> myArray = setParameters();
 128
 129                         OptionParser parser(option);
 130                         map<string,string> parameters = parser.getParameters();
 131
 132                         ValidParameters validParameter;
 133                         map<string,string>::iterator it;
 134
 135                         //check to make sure all parameters are valid for command
 136                         for (it = parameters.begin(); it != parameters.end(); it++) {
 137                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 138                         }
 139
 140                         //initialize outputTypes
 141                         vector<string> tempOutNames;
 142                         outputTypes["errorsummary"] = tempOutNames;
 143                         outputTypes["errorseq"] = tempOutNames;
 144                         outputTypes["errorquality"] = tempOutNames;
 145                         outputTypes["errorqualforward"] = tempOutNames;
 146                         outputTypes["errorqualreverse"] = tempOutNames;
 147                         outputTypes["errorforward"] = tempOutNames;
 148                         outputTypes["errorreverse"] = tempOutNames;
 149                         outputTypes["errorcount"] = tempOutNames;
 150                         outputTypes["errormatrix"] = tempOutNames;
 151             outputTypes["errorchimera"] = tempOutNames;
 152             outputTypes["errorref-query"] = tempOutNames;
 153
 154
 155                         //if the user changes the input directory command factory will send this info to us in the output parameter
 156                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 157                         if (inputDir == "not found"){   inputDir = "";          }
 158                         else {
 159                                 string path;
 160                                 it = parameters.find("fasta");
 161                                 //user has given a template file
 162                                 if(it != parameters.end()){
 163                                         path = m->hasPath(it->second);
 164                                         //if the user has not given a path then, add inputdir. else leave path alone.
 165                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 166                                 }
 167
 168                                 it = parameters.find("reference");
 169                                 //user has given a template file
 170                                 if(it != parameters.end()){
 171                                         path = m->hasPath(it->second);
 172                                         //if the user has not given a path then, add inputdir. else leave path alone.
 173                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 174                                 }
 175
 176                                 it = parameters.find("name");
 177                                 //user has given a names file
 178                                 if(it != parameters.end()){
 179                                         path = m->hasPath(it->second);
 180                                         //if the user has not given a path then, add inputdir. else leave path alone.
 181                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 182                                 }
 183
 184                                 it = parameters.find("qfile");
 185                                 //user has given a quality score file
 186                                 if(it != parameters.end()){
 187                                         path = m->hasPath(it->second);
 188                                         //if the user has not given a path then, add inputdir. else leave path alone.
 189                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 190                                 }
 191
 192                                 it = parameters.find("report");
 193                                 //user has given a alignment report file
 194                                 if(it != parameters.end()){
 195                                         path = m->hasPath(it->second);
 196                                         //if the user has not given a path then, add inputdir. else leave path alone.
 197                                         if (path == "") {       parameters["report"] = inputDir + it->second;           }
 198                                 }
 199
 200                         }
 201                         //check for required parameters
 202                         queryFileName = validParameter.validFile(parameters, "fasta", true);
 203                         if (queryFileName == "not found") {
 204                                 queryFileName = m->getFastaFile();
 205                                 if (queryFileName != "") { m->mothurOut("Using " + queryFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 206                                 else {  m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 207                         }
 208                         else if (queryFileName == "not open") { queryFileName = ""; abort = true; }
 209                         else { m->setFastaFile(queryFileName); }
 210
 211                         referenceFileName = validParameter.validFile(parameters, "reference", true);
 212                         if (referenceFileName == "not found") { m->mothurOut("reference is a required parameter for the seq.error command."); m->mothurOutEndLine(); abort = true; }
 213                         else if (referenceFileName == "not open") { abort = true; }
 214
 215                         //check for optional parameters
 216                         namesFileName = validParameter.validFile(parameters, "name", true);
 217                         if(namesFileName == "not found"){       namesFileName = "";     }
 218                         else if (namesFileName == "not open") { namesFileName = ""; abort = true; }
 219                         else { m->setNameFile(namesFileName); }
 220
 221                         qualFileName = validParameter.validFile(parameters, "qfile", true);
 222                         if(qualFileName == "not found"){        qualFileName = "";      }
 223                         else if (qualFileName == "not open") { qualFileName = ""; abort = true; }
 224                         else { m->setQualFile(qualFileName); }
 225
 226                         reportFileName = validParameter.validFile(parameters, "report", true);
 227                         if(reportFileName == "not found"){      reportFileName = "";    }
 228                         else if (reportFileName == "not open") { reportFileName = ""; abort = true; }
 229
 230                         if((reportFileName != "" && qualFileName == "") || (reportFileName == "" && qualFileName != "")){
 231                                 m->mothurOut("if you use either a qual file or a report file, you have to have both.");
 232                                 m->mothurOutEndLine();
 233                                 abort = true;
 234                         }
 235
 236                         outputDir = validParameter.validFile(parameters, "outputdir", false);
 237                         if (outputDir == "not found"){
 238                                 outputDir = "";
 239                                 outputDir += m->hasPath(queryFileName); //if user entered a file with a path then preserve it
 240                         }
 241
 242                         //check for optional parameter and set defaults
 243                         // ...at some point should added some additional type checking...
 244                         temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found") { temp = "1.00"; }
 245                         m->mothurConvert(temp, threshold);
 246
 247                         temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
 248                         save = m->isTrue(temp);
 249                         rdb->save = save;
 250                         if (save) { //clear out old references
 251                                 rdb->clearMemory();
 252                         }
 253
 254                         //this has to go after save so that if the user sets save=t and provides no reference we abort
 255                         referenceFileName = validParameter.validFile(parameters, "reference", true);
 256                         if (referenceFileName == "not found") {
 257                                 //check for saved reference sequences
 258                                 if (rdb->referenceSeqs.size() != 0) {
 259                                         referenceFileName = "saved";
 260                                 }else {
 261                                         m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required.");
 262                                         m->mothurOutEndLine();
 263                                         abort = true;
 264                                 }
 265                         }else if (referenceFileName == "not open") { abort = true; }
 266                         else {  if (save) {     rdb->setSavedReference(referenceFileName);      }       }
 267
 268
 269                         temp = validParameter.validFile(parameters, "ignorechimeras", false);   if (temp == "not found") { temp = "T"; }
 270                         ignoreChimeras = m->isTrue(temp);
 271
 272                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 273                         m->setProcessors(temp);
 274                         m->mothurConvert(temp, processors);
 275
 276                         substitutionMatrix.resize(6);
 277                         for(int i=0;i<6;i++){   substitutionMatrix[i].resize(6,0);      }
 278
 279                         if ((namesFileName == "") && (queryFileName != "")){
 280                                 vector<string> files; files.push_back(queryFileName);
 281                                 parser.getNameFile(files);
 282                         }
 283                 }
 284         }
 285         catch(exception& e) {
 286                 m->errorOut(e, "SeqErrorCommand", "SeqErrorCommand");
 287                 exit(1);
 288         }
 289 }
 290 //***************************************************************************************************************
 291
 292 int SeqErrorCommand::execute(){
 293         try{
 294                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 295
 296                 int start = time(NULL);
 297                 maxLength = 2000;
 298                 totalBases = 0;
 299                 totalMatches = 0;
 300
 301         string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(queryFileName));
 302         map<string, string> variables;
 303                 variables["[filename]"] = fileNameRoot;
 304                 string errorSummaryFileName = getOutputFileName("errorsummary",variables);
 305                 outputNames.push_back(errorSummaryFileName); outputTypes["errorsummary"].push_back(errorSummaryFileName);
 306
 307                 string errorSeqFileName = getOutputFileName("errorseq",variables);
 308                 outputNames.push_back(errorSeqFileName); outputTypes["errorseq"].push_back(errorSeqFileName);
 309
 310                 string errorChimeraFileName = getOutputFileName("errorchimera",variables);
 311                 outputNames.push_back(errorChimeraFileName); outputTypes["errorchimera"].push_back(errorChimeraFileName);
 312
 313                 getReferences();        //read in reference sequences - make sure there's no ambiguous bases
 314
 315                 if(namesFileName != ""){        weights = getWeights(); }
 316
 317                 vector<unsigned long long> fastaFilePos;
 318                 vector<unsigned long long> qFilePos;
 319                 vector<unsigned long long> reportFilePos;
 320
 321                 setLines(queryFileName, qualFileName, reportFileName, fastaFilePos, qFilePos, reportFilePos);
 322
 323                 if (m->control_pressed) { return 0; }
 324
 325                 for (int i = 0; i < (fastaFilePos.size()-1); i++) {
 326                         lines.push_back(linePair(fastaFilePos[i], fastaFilePos[(i+1)]));
 327                         if (qualFileName != "") {  qLines.push_back(linePair(qFilePos[i], qFilePos[(i+1)]));  }
 328                         if (reportFileName != "") {  rLines.push_back(linePair(reportFilePos[i], reportFilePos[(i+1)]));  }
 329                 }
 330                 if(qualFileName == "")  {       qLines = lines; rLines = lines; } //fills with duds
 331
 332                 int numSeqs = 0;
 333 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 334                 if(processors == 1){
 335                         numSeqs = driver(queryFileName, qualFileName, reportFileName, errorSummaryFileName, errorSeqFileName, errorChimeraFileName, lines[0], qLines[0], rLines[0]);
 336                 }else{
 337                         numSeqs = createProcesses(queryFileName, qualFileName, reportFileName, errorSummaryFileName, errorSeqFileName, errorChimeraFileName);
 338                 }
 339 #else
 340                 numSeqs = driver(queryFileName, qualFileName, reportFileName, errorSummaryFileName, errorSeqFileName, errorChimeraFileName, lines[0], qLines[0], rLines[0]);
 341 #endif
 342
 343                 if(qualFileName != "" && reportFileName != ""){
 344                         printErrorQuality(qScoreErrorMap);
 345                         printQualityFR(qualForwardMap, qualReverseMap);
 346                 }
 347
 348                 printErrorFRFile(errorForward, errorReverse);
 349
 350                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
 351
 352                 string errorCountFileName = getOutputFileName("errorcount",variables);
 353                 ofstream errorCountFile;
 354                 m->openOutputFile(errorCountFileName, errorCountFile);
 355                 outputNames.push_back(errorCountFileName);  outputTypes["errorcount"].push_back(errorCountFileName);
 356                 m->mothurOut("Overall error rate:\t" + toString((double)(totalBases - totalMatches) / (double)totalBases) + "\n");
 357                 m->mothurOut("Errors\tSequences\n");
 358                 errorCountFile << "Errors\tSequences\n";
 359                 for(int i=0;i<misMatchCounts.size();i++){
 360                         m->mothurOut(toString(i) + '\t' + toString(misMatchCounts[i]) + '\n');
 361                         errorCountFile << i << '\t' << misMatchCounts[i] << endl;
 362                 }
 363                 errorCountFile.close();
 364
 365                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
 366
 367                 printSubMatrix();
 368
 369                 string megAlignmentFileName = getOutputFileName("errorref-query",variables);
 370                 ofstream megAlignmentFile;
 371                 m->openOutputFile(megAlignmentFileName, megAlignmentFile);
 372                 outputNames.push_back(megAlignmentFileName);  outputTypes["errorref-query"].push_back(megAlignmentFileName);
 373
 374                 for(int i=0;i<numRefs;i++){
 375                         megAlignmentFile << referenceSeqs[i].getInlineSeq() << endl;
 376                         megAlignmentFile << megaAlignVector[i] << endl;
 377                 }
 378
 379                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences.");
 380                 m->mothurOutEndLine();
 381
 382                 m->mothurOutEndLine();
 383                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 384                 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
 385                 m->mothurOutEndLine();
 386
 387                 return 0;
 388         }
 389         catch(exception& e) {
 390                 m->errorOut(e, "SeqErrorCommand", "execute");
 391                 exit(1);
 392         }
 393 }
 394 //**********************************************************************************************************************
 395 int SeqErrorCommand::createProcesses(string filename, string qFileName, string rFileName, string summaryFileName, string errorOutputFileName, string chimeraOutputFileName) {
 396         try {
 397                 int process = 1;
 398                 processIDS.clear();
 399                 map<char, vector<int> >::iterator it;
 400                 int num = 0;
 401 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 402
 403                 //loop through and create all the processes you want
 404                 while (process != processors) {
 405                         int pid = fork();
 406
 407                         if (pid > 0) {
 408                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 409                                 process++;
 410                         }else if (pid == 0){
 411
 412                                 num = driver(filename, qFileName, rFileName, summaryFileName + toString(getpid()) + ".temp", errorOutputFileName+ toString(getpid()) + ".temp", chimeraOutputFileName + toString(getpid()) + ".temp", lines[process], qLines[process], rLines[process]);
 413
 414                                 //pass groupCounts to parent
 415                                 ofstream out;
 416                                 string tempFile = filename + toString(getpid()) + ".info.temp";
 417                                 m->openOutputFile(tempFile, out);
 418
 419                                 //output totalBases and totalMatches
 420                                 out << num << '\t' << totalBases << '\t' << totalMatches << endl << endl;
 421
 422                                 //output substitutionMatrix
 423                                 for(int i = 0; i < substitutionMatrix.size(); i++) {
 424                                         for (int j = 0; j < substitutionMatrix[i].size(); j++) {
 425                                                 out << substitutionMatrix[i][j] << '\t';
 426                                         }
 427                                         out << endl;
 428                                 }
 429                                 out << endl;
 430
 431                                 //output qScoreErrorMap
 432                                 for (it = qScoreErrorMap.begin(); it != qScoreErrorMap.end(); it++) {
 433                                         vector<int> thisScoreErrorMap = it->second;
 434                                         out << it->first << '\t';
 435                                         for (int i = 0; i < thisScoreErrorMap.size(); i++) {
 436                                                 out << thisScoreErrorMap[i] << '\t';
 437                                         }
 438                                         out << endl;
 439                                 }
 440                                 out << endl;
 441
 442                                 //output qualForwardMap
 443                                 for(int i = 0; i < qualForwardMap.size(); i++) {
 444                                         for (int j = 0; j < qualForwardMap[i].size(); j++) {
 445                                                 out << qualForwardMap[i][j] << '\t';
 446                                         }
 447                                         out << endl;
 448                                 }
 449                                 out << endl;
 450
 451                                 //output qualReverseMap
 452                                 for(int i = 0; i < qualReverseMap.size(); i++) {
 453                                         for (int j = 0; j < qualReverseMap[i].size(); j++) {
 454                                                 out << qualReverseMap[i][j] << '\t';
 455                                         }
 456                                         out << endl;
 457                                 }
 458                                 out << endl;
 459
 460
 461                                 //output errorForward
 462                                 for (it = errorForward.begin(); it != errorForward.end(); it++) {
 463                                         vector<int> thisErrorForward = it->second;
 464                                         out << it->first << '\t';
 465                                         for (int i = 0; i < thisErrorForward.size(); i++) {
 466                                                 out << thisErrorForward[i] << '\t';
 467                                         }
 468                                         out << endl;
 469                                 }
 470                                 out << endl;
 471
 472                                 //output errorReverse
 473                                 for (it = errorReverse.begin(); it != errorReverse.end(); it++) {
 474                                         vector<int> thisErrorReverse = it->second;
 475                                         out << it->first << '\t';
 476                                         for (int i = 0; i < thisErrorReverse.size(); i++) {
 477                                                 out << thisErrorReverse[i] << '\t';
 478                                         }
 479                                         out << endl;
 480                                 }
 481                                 out << endl;
 482
 483                                 //output misMatchCounts
 484                                 out << misMatchCounts.size() << endl;
 485                                 for (int j = 0; j < misMatchCounts.size(); j++) {
 486                                         out << misMatchCounts[j] << '\t';
 487                                 }
 488                                 out << endl;
 489
 490
 491                                 //output megaAlignVector
 492                                 for (int j = 0; j < megaAlignVector.size(); j++) {
 493                                         out << megaAlignVector[j] << endl;
 494                                 }
 495                                 out << endl;
 496
 497                                 out.close();
 498
 499                                 exit(0);
 500                         }else {
 501                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 502                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 503                                 exit(0);
 504                         }
 505                 }
 506
 507                 //do my part
 508                 num = driver(filename, qFileName, rFileName, summaryFileName, errorOutputFileName, chimeraOutputFileName, lines[0], qLines[0], rLines[0]);
 509
 510                 //force parent to wait until all the processes are done
 511                 for (int i=0;i<processIDS.size();i++) {
 512                         int temp = processIDS[i];
 513                         wait(&temp);
 514                 }
 515
 516                 //append files
 517                 for(int i=0;i<processIDS.size();i++){
 518
 519                         m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
 520
 521                         m->appendFiles((summaryFileName + toString(processIDS[i]) + ".temp"), summaryFileName);
 522                         m->mothurRemove((summaryFileName + toString(processIDS[i]) + ".temp"));
 523                         m->appendFiles((errorOutputFileName + toString(processIDS[i]) + ".temp"), errorOutputFileName);
 524                         m->mothurRemove((errorOutputFileName + toString(processIDS[i]) + ".temp"));
 525                         m->appendFiles((chimeraOutputFileName + toString(processIDS[i]) + ".temp"), chimeraOutputFileName);
 526                         m->mothurRemove((chimeraOutputFileName + toString(processIDS[i]) + ".temp"));
 527
 528                         ifstream in;
 529                         string tempFile =  filename + toString(processIDS[i]) + ".info.temp";
 530                         m->openInputFile(tempFile, in);
 531
 532                         //input totalBases and totalMatches
 533                         int tempBases, tempMatches, tempNumSeqs;
 534                         in >> tempNumSeqs >> tempBases >> tempMatches; m->gobble(in);
 535                         totalBases += tempBases; totalMatches += tempMatches; num += tempNumSeqs;
 536
 537                         //input substitutionMatrix
 538                         int tempNum;
 539                         for(int i = 0; i < substitutionMatrix.size(); i++) {
 540                                 for (int j = 0; j < substitutionMatrix[i].size(); j++) {
 541                                         in >> tempNum; substitutionMatrix[i][j] += tempNum;
 542                                 }
 543                                 m->gobble(in);
 544                         }
 545                         m->gobble(in);
 546
 547                         //input qScoreErrorMap
 548                         char first;
 549                         for (int i = 0; i < qScoreErrorMap.size(); i++) {
 550                                 in >> first;
 551                                 vector<int> thisScoreErrorMap = qScoreErrorMap[first];
 552
 553                                 for (int i = 0; i < thisScoreErrorMap.size(); i++) {
 554                                         in >> tempNum; thisScoreErrorMap[i] += tempNum;
 555                                 }
 556                                 qScoreErrorMap[first] = thisScoreErrorMap;
 557                                 m->gobble(in);
 558                         }
 559                         m->gobble(in);
 560
 561                         //input qualForwardMap
 562                         for(int i = 0; i < qualForwardMap.size(); i++) {
 563                                 for (int j = 0; j < qualForwardMap[i].size(); j++) {
 564                                         in >> tempNum; qualForwardMap[i][j] += tempNum;
 565                                 }
 566                                 m->gobble(in);
 567                         }
 568                         m->gobble(in);
 569
 570                         //input qualReverseMap
 571                         for(int i = 0; i < qualReverseMap.size(); i++) {
 572                                 for (int j = 0; j < qualReverseMap[i].size(); j++) {
 573                                         in >> tempNum; qualReverseMap[i][j] += tempNum;
 574                                 }
 575                                 m->gobble(in);
 576                         }
 577                         m->gobble(in);
 578
 579                         //input errorForward
 580                         for (int i = 0; i < errorForward.size(); i++) {
 581                                 in >> first;
 582                                 vector<int> thisErrorForward = errorForward[first];
 583
 584                                 for (int i = 0; i < thisErrorForward.size(); i++) {
 585                                         in >> tempNum; thisErrorForward[i] += tempNum;
 586                                 }
 587                                 errorForward[first] = thisErrorForward;
 588                                 m->gobble(in);
 589                         }
 590                         m->gobble(in);
 591
 592                         //input errorReverse
 593                         for (int i = 0; i < errorReverse.size(); i++) {
 594                                 in >> first;
 595                                 vector<int> thisErrorReverse = errorReverse[first];
 596
 597                                 for (int i = 0; i < thisErrorReverse.size(); i++) {
 598                                         in >> tempNum; thisErrorReverse[i] += tempNum;
 599                                 }
 600                                 errorReverse[first] = thisErrorReverse;
 601                                 m->gobble(in);
 602                         }
 603                         m->gobble(in);
 604
 605                         //input misMatchCounts
 606                         int misMatchSize;
 607                         in >> misMatchSize; m->gobble(in);
 608                         if (misMatchSize > misMatchCounts.size()) {     misMatchCounts.resize(misMatchSize, 0); }
 609                         for (int j = 0; j < misMatchCounts.size(); j++) {
 610                                 in >> tempNum; misMatchCounts[j] += tempNum;
 611                         }
 612                         m->gobble(in);
 613
 614                         //input megaAlignVector
 615                         string thisLine;
 616                         for (int j = 0; j < megaAlignVector.size(); j++) {
 617                                 thisLine = m->getline(in); m->gobble(in); megaAlignVector[j] += thisLine + '\n';
 618                         }
 619                         m->gobble(in);
 620
 621                         in.close(); m->mothurRemove(tempFile);
 622
 623                 }
 624 #endif
 625                 return num;
 626         }
 627         catch(exception& e) {
 628                 m->errorOut(e, "SeqErrorCommand", "createProcesses");
 629                 exit(1);
 630         }
 631 }
 632 //**********************************************************************************************************************
 633 int SeqErrorCommand::driver(string filename, string qFileName, string rFileName, string summaryFileName, string errorOutputFileName, string chimeraOutputFileName, linePair line, linePair qline, linePair rline) {
 634
 635         try {
 636                 ReportFile report;
 637                 QualityScores quality;
 638
 639                 misMatchCounts.resize(11, 0);
 640                 int maxMismatch = 0;
 641                 int numSeqs = 0;
 642
 643                 map<string, int>::iterator it;
 644                 qScoreErrorMap['m'].assign(41, 0);
 645                 qScoreErrorMap['s'].assign(41, 0);
 646                 qScoreErrorMap['i'].assign(41, 0);
 647                 qScoreErrorMap['a'].assign(41, 0);
 648
 649                 errorForward['m'].assign(maxLength,0);
 650                 errorForward['s'].assign(maxLength,0);
 651                 errorForward['i'].assign(maxLength,0);
 652                 errorForward['d'].assign(maxLength,0);
 653                 errorForward['a'].assign(maxLength,0);
 654
 655                 errorReverse['m'].assign(maxLength,0);
 656                 errorReverse['s'].assign(maxLength,0);
 657                 errorReverse['i'].assign(maxLength,0);
 658                 errorReverse['d'].assign(maxLength,0);
 659                 errorReverse['a'].assign(maxLength,0);
 660
 661                 //open inputfiles and go to beginning place for this processor
 662                 ifstream queryFile;
 663                 m->openInputFile(filename, queryFile);
 664                 queryFile.seekg(line.start);
 665
 666                 ifstream reportFile;
 667                 ifstream qualFile;
 668                 if(qFileName != "" && rFileName != ""){
 669                         m->openInputFile(qFileName, qualFile);
 670                         qualFile.seekg(qline.start);
 671
 672                         //gobble headers
 673                         if (rline.start == 0) {  report = ReportFile(reportFile, rFileName); }
 674                         else{
 675                                 m->openInputFile(rFileName, reportFile);
 676                                 reportFile.seekg(rline.start);
 677                         }
 678
 679                         qualForwardMap.resize(maxLength);
 680                         qualReverseMap.resize(maxLength);
 681                         for(int i=0;i<maxLength;i++){
 682                                 qualForwardMap[i].assign(41,0);
 683                                 qualReverseMap[i].assign(41,0);
 684                         }
 685                 }
 686
 687                 ofstream outChimeraReport;
 688                 m->openOutputFile(chimeraOutputFileName, outChimeraReport);
 689                 RefChimeraTest chimeraTest(referenceSeqs);
 690                 if (line.start == 0) { chimeraTest.printHeader(outChimeraReport); }
 691
 692                 ofstream errorSummaryFile;
 693                 m->openOutputFile(summaryFileName, errorSummaryFile);
 694                 if (line.start == 0) { printErrorHeader(errorSummaryFile); }
 695
 696                 ofstream errorSeqFile;
 697                 m->openOutputFile(errorOutputFileName, errorSeqFile);
 698
 699                 megaAlignVector.resize(numRefs, "");
 700
 701                 int index = 0;
 702                 bool ignoreSeq = 0;
 703
 704                 bool moreSeqs = 1;
 705                 while (moreSeqs) {
 706
 707                         if (m->control_pressed) { queryFile.close(); if(qFileName != "" && rFileName != ""){  reportFile.close(); qualFile.close(); } outChimeraReport.close(); errorSummaryFile.close();errorSeqFile.close(); return 0; }
 708
 709                         Sequence query(queryFile);
 710
 711                         int numParentSeqs = chimeraTest.analyzeQuery(query.getName(), query.getAligned(), outChimeraReport);
 712                         int closestRefIndex = chimeraTest.getClosestRefIndex();
 713
 714                         if(numParentSeqs > 1 && ignoreChimeras == 1)    {       ignoreSeq = 1;  }
 715                         else                                                                                    {       ignoreSeq = 0;  }
 716
 717                         Compare minCompare;
 718             getErrors(query, referenceSeqs[closestRefIndex], minCompare);
 719
 720                         if(namesFileName != ""){
 721                                 it = weights.find(query.getName());
 722                                 minCompare.weight = it->second;
 723                         }
 724                         else{   minCompare.weight = 1;  }
 725
 726                         printErrorData(minCompare, numParentSeqs, errorSummaryFile, errorSeqFile);
 727
 728                         if(!ignoreSeq){
 729
 730                                 for(int i=0;i<minCompare.sequence.length();i++){
 731                                         char letter = minCompare.sequence[i];
 732
 733                                         if(letter != 'r'){
 734                                                 errorForward[letter][i] += minCompare.weight;
 735                                                 errorReverse[letter][minCompare.total-i-1] += minCompare.weight;
 736                                         }
 737                                 }
 738                         }
 739
 740                         if(qualFileName != "" && reportFileName != ""){
 741                                 report = ReportFile(reportFile);
 742
 743                                 //                              int origLength = report.getQueryLength();
 744                                 int startBase = report.getQueryStart();
 745                                 int endBase = report.getQueryEnd();
 746
 747                                 quality = QualityScores(qualFile);
 748
 749                                 if(!ignoreSeq){
 750 //                                      cout << query.getName() << '\t';
 751
 752                                         quality.updateQScoreErrorMap(qScoreErrorMap, minCompare.sequence, startBase, endBase, minCompare.weight);
 753                                         quality.updateForwardMap(qualForwardMap, startBase, endBase, minCompare.weight);
 754                                         quality.updateReverseMap(qualReverseMap, startBase, endBase, minCompare.weight);
 755
 756 //                                      cout << endl;
 757                                 }
 758                         }
 759
 760                         if(minCompare.errorRate < threshold && !ignoreSeq){
 761                                 totalBases += (minCompare.total * minCompare.weight);
 762                                 totalMatches += minCompare.matches * minCompare.weight;
 763                                 if(minCompare.mismatches > maxMismatch){
 764                                         maxMismatch = minCompare.mismatches;
 765                                         misMatchCounts.resize(maxMismatch + 1, 0);
 766                                 }
 767                                 misMatchCounts[minCompare.mismatches] += minCompare.weight;
 768                                 numSeqs++;
 769
 770                                 megaAlignVector[closestRefIndex] += query.getInlineSeq() + '\n';
 771                         }
 772
 773                         index++;
 774
 775                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 776                                 unsigned long long pos = queryFile.tellg();
 777                                 if ((pos == -1) || (pos >= line.end)) { break; }
 778                         #else
 779                                 if (queryFile.eof()) { break; }
 780                         #endif
 781
 782                         if(index % 100 == 0){   m->mothurOut(toString(index));  m->mothurOutEndLine(); }
 783                 }
 784                 queryFile.close();
 785                 if(qFileName != "" && rFileName != ""){  reportFile.close(); qualFile.close(); }
 786                 errorSummaryFile.close();
 787                 errorSeqFile.close();
 788
 789                 //report progress
 790                 if(index % 100 != 0){   m->mothurOut(toString(index));  m->mothurOutEndLine(); }
 791
 792                 return index;
 793         }
 794         catch(exception& e) {
 795                 m->errorOut(e, "SeqErrorCommand", "driver");
 796                 exit(1);
 797         }
 798 }
 799 //***************************************************************************************************************
 800
 801 void SeqErrorCommand::getReferences(){
 802         try {
 803                 int numAmbigSeqs = 0;
 804
 805                 int maxStartPos = 0;
 806                 int minEndPos = 100000;
 807
 808                 if (referenceFileName == "saved") {
 809                         int start = time(NULL);
 810                         m->mothurOutEndLine();  m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory.");        m->mothurOutEndLine();
 811
 812                         for (int i = 0; i < rdb->referenceSeqs.size(); i++) {
 813                                 int numAmbigs = rdb->referenceSeqs[i].getAmbigBases();
 814                                 if(numAmbigs > 0){      numAmbigSeqs++; }
 815
 816                                 //                      int startPos = rdb->referenceSeqs[i].getStartPos();
 817                                 //                      if(startPos > maxStartPos)      {       maxStartPos = startPos; }
 818                                 //
 819                                 //                      int endPos = rdb->referenceSeqs[i].getEndPos();
 820                                 //                      if(endPos < minEndPos)          {       minEndPos = endPos;             }
 821                                 if (rdb->referenceSeqs[i].getNumBases() == 0) {
 822                     m->mothurOut("[WARNING]: " + rdb->referenceSeqs[i].getName() + " is blank, ignoring.");m->mothurOutEndLine();
 823                 }else {
 824                     referenceSeqs.push_back(rdb->referenceSeqs[i]);
 825                 }
 826
 827                         }
 828                         referenceFileName = rdb->getSavedReference();
 829
 830                         m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(referenceSeqs.size()) + " sequences.");m->mothurOutEndLine();
 831
 832                 }else {
 833                         int start = time(NULL);
 834
 835                         ifstream referenceFile;
 836                         m->openInputFile(referenceFileName, referenceFile);
 837
 838                         while(referenceFile){
 839                                 Sequence currentSeq(referenceFile);
 840                                 int numAmbigs = currentSeq.getAmbigBases();
 841                                 if(numAmbigs > 0){      numAmbigSeqs++; }
 842
 843         //                      int startPos = currentSeq.getStartPos();
 844         //                      if(startPos > maxStartPos)      {       maxStartPos = startPos; }
 845         //
 846         //                      int endPos = currentSeq.getEndPos();
 847         //                      if(endPos < minEndPos)          {       minEndPos = endPos;             }
 848                 if (currentSeq.getNumBases() == 0) {
 849                     m->mothurOut("[WARNING]: " + currentSeq.getName() + " is blank, ignoring.");m->mothurOutEndLine();
 850                 }else {
 851                     referenceSeqs.push_back(currentSeq);
 852                     if (rdb->save) { rdb->referenceSeqs.push_back(currentSeq); }
 853                 }
 854
 855                                 m->gobble(referenceFile);
 856                         }
 857                         referenceFile.close();
 858
 859                         m->mothurOut("It took " + toString(time(NULL) - start) + " to read " + toString(referenceSeqs.size()) + " sequences.");m->mothurOutEndLine();
 860                 }
 861
 862                 numRefs = referenceSeqs.size();
 863
 864                 for(int i=0;i<numRefs;i++){
 865                         referenceSeqs[i].padToPos(maxStartPos);
 866                         referenceSeqs[i].padFromPos(minEndPos);
 867         }
 868
 869                 if(numAmbigSeqs != 0){
 870                         m->mothurOut("Warning: " + toString(numAmbigSeqs) + " reference sequences have ambiguous bases, these bases will be ignored\n");
 871                 }
 872
 873         }
 874         catch(exception& e) {
 875                 m->errorOut(e, "SeqErrorCommand", "getReferences");
 876                 exit(1);
 877         }
 878 }
 879
 880 //***************************************************************************************************************
 881
 882 int SeqErrorCommand::getErrors(Sequence query, Sequence reference, Compare& errors){
 883         try {
 884                 if(query.getAlignLength() != reference.getAlignLength()){
 885                         m->mothurOut("Warning: " + toString(query.getName()) + " and " + toString(reference.getName()) + " are different lengths\n");
 886                 }
 887                 int alignLength = query.getAlignLength();
 888
 889                 string q = query.getAligned();
 890                 string r = reference.getAligned();
 891
 892                 int started = 0;
 893                 //Compare errors;
 894
 895                 for(int i=0;i<alignLength;i++){
 896 //                      cout << r[i] << '\t' << q[i] << '\t';
 897                         if(q[i] != '.' && r[i] != '.' && (q[i] != '-' || r[i] != '-')){                 //      no missing data and no double gaps
 898                                 if(r[i] != 'N'){
 899                                         started = 1;
 900
 901                                         if(q[i] == 'A'){
 902                                                 if(r[i] == 'A'){        errors.AA++;    errors.matches++;       errors.sequence += 'm'; }
 903                                                 if(r[i] == 'T'){        errors.AT++;    errors.sequence += 's'; }
 904                                                 if(r[i] == 'G'){        errors.AG++;    errors.sequence += 's'; }
 905                                                 if(r[i] == 'C'){        errors.AC++;    errors.sequence += 's'; }
 906                                                 if(r[i] == '-'){        errors.Ai++;    errors.sequence += 'i'; }
 907                                         }
 908                                         else if(q[i] == 'T'){
 909                                                 if(r[i] == 'A'){        errors.TA++;    errors.sequence += 's'; }
 910                                                 if(r[i] == 'T'){        errors.TT++;    errors.matches++;       errors.sequence += 'm'; }
 911                                                 if(r[i] == 'G'){        errors.TG++;    errors.sequence += 's'; }
 912                                                 if(r[i] == 'C'){        errors.TC++;    errors.sequence += 's'; }
 913                                                 if(r[i] == '-'){        errors.Ti++;    errors.sequence += 'i'; }
 914                                         }
 915                                         else if(q[i] == 'G'){
 916                                                 if(r[i] == 'A'){        errors.GA++;    errors.sequence += 's'; }
 917                                                 if(r[i] == 'T'){        errors.GT++;    errors.sequence += 's'; }
 918                                                 if(r[i] == 'G'){        errors.GG++;    errors.matches++;       errors.sequence += 'm'; }
 919                                                 if(r[i] == 'C'){        errors.GC++;    errors.sequence += 's'; }
 920                                                 if(r[i] == '-'){        errors.Gi++;    errors.sequence += 'i'; }
 921                                         }
 922                                         else if(q[i] == 'C'){
 923                                                 if(r[i] == 'A'){        errors.CA++;    errors.sequence += 's'; }
 924                                                 if(r[i] == 'T'){        errors.CT++;    errors.sequence += 's'; }
 925                                                 if(r[i] == 'G'){        errors.CG++;    errors.sequence += 's'; }
 926                                                 if(r[i] == 'C'){        errors.CC++;    errors.matches++;       errors.sequence += 'm'; }
 927                                                 if(r[i] == '-'){        errors.Ci++;    errors.sequence += 'i'; }
 928                                         }
 929                                         else if(q[i] == 'N'){
 930                                                 if(r[i] == 'A'){        errors.NA++;    errors.sequence += 'a'; }
 931                                                 if(r[i] == 'T'){        errors.NT++;    errors.sequence += 'a'; }
 932                                                 if(r[i] == 'G'){        errors.NG++;    errors.sequence += 'a'; }
 933                                                 if(r[i] == 'C'){        errors.NC++;    errors.sequence += 'a'; }
 934                                                 if(r[i] == '-'){        errors.Ni++;    errors.sequence += 'a'; }
 935                                         }
 936                                         else if(q[i] == '-' && r[i] != '-'){
 937                                                 if(r[i] == 'A'){        errors.dA++;    errors.sequence += 'd'; }
 938                                                 if(r[i] == 'T'){        errors.dT++;    errors.sequence += 'd'; }
 939                                                 if(r[i] == 'G'){        errors.dG++;    errors.sequence += 'd'; }
 940                                                 if(r[i] == 'C'){        errors.dC++;    errors.sequence += 'd'; }
 941                                         }
 942                                         errors.total++;
 943                                 }
 944                                 else{
 945
 946                                         if(q[i] == '-'){
 947                                                 errors.sequence += 'd'; errors.total++;
 948                                         }
 949                                         else{
 950                                                 errors.sequence += 'r';
 951                                         }
 952                                 }
 953                         }
 954
 955                         else if(q[i] == '.' && r[i] != '.'){            //      reference extends beyond query
 956                                 if(started == 1){       break;  }
 957                         }
 958                         else if(q[i] != '.' && r[i] == '.'){            //      query extends beyond reference
 959                                 if(started == 1){       break;  }
 960                         }
 961                         else if(q[i] == '.' && r[i] == '.'){            //      both are missing data
 962                                 if(started == 1){       break;  }
 963                         }
 964 //                      cout << errors.sequence[errors.sequence.length()-1] << endl;
 965                 }
 966 //              cout << errors.sequence << endl;
 967                 errors.mismatches = errors.total-errors.matches;
 968                 errors.errorRate = (double)(errors.total-errors.matches) / (double)errors.total;
 969                 errors.queryName = query.getName();
 970                 errors.refName = reference.getName();
 971                 //return errors;
 972         return 0;
 973         }
 974         catch(exception& e) {
 975                 m->errorOut(e, "SeqErrorCommand", "getErrors");
 976                 exit(1);
 977         }
 978 }
 979
 980 //***************************************************************************************************************
 981
 982 map<string, int> SeqErrorCommand::getWeights(){
 983         ifstream nameFile;
 984         m->openInputFile(namesFileName, nameFile);
 985
 986         string seqName;
 987         string redundantSeqs;
 988         map<string, int> nameCountMap;
 989
 990         while(nameFile){
 991                 nameFile >> seqName >> redundantSeqs;
 992                 nameCountMap[seqName] = m->getNumNames(redundantSeqs);
 993                 m->gobble(nameFile);
 994         }
 995         return nameCountMap;
 996 }
 997
 998
 999 //***************************************************************************************************************
1000
1001 void SeqErrorCommand::printErrorHeader(ofstream& errorSummaryFile){
1002         try {
1003                 errorSummaryFile << "query\treference\tweight\t";
1004                 errorSummaryFile << "AA\tAT\tAG\tAC\tTA\tTT\tTG\tTC\tGA\tGT\tGG\tGC\tCA\tCT\tCG\tCC\tNA\tNT\tNG\tNC\tAi\tTi\tGi\tCi\tNi\tdA\tdT\tdG\tdC\t";
1005                 errorSummaryFile << "insertions\tdeletions\tsubstitutions\tambig\tmatches\tmismatches\ttotal\terror\tnumparents\n";
1006
1007                 errorSummaryFile << setprecision(6);
1008                 errorSummaryFile.setf(ios::fixed);
1009         }
1010         catch(exception& e) {
1011                 m->errorOut(e, "SeqErrorCommand", "printErrorHeader");
1012                 exit(1);
1013         }
1014 }
1015
1016 //***************************************************************************************************************
1017
1018 void SeqErrorCommand::printErrorData(Compare error, int numParentSeqs, ofstream& errorSummaryFile, ofstream& errorSeqFile){
1019         try {
1020
1021                 errorSummaryFile << error.queryName << '\t' << error.refName << '\t' << error.weight << '\t';
1022                 errorSummaryFile << error.AA << '\t' << error.AT << '\t' << error.AG << '\t' << error.AC << '\t';
1023                 errorSummaryFile << error.TA << '\t' << error.TT << '\t' << error.TG << '\t' << error.TC << '\t';
1024                 errorSummaryFile << error.GA << '\t' << error.GT << '\t' << error.GG << '\t' << error.GC << '\t';
1025                 errorSummaryFile << error.CA << '\t' << error.CT << '\t' << error.CG << '\t' << error.CC << '\t';
1026                 errorSummaryFile << error.NA << '\t' << error.NT << '\t' << error.NG << '\t' << error.NC << '\t';
1027                 errorSummaryFile << error.Ai << '\t' << error.Ti << '\t' << error.Gi << '\t' << error.Ci << '\t' << error.Ni << '\t';
1028                 errorSummaryFile << error.dA << '\t' << error.dT << '\t' << error.dG << '\t' << error.dC << '\t';
1029
1030                 errorSummaryFile << error.Ai + error.Ti + error.Gi + error.Ci << '\t';                  //insertions
1031                 errorSummaryFile << error.dA + error.dT + error.dG + error.dC << '\t';                  //deletions
1032                 errorSummaryFile << error.mismatches - (error.Ai + error.Ti + error.Gi + error.Ci) - (error.dA + error.dT + error.dG + error.dC) - (error.NA + error.NT + error.NG + error.NC + error.Ni) << '\t';      //substitutions
1033                 errorSummaryFile << error.NA + error.NT + error.NG + error.NC + error.Ni << '\t';       //ambiguities
1034                 errorSummaryFile << error.matches << '\t' << error.mismatches << '\t' << error.total << '\t' << error.errorRate << '\t' << numParentSeqs << endl;
1035
1036                 errorSeqFile << '>' << error.queryName << "\tref:" << error.refName << '\n' << error.sequence << endl;
1037
1038                 int a=0;                int t=1;                int g=2;                int c=3;
1039                 int gap=4;              int n=5;
1040
1041                 if(numParentSeqs == 1 || ignoreChimeras == 0){
1042                         substitutionMatrix[a][a] += error.weight * error.AA;
1043                         substitutionMatrix[a][t] += error.weight * error.TA;
1044                         substitutionMatrix[a][g] += error.weight * error.GA;
1045                         substitutionMatrix[a][c] += error.weight * error.CA;
1046                         substitutionMatrix[a][gap] += error.weight * error.dA;
1047                         substitutionMatrix[a][n] += error.weight * error.NA;
1048
1049                         substitutionMatrix[t][a] += error.weight * error.AT;
1050                         substitutionMatrix[t][t] += error.weight * error.TT;
1051                         substitutionMatrix[t][g] += error.weight * error.GT;
1052                         substitutionMatrix[t][c] += error.weight * error.CT;
1053                         substitutionMatrix[t][gap] += error.weight * error.dT;
1054                         substitutionMatrix[t][n] += error.weight * error.NT;
1055
1056                         substitutionMatrix[g][a] += error.weight * error.AG;
1057                         substitutionMatrix[g][t] += error.weight * error.TG;
1058                         substitutionMatrix[g][g] += error.weight * error.GG;
1059                         substitutionMatrix[g][c] += error.weight * error.CG;
1060                         substitutionMatrix[g][gap] += error.weight * error.dG;
1061                         substitutionMatrix[g][n] += error.weight * error.NG;
1062
1063                         substitutionMatrix[c][a] += error.weight * error.AC;
1064                         substitutionMatrix[c][t] += error.weight * error.TC;
1065                         substitutionMatrix[c][g] += error.weight * error.GC;
1066                         substitutionMatrix[c][c] += error.weight * error.CC;
1067                         substitutionMatrix[c][gap] += error.weight * error.dC;
1068                         substitutionMatrix[c][n] += error.weight * error.NC;
1069
1070                         substitutionMatrix[gap][a] += error.weight * error.Ai;
1071                         substitutionMatrix[gap][t] += error.weight * error.Ti;
1072                         substitutionMatrix[gap][g] += error.weight * error.Gi;
1073                         substitutionMatrix[gap][c] += error.weight * error.Ci;
1074                         substitutionMatrix[gap][n] += error.weight * error.Ni;
1075                 }
1076         }
1077         catch(exception& e) {
1078                 m->errorOut(e, "SeqErrorCommand", "printErrorData");
1079                 exit(1);
1080         }
1081 }
1082
1083 //***************************************************************************************************************
1084
1085 void SeqErrorCommand::printSubMatrix(){
1086         try {
1087         string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(queryFileName));
1088         map<string, string> variables;
1089                 variables["[filename]"] = fileNameRoot;
1090                 string subMatrixFileName = getOutputFileName("errormatrix",variables);
1091                 ofstream subMatrixFile;
1092                 m->openOutputFile(subMatrixFileName, subMatrixFile);
1093                 outputNames.push_back(subMatrixFileName);  outputTypes["errormatrix"].push_back(subMatrixFileName);
1094                 vector<string> bases(6);
1095                 bases[0] = "A";
1096                 bases[1] = "T";
1097                 bases[2] = "G";
1098                 bases[3] = "C";
1099                 bases[4] = "Gap";
1100                 bases[5] = "N";
1101                 vector<int> refSums(5,1);
1102
1103                 for(int i=0;i<5;i++){
1104                         subMatrixFile << "\tr" << bases[i];
1105
1106                         for(int j=0;j<6;j++){
1107                                 refSums[i] += substitutionMatrix[i][j];
1108                         }
1109                 }
1110                 subMatrixFile << endl;
1111
1112                 for(int i=0;i<6;i++){
1113                         subMatrixFile << 'q' << bases[i];
1114                         for(int j=0;j<5;j++){
1115                                 subMatrixFile << '\t' << substitutionMatrix[j][i];
1116                         }
1117                         subMatrixFile << endl;
1118                 }
1119
1120                 subMatrixFile << "total";
1121                 for(int i=0;i<5;i++){
1122                         subMatrixFile << '\t' << refSums[i];
1123                 }
1124                 subMatrixFile << endl;
1125                 subMatrixFile.close();
1126         }
1127         catch(exception& e) {
1128                 m->errorOut(e, "SeqErrorCommand", "printSubMatrix");
1129                 exit(1);
1130         }
1131 }
1132 //***************************************************************************************************************
1133
1134 void SeqErrorCommand::printErrorFRFile(map<char, vector<int> > errorForward, map<char, vector<int> > errorReverse){
1135         try{
1136         string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(queryFileName));
1137         map<string, string> variables;
1138                 variables["[filename]"] = fileNameRoot;
1139                 string errorForwardFileName = getOutputFileName("errorforward",variables);
1140                 ofstream errorForwardFile;
1141                 m->openOutputFile(errorForwardFileName, errorForwardFile);
1142                 outputNames.push_back(errorForwardFileName);  outputTypes["errorforward"].push_back(errorForwardFileName);
1143
1144                 errorForwardFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl;
1145                 for(int i=0;i<maxLength;i++){
1146                         float match = (float)errorForward['m'][i];
1147                         float subst = (float)errorForward['s'][i];
1148                         float insert = (float)errorForward['i'][i];
1149                         float del = (float)errorForward['d'][i];
1150                         float amb = (float)errorForward['a'][i];
1151                         float total = match + subst + insert + del + amb;
1152                         if(total == 0){ break;  }
1153                         errorForwardFile << i+1 << '\t' << total << '\t' << match/total  << '\t' << subst/total  << '\t' << insert/total  << '\t' << del/total  << '\t' << amb/total << endl;
1154                 }
1155                 errorForwardFile.close();
1156
1157                 string errorReverseFileName = getOutputFileName("errorreverse",variables);
1158                 ofstream errorReverseFile;
1159                 m->openOutputFile(errorReverseFileName, errorReverseFile);
1160                 outputNames.push_back(errorReverseFileName);  outputTypes["errorreverse"].push_back(errorReverseFileName);
1161
1162                 errorReverseFile << "position\ttotalseqs\tmatch\tsubstitution\tinsertion\tdeletion\tambiguous" << endl;
1163                 for(int i=0;i<maxLength;i++){
1164                         float match = (float)errorReverse['m'][i];
1165                         float subst = (float)errorReverse['s'][i];
1166                         float insert = (float)errorReverse['i'][i];
1167                         float del = (float)errorReverse['d'][i];
1168                         float amb = (float)errorReverse['a'][i];
1169                         float total = match + subst + insert + del + amb;
1170                         if(total == 0){ break;  }
1171                         errorReverseFile << i+1 << '\t' << total << '\t' << match/total  << '\t' << subst/total  << '\t' << insert/total  << '\t' << del/total  << '\t' << amb/total << endl;
1172                 }
1173                 errorReverseFile.close();
1174         }
1175         catch(exception& e) {
1176                 m->errorOut(e, "SeqErrorCommand", "printErrorFRFile");
1177                 exit(1);
1178         }
1179 }
1180
1181 //***************************************************************************************************************
1182
1183 void SeqErrorCommand::printErrorQuality(map<char, vector<int> > qScoreErrorMap){
1184         try{
1185         string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(queryFileName));
1186         map<string, string> variables;
1187                 variables["[filename]"] = fileNameRoot;
1188                 string errorQualityFileName = getOutputFileName("errorquality",variables);
1189                 ofstream errorQualityFile;
1190                 m->openOutputFile(errorQualityFileName, errorQualityFile);
1191                 outputNames.push_back(errorQualityFileName);  outputTypes["errorquality"].push_back(errorQualityFileName);
1192
1193                 errorQualityFile << "qscore\tmatches\tsubstitutions\tinsertions\tambiguous" << endl;
1194                 for(int i=0;i<41;i++){
1195                         errorQualityFile << i << '\t' << qScoreErrorMap['m'][i] << '\t' << qScoreErrorMap['s'][i] << '\t' << qScoreErrorMap['i'][i] << '\t'<< qScoreErrorMap['a'][i] << endl;
1196                 }
1197                 errorQualityFile.close();
1198         }
1199         catch(exception& e) {
1200                 m->errorOut(e, "SeqErrorCommand", "printErrorFRFile");
1201                 exit(1);
1202         }
1203 }
1204
1205
1206 //***************************************************************************************************************
1207
1208 void SeqErrorCommand::printQualityFR(vector<vector<int> > qualForwardMap, vector<vector<int> > qualReverseMap){
1209
1210         try{
1211                 int numRows = 0;
1212                 int numColumns = qualForwardMap[0].size();
1213
1214                 for(int i=0;i<qualForwardMap.size();i++){
1215                         for(int j=0;j<numColumns;j++){
1216                                 if(qualForwardMap[i][j] != 0){
1217                                         if(numRows < i)         {       numRows = i+20;         }
1218                                 }
1219                         }
1220                 }
1221         string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(queryFileName));
1222         map<string, string> variables;
1223                 variables["[filename]"] = fileNameRoot;
1224                 string qualityForwardFileName = getOutputFileName("errorqualforward",variables);
1225                 ofstream qualityForwardFile;
1226                 m->openOutputFile(qualityForwardFileName, qualityForwardFile);
1227                 outputNames.push_back(qualityForwardFileName);  outputTypes["errorqualforward"].push_back(qualityForwardFileName);
1228
1229                 for(int i=0;i<numColumns;i++){  qualityForwardFile << '\t' << i;        }       qualityForwardFile << endl;
1230
1231                 for(int i=0;i<numRows;i++){
1232                         qualityForwardFile << i+1;
1233                         for(int j=0;j<numColumns;j++){
1234                                 qualityForwardFile << '\t' << qualForwardMap[i][j];
1235                         }
1236
1237                         qualityForwardFile << endl;
1238                 }
1239                 qualityForwardFile.close();
1240
1241
1242                 string qualityReverseFileName = getOutputFileName("errorqualreverse",variables);
1243                 ofstream qualityReverseFile;
1244                 m->openOutputFile(qualityReverseFileName, qualityReverseFile);
1245                 outputNames.push_back(qualityReverseFileName);  outputTypes["errorqualreverse"].push_back(qualityReverseFileName);
1246
1247                 for(int i=0;i<numColumns;i++){  qualityReverseFile << '\t' << i;        }       qualityReverseFile << endl;
1248                 for(int i=0;i<numRows;i++){
1249
1250                         qualityReverseFile << i+1;
1251                         for(int j=0;j<numColumns;j++){
1252                                 qualityReverseFile << '\t' << qualReverseMap[i][j];
1253                         }
1254                         qualityReverseFile << endl;
1255                 }
1256                 qualityReverseFile.close();
1257         }
1258         catch(exception& e) {
1259                 m->errorOut(e, "SeqErrorCommand", "printErrorFRFile");
1260                 exit(1);
1261         }
1262
1263 }
1264 /**************************************************************************************************/
1265
1266 int SeqErrorCommand::setLines(string filename, string qfilename, string rfilename, vector<unsigned long long>& fastaFilePos, vector<unsigned long long>& qfileFilePos, vector<unsigned long long>& rfileFilePos) {
1267         try {
1268 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1269                 //set file positions for fasta file
1270                 fastaFilePos = m->divideFile(filename, processors);
1271
1272                 if (qfilename == "") { return processors; }
1273
1274                 //get name of first sequence in each chunk
1275                 map<string, int> firstSeqNames;
1276                 for (int i = 0; i < (fastaFilePos.size()-1); i++) {
1277                         ifstream in;
1278                         m->openInputFile(filename, in);
1279                         in.seekg(fastaFilePos[i]);
1280
1281                         Sequence temp(in);
1282                         firstSeqNames[temp.getName()] = i;
1283
1284                         in.close();
1285                 }
1286
1287                 //make copy to use below
1288                 map<string, int> firstSeqNamesReport = firstSeqNames;
1289
1290                 //seach for filePos of each first name in the qfile and save in qfileFilePos
1291                 ifstream inQual;
1292                 m->openInputFile(qfilename, inQual);
1293
1294                 string input;
1295                 while(!inQual.eof()){
1296                         input = m->getline(inQual);
1297
1298                         if (input.length() != 0) {
1299                                 if(input[0] == '>'){ //this is a sequence name line
1300                                         istringstream nameStream(input);
1301
1302                                         string sname = "";  nameStream >> sname;
1303                                         sname = sname.substr(1);
1304
1305                                         map<string, int>::iterator it = firstSeqNames.find(sname);
1306
1307                                         if(it != firstSeqNames.end()) { //this is the start of a new chunk
1308                                                 unsigned long long pos = inQual.tellg();
1309                                                 qfileFilePos.push_back(pos - input.length() - 1);
1310                                                 firstSeqNames.erase(it);
1311                                         }
1312                                 }
1313                         }
1314
1315                         if (firstSeqNames.size() == 0) { break; }
1316                 }
1317                 inQual.close();
1318
1319                 if (firstSeqNames.size() != 0) {
1320                         for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
1321                                 m->mothurOut(it->first + " is in your fasta file and not in your quality file, aborting."); m->mothurOutEndLine();
1322                         }
1323                         m->control_pressed = true;
1324                         return processors;
1325                 }
1326
1327                 //get last file position of qfile
1328                 FILE * pFile;
1329                 unsigned long long size;
1330
1331                 //get num bytes in file
1332                 pFile = fopen (qfilename.c_str(),"rb");
1333                 if (pFile==NULL) perror ("Error opening file");
1334                 else{
1335                         fseek (pFile, 0, SEEK_END);
1336                         size=ftell (pFile);
1337                         fclose (pFile);
1338                 }
1339
1340                 qfileFilePos.push_back(size);
1341
1342                 //seach for filePos of each first name in the rfile and save in rfileFilePos
1343                 string junk;
1344                 ifstream inR;
1345                 m->openInputFile(rfilename, inR);
1346
1347                 //read column headers
1348                 for (int i = 0; i < 16; i++) {
1349                         if (!inR.eof()) {       inR >> junk;    }
1350                         else                    {       break;                  }
1351                 }
1352
1353                 while(!inR.eof()){
1354
1355                         if (m->control_pressed) { inR.close();  return processors; }
1356
1357                         input = m->getline(inR);
1358
1359                         if (input.length() != 0) {
1360
1361                                 istringstream nameStream(input);
1362                                 string sname = "";  nameStream >> sname;
1363
1364                                 map<string, int>::iterator it = firstSeqNamesReport.find(sname);
1365
1366                                 if(it != firstSeqNamesReport.end()) { //this is the start of a new chunk
1367                                         unsigned long long pos = inR.tellg();
1368                                         rfileFilePos.push_back(pos - input.length() - 1);
1369                                         firstSeqNamesReport.erase(it);
1370                                 }
1371                         }
1372
1373                         if (firstSeqNamesReport.size() == 0) { break; }
1374                         m->gobble(inR);
1375                 }
1376                 inR.close();
1377
1378                 if (firstSeqNamesReport.size() != 0) {
1379                         for (map<string, int>::iterator it = firstSeqNamesReport.begin(); it != firstSeqNamesReport.end(); it++) {
1380                                 m->mothurOut(it->first + " is in your fasta file and not in your report file, aborting."); m->mothurOutEndLine();
1381                         }
1382                         m->control_pressed = true;
1383                         return processors;
1384                 }
1385
1386                 //get last file position of qfile
1387                 FILE * rFile;
1388                 unsigned long long sizeR;
1389
1390                 //get num bytes in file
1391                 rFile = fopen (rfilename.c_str(),"rb");
1392                 if (rFile==NULL) perror ("Error opening file");
1393                 else{
1394                         fseek (rFile, 0, SEEK_END);
1395                         sizeR=ftell (rFile);
1396                         fclose (rFile);
1397                 }
1398
1399                 rfileFilePos.push_back(sizeR);
1400
1401                 return processors;
1402
1403 #else
1404
1405                 fastaFilePos.push_back(0); qfileFilePos.push_back(0);
1406                 //get last file position of fastafile
1407                 FILE * pFile;
1408                 unsigned long long size;
1409
1410                 //get num bytes in file
1411                 pFile = fopen (filename.c_str(),"rb");
1412                 if (pFile==NULL) perror ("Error opening file");
1413                 else{
1414                         fseek (pFile, 0, SEEK_END);
1415                         size=ftell (pFile);
1416                         fclose (pFile);
1417                 }
1418                 fastaFilePos.push_back(size);
1419
1420                 //get last file position of fastafile
1421                 FILE * qFile;
1422
1423                 //get num bytes in file
1424                 qFile = fopen (qfilename.c_str(),"rb");
1425                 if (qFile==NULL) perror ("Error opening file");
1426                 else{
1427                         fseek (qFile, 0, SEEK_END);
1428                         size=ftell (qFile);
1429                         fclose (qFile);
1430                 }
1431                 qfileFilePos.push_back(size);
1432
1433                 return 1;
1434
1435 #endif
1436         }
1437         catch(exception& e) {
1438                 m->errorOut(e, "SeqErrorCommand", "setLines");
1439                 exit(1);
1440         }
1441 }
1442 //***************************************************************************************************************