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