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