screenseqscommand.cpp

   1 /*
   2  *  screenseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 6/3/09.
   6  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "screenseqscommand.h"
  11 #include "counttable.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> ScreenSeqsCommand::setParameters(){
  15         try {
  16                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  17         CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
  18         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
  19                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
  20                 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
  21                 CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(palignreport);
  22                 CommandParameter ptax("taxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptax);
  23                 CommandParameter pstart("start", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pstart);
  24                 CommandParameter pend("end", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pend);
  25                 CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxambig);
  26                 CommandParameter pmaxhomop("maxhomop", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxhomop);
  27                 CommandParameter pminlength("minlength", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pminlength);
  28                 CommandParameter pmaxlength("maxlength", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxlength);
  29                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  30                 CommandParameter pcriteria("criteria", "Number", "", "90", "", "", "",false,false); parameters.push_back(pcriteria);
  31                 CommandParameter poptimize("optimize", "Multiple", "none-start-end-maxambig-maxhomop-minlength-maxlength", "none", "", "", "",true,false); parameters.push_back(poptimize);
  32                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  33                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  34
  35                 vector<string> myArray;
  36                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  37                 return myArray;
  38         }
  39         catch(exception& e) {
  40                 m->errorOut(e, "ScreenSeqsCommand", "setParameters");
  41                 exit(1);
  42         }
  43 }
  44 //**********************************************************************************************************************
  45 string ScreenSeqsCommand::getHelpString(){
  46         try {
  47                 string helpString = "";
  48                 helpString += "The screen.seqs command reads a fastafile and screens sequences.\n";
  49                 helpString += "The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group, count, qfile, alignreport, taxonomy, optimize, criteria and processors.\n";
  50                 helpString += "The fasta parameter is required.\n";
  51                 helpString += "The alignreport and taxonomy parameters allow you to remove bad seqs from taxonomy and alignreport files.\n";
  52                 helpString += "The start parameter is used to set a position the \"good\" sequences must start by. The default is -1.\n";
  53                 helpString += "The end parameter is used to set a position the \"good\" sequences must end after. The default is -1.\n";
  54                 helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
  55                 helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
  56                 helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
  57                 helpString += "The maxlength parameter allows you to set and maximum sequence length. \n";
  58                 helpString += "The processors parameter allows you to specify the number of processors to use while running the command. The default is 1.\n";
  59                 helpString += "The optimize and criteria parameters allow you set the start, end, maxabig, maxhomop, minlength and maxlength parameters relative to your set of sequences .\n";
  60                 helpString += "For example optimize=start-end, criteria=90, would set the start and end values to the position 90% of your sequences started and ended.\n";
  61                 helpString += "The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n";
  62                 helpString += "The screen.seqs command should be in the following format: \n";
  63                 helpString += "screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig,  \n";
  64                 helpString += "maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n";
  65                 helpString += "Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n";
  66                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  67                 return helpString;
  68         }
  69         catch(exception& e) {
  70                 m->errorOut(e, "ScreenSeqsCommand", "getHelpString");
  71                 exit(1);
  72         }
  73 }
  74 //**********************************************************************************************************************
  75 string ScreenSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
  76         try {
  77         string outputFileName = "";
  78                 map<string, vector<string> >::iterator it;
  79
  80         //is this a type this command creates
  81         it = outputTypes.find(type);
  82         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  83         else {
  84             if (type == "fasta")            {   outputFileName =  "good" + m->getExtension(inputName);   }
  85             else if (type == "taxonomy")    {   outputFileName =  "good" + m->getExtension(inputName);   }
  86             else if (type == "name")        {   outputFileName =  "good" + m->getExtension(inputName);   }
  87             else if (type == "count")        {   outputFileName =  "good" + m->getExtension(inputName);   }
  88             else if (type == "group")       {   outputFileName =  "good" + m->getExtension(inputName);   }
  89             else if (type == "accnos")      {   outputFileName =  "bad.accnos";   }
  90             else if (type == "qfile")       {   outputFileName =  "good" + m->getExtension(inputName);   }
  91             else if (type == "alignreport") {   outputFileName =  "good.align.report";                   }
  92             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  93         }
  94         return outputFileName;
  95         }
  96         catch(exception& e) {
  97                 m->errorOut(e, "ScreenSeqsCommand", "getOutputFileNameTag");
  98                 exit(1);
  99         }
 100 }
 101
 102 //**********************************************************************************************************************
 103 ScreenSeqsCommand::ScreenSeqsCommand(){
 104         try {
 105                 abort = true; calledHelp = true;
 106                 setParameters();
 107                 vector<string> tempOutNames;
 108                 outputTypes["fasta"] = tempOutNames;
 109                 outputTypes["name"] = tempOutNames;
 110                 outputTypes["group"] = tempOutNames;
 111                 outputTypes["alignreport"] = tempOutNames;
 112                 outputTypes["accnos"] = tempOutNames;
 113                 outputTypes["qfile"] = tempOutNames;
 114                 outputTypes["taxonomy"] = tempOutNames;
 115         outputTypes["count"] = tempOutNames;
 116         }
 117         catch(exception& e) {
 118                 m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
 119                 exit(1);
 120         }
 121 }
 122 //***************************************************************************************************************
 123
 124 ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
 125         try {
 126                 abort = false; calledHelp = false;
 127
 128                 //allow user to run help
 129                 if(option == "help") { help(); abort = true; calledHelp = true; }
 130                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 131
 132                 else {
 133                         vector<string> myArray = setParameters();
 134
 135                         OptionParser parser(option);
 136                         map<string,string> parameters = parser.getParameters();
 137
 138                         ValidParameters validParameter("screen.seqs");
 139                         map<string,string>::iterator it;
 140
 141                         //check to make sure all parameters are valid for command
 142                         for (it = parameters.begin(); it != parameters.end(); it++) {
 143                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 144                         }
 145
 146                         //initialize outputTypes
 147                         vector<string> tempOutNames;
 148                         outputTypes["fasta"] = tempOutNames;
 149                         outputTypes["name"] = tempOutNames;
 150                         outputTypes["group"] = tempOutNames;
 151                         outputTypes["alignreport"] = tempOutNames;
 152                         outputTypes["accnos"] = tempOutNames;
 153                         outputTypes["qfile"] = tempOutNames;
 154                         outputTypes["taxonomy"] = tempOutNames;
 155             outputTypes["count"] = tempOutNames;
 156
 157                         //if the user changes the input directory command factory will send this info to us in the output parameter
 158                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 159                         if (inputDir == "not found"){   inputDir = "";          }
 160                         else {
 161                                 string path;
 162                                 it = parameters.find("fasta");
 163                                 //user has given a template file
 164                                 if(it != parameters.end()){
 165                                         path = m->hasPath(it->second);
 166                                         //if the user has not given a path then, add inputdir. else leave path alone.
 167                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 168                                 }
 169
 170                                 it = parameters.find("group");
 171                                 //user has given a template file
 172                                 if(it != parameters.end()){
 173                                         path = m->hasPath(it->second);
 174                                         //if the user has not given a path then, add inputdir. else leave path alone.
 175                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 176                                 }
 177
 178                                 it = parameters.find("name");
 179                                 //user has given a template file
 180                                 if(it != parameters.end()){
 181                                         path = m->hasPath(it->second);
 182                                         //if the user has not given a path then, add inputdir. else leave path alone.
 183                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 184                                 }
 185
 186                                 it = parameters.find("alignreport");
 187                                 //user has given a template file
 188                                 if(it != parameters.end()){
 189                                         path = m->hasPath(it->second);
 190                                         //if the user has not given a path then, add inputdir. else leave path alone.
 191                                         if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
 192                                 }
 193
 194                                 it = parameters.find("qfile");
 195                                 //user has given a template file
 196                                 if(it != parameters.end()){
 197                                         path = m->hasPath(it->second);
 198                                         //if the user has not given a path then, add inputdir. else leave path alone.
 199                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 200                                 }
 201
 202                                 it = parameters.find("taxonomy");
 203                                 //user has given a template file
 204                                 if(it != parameters.end()){
 205                                         path = m->hasPath(it->second);
 206                                         //if the user has not given a path then, add inputdir. else leave path alone.
 207                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 208                                 }
 209
 210                 it = parameters.find("count");
 211                                 //user has given a template file
 212                                 if(it != parameters.end()){
 213                                         path = m->hasPath(it->second);
 214                                         //if the user has not given a path then, add inputdir. else leave path alone.
 215                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 216                                 }
 217                         }
 218
 219                         //check for required parameters
 220                         fastafile = validParameter.validFile(parameters, "fasta", true);
 221                         if (fastafile == "not found") {
 222                                 fastafile = m->getFastaFile();
 223                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 224                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 225                         }
 226                         else if (fastafile == "not open") { abort = true; }
 227                         else { m->setFastaFile(fastafile); }
 228
 229                         groupfile = validParameter.validFile(parameters, "group", true);
 230                         if (groupfile == "not open") { abort = true; }
 231                         else if (groupfile == "not found") { groupfile = ""; }
 232                         else { m->setGroupFile(groupfile); }
 233
 234                         qualfile = validParameter.validFile(parameters, "qfile", true);
 235                         if (qualfile == "not open") { abort = true; }
 236                         else if (qualfile == "not found") { qualfile = ""; }
 237                         else { m->setQualFile(qualfile); }
 238
 239                         namefile = validParameter.validFile(parameters, "name", true);
 240                         if (namefile == "not open") { namefile = ""; abort = true; }
 241                         else if (namefile == "not found") { namefile = ""; }
 242                         else { m->setNameFile(namefile); }
 243
 244             countfile = validParameter.validFile(parameters, "count", true);
 245                         if (countfile == "not open") { countfile = ""; abort = true; }
 246                         else if (countfile == "not found") { countfile = "";  }
 247                         else { m->setCountTableFile(countfile); }
 248
 249             if ((namefile != "") && (countfile != "")) {
 250                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
 251             }
 252
 253             if ((groupfile != "") && (countfile != "")) {
 254                 m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
 255             }
 256
 257                         alignreport = validParameter.validFile(parameters, "alignreport", true);
 258                         if (alignreport == "not open") { abort = true; }
 259                         else if (alignreport == "not found") { alignreport = ""; }
 260
 261                         taxonomy = validParameter.validFile(parameters, "taxonomy", true);
 262                         if (taxonomy == "not open") { abort = true; }
 263                         else if (taxonomy == "not found") { taxonomy = ""; }
 264
 265                         //if the user changes the output directory command factory will send this info to us in the output parameter
 266                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 267                                 outputDir = "";
 268                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 269                         }
 270
 271                         //check for optional parameter and set defaults
 272                         // ...at some point should added some additional type checking...
 273                         string temp;
 274                         temp = validParameter.validFile(parameters, "start", false);            if (temp == "not found") { temp = "-1"; }
 275                         m->mothurConvert(temp, startPos);
 276
 277                         temp = validParameter.validFile(parameters, "end", false);                      if (temp == "not found") { temp = "-1"; }
 278                         m->mothurConvert(temp, endPos);
 279
 280                         temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
 281                         m->mothurConvert(temp, maxAmbig);
 282
 283                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "-1"; }
 284                         m->mothurConvert(temp, maxHomoP);
 285
 286                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "-1"; }
 287                         m->mothurConvert(temp, minLength);
 288
 289                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "-1"; }
 290                         m->mothurConvert(temp, maxLength);
 291
 292                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 293                         m->setProcessors(temp);
 294                         m->mothurConvert(temp, processors);
 295
 296                         temp = validParameter.validFile(parameters, "optimize", false); //optimizing trumps the optimized values original value
 297                         if (temp == "not found"){       temp = "none";          }
 298                         m->splitAtDash(temp, optimize);
 299
 300                         //check for invalid optimize options
 301                         set<string> validOptimizers;
 302                         validOptimizers.insert("none"); validOptimizers.insert("start"); validOptimizers.insert("end"); validOptimizers.insert("maxambig"); validOptimizers.insert("maxhomop"); validOptimizers.insert("minlength"); validOptimizers.insert("maxlength");
 303                         for (int i = 0; i < optimize.size(); i++) {
 304                                 if (validOptimizers.count(optimize[i]) == 0) {
 305                                         m->mothurOut(optimize[i] + " is not a valid optimizer. Valid options are start, end, maxambig, maxhomop, minlength and maxlength."); m->mothurOutEndLine();
 306                                         optimize.erase(optimize.begin()+i);
 307                                         i--;
 308                                 }
 309                         }
 310
 311                         if (optimize.size() == 1) { if (optimize[0] == "none") { optimize.clear(); } }
 312
 313                         temp = validParameter.validFile(parameters, "criteria", false); if (temp == "not found"){       temp = "90";                            }
 314                         m->mothurConvert(temp, criteria);
 315
 316                         if (countfile == "") {
 317                 if (namefile == "") {
 318                     vector<string> files; files.push_back(fastafile);
 319                     parser.getNameFile(files);
 320                 }
 321             }
 322                 }
 323
 324         }
 325         catch(exception& e) {
 326                 m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
 327                 exit(1);
 328         }
 329 }
 330 //***************************************************************************************************************
 331
 332 int ScreenSeqsCommand::execute(){
 333         try{
 334
 335                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 336
 337                 //if the user want to optimize we need to know the 90% mark
 338                 vector<unsigned long long> positions;
 339                 if (optimize.size() != 0) {  //get summary is paralellized so we need to divideFile, no need to do this step twice so I moved it here
 340                         //use the namefile to optimize correctly
 341                         if (namefile != "") { nameMap = m->readNames(namefile); }
 342             else if (countfile != "") {
 343                 CountTable ct;
 344                 ct.readTable(countfile);
 345                 nameMap = ct.getNameMap();
 346             }
 347                         getSummary(positions);
 348                 }
 349                 else {
 350                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 351                 positions = m->divideFile(fastafile, processors);
 352                 for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
 353                         #else
 354                 if(processors == 1){ lines.push_back(linePair(0, 1000));  }
 355                 else {
 356                     int numFastaSeqs = 0;
 357                     positions = m->setFilePosFasta(fastafile, numFastaSeqs);
 358                     if (positions.size() < processors) { processors = positions.size(); }
 359
 360                     //figure out how many sequences you have to process
 361                     int numSeqsPerProcessor = numFastaSeqs / processors;
 362                     for (int i = 0; i < processors; i++) {
 363                         int startIndex =  i * numSeqsPerProcessor;
 364                         if(i == (processors - 1)){      numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
 365                         lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
 366                     }
 367                 }
 368                         #endif
 369                 }
 370
 371                 string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
 372                 string badAccnosFile =  outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("accnos");
 373
 374                 int numFastaSeqs = 0;
 375                 set<string> badSeqNames;
 376                 int start = time(NULL);
 377
 378 #ifdef USE_MPI
 379                         int pid, numSeqsPerProcessor;
 380                         int tag = 2001;
 381                         vector<unsigned long long> MPIPos;
 382
 383                         MPI_Status status;
 384                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 385                         MPI_Comm_size(MPI_COMM_WORLD, &processors);
 386
 387                         MPI_File inMPI;
 388                         MPI_File outMPIGood;
 389                         MPI_File outMPIBadAccnos;
 390
 391                         int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 392                         int inMode=MPI_MODE_RDONLY;
 393
 394                         char outGoodFilename[1024];
 395                         strcpy(outGoodFilename, goodSeqFile.c_str());
 396
 397                         char outBadAccnosFilename[1024];
 398                         strcpy(outBadAccnosFilename, badAccnosFile.c_str());
 399
 400                         char inFileName[1024];
 401                         strcpy(inFileName, fastafile.c_str());
 402
 403                         MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 404                         MPI_File_open(MPI_COMM_WORLD, outGoodFilename, outMode, MPI_INFO_NULL, &outMPIGood);
 405                         MPI_File_open(MPI_COMM_WORLD, outBadAccnosFilename, outMode, MPI_INFO_NULL, &outMPIBadAccnos);
 406
 407                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
 408
 409                         if (pid == 0) { //you are the root process
 410
 411                                 MPIPos = m->setFilePosFasta(fastafile, numFastaSeqs); //fills MPIPos, returns numSeqs
 412
 413                                 //send file positions to all processes
 414                                 for(int i = 1; i < processors; i++) {
 415                                         MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 416                                         MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 417                                 }
 418
 419                                 //figure out how many sequences you have to align
 420                                 numSeqsPerProcessor = numFastaSeqs / processors;
 421                                 int startIndex =  pid * numSeqsPerProcessor;
 422                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 423
 424                                 //align your part
 425                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 426
 427                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos);  return 0; }
 428
 429                                 for (int i = 1; i < processors; i++) {
 430                                         //get bad lists
 431                                         int badSize;
 432                                         MPI_Recv(&badSize, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 433                                 }
 434                         }else{ //you are a child process
 435                                 MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 436                                 MPIPos.resize(numFastaSeqs+1);
 437                                 MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 438
 439                                 //figure out how many sequences you have to align
 440                                 numSeqsPerProcessor = numFastaSeqs / processors;
 441                                 int startIndex =  pid * numSeqsPerProcessor;
 442                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 443
 444                                 //align your part
 445                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 446
 447                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos); return 0; }
 448
 449                                 //send bad list
 450                                 int badSize = badSeqNames.size();
 451                                 MPI_Send(&badSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 452                         }
 453
 454                         //close files
 455                         MPI_File_close(&inMPI);
 456                         MPI_File_close(&outMPIGood);
 457                         MPI_File_close(&outMPIBadAccnos);
 458                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 459
 460 #else
 461         if(processors == 1){ numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);       }
 462         else{ numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames); }
 463
 464         if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; }
 465 #endif
 466
 467                 #ifdef USE_MPI
 468                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 469
 470                         if (pid == 0) { //only one process should fix files
 471
 472                                 //read accnos file with all names in it, process 0 just has its names
 473                                 MPI_File inMPIAccnos;
 474                                 MPI_Offset size;
 475
 476                                 char inFileName[1024];
 477                                 strcpy(inFileName, badAccnosFile.c_str());
 478
 479                                 MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPIAccnos);  //comm, filename, mode, info, filepointer
 480                                 MPI_File_get_size(inMPIAccnos, &size);
 481
 482                                 char* buffer = new char[size];
 483                                 MPI_File_read(inMPIAccnos, buffer, size, MPI_CHAR, &status);
 484
 485                                 string tempBuf = buffer;
 486                                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 487                                 istringstream iss (tempBuf,istringstream::in);
 488
 489                                 delete buffer;
 490                                 MPI_File_close(&inMPIAccnos);
 491
 492                                 badSeqNames.clear();
 493                                 string tempName;
 494                                 while (!iss.eof()) {
 495                                         iss >> tempName; m->gobble(iss);
 496                                         badSeqNames.insert(tempName);
 497                                 }
 498                 #endif
 499
 500                 if(namefile != "" && groupfile != "")   {
 501                         screenNameGroupFile(badSeqNames);
 502                         if (m->control_pressed) {  m->mothurRemove(goodSeqFile); return 0; }
 503                 }else if(namefile != "")        {
 504                         screenNameGroupFile(badSeqNames);
 505                         if (m->control_pressed) {  m->mothurRemove(goodSeqFile);  return 0; }
 506                 }else if(groupfile != "")                               {       screenGroupFile(badSeqNames);           }       // this screens just the group
 507                 else if (countfile != "") {     screenCountFile(badSeqNames);           }
 508
 509
 510                 if (m->control_pressed) { m->mothurRemove(goodSeqFile);  return 0; }
 511
 512                 if(alignreport != "")                                   {       screenAlignReport(badSeqNames);         }
 513                 if(qualfile != "")                                              {       screenQual(badSeqNames);                        }
 514                 if(taxonomy != "")                                              {       screenTaxonomy(badSeqNames);            }
 515
 516                 if (m->control_pressed) { m->mothurRemove(goodSeqFile);  return 0; }
 517
 518                 #ifdef USE_MPI
 519                         }
 520                 #endif
 521
 522                 m->mothurOutEndLine();
 523                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 524                 m->mothurOut(goodSeqFile); m->mothurOutEndLine();       outputTypes["fasta"].push_back(goodSeqFile);
 525                 m->mothurOut(badAccnosFile); m->mothurOutEndLine();      outputTypes["accnos"].push_back(badAccnosFile);
 526                 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
 527                 m->mothurOutEndLine();
 528                 m->mothurOutEndLine();
 529
 530                 //set fasta file as new current fastafile
 531                 string current = "";
 532                 itTypes = outputTypes.find("fasta");
 533                 if (itTypes != outputTypes.end()) {
 534                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 535                 }
 536
 537                 itTypes = outputTypes.find("name");
 538                 if (itTypes != outputTypes.end()) {
 539                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 540                 }
 541
 542                 itTypes = outputTypes.find("group");
 543                 if (itTypes != outputTypes.end()) {
 544                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 545                 }
 546
 547                 itTypes = outputTypes.find("qfile");
 548                 if (itTypes != outputTypes.end()) {
 549                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 550                 }
 551
 552                 itTypes = outputTypes.find("taxonomy");
 553                 if (itTypes != outputTypes.end()) {
 554                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 555                 }
 556
 557         itTypes = outputTypes.find("count");
 558                 if (itTypes != outputTypes.end()) {
 559                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 560                 }
 561
 562                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.");
 563                 m->mothurOutEndLine();
 564
 565                 return 0;
 566         }
 567         catch(exception& e) {
 568                 m->errorOut(e, "ScreenSeqsCommand", "execute");
 569                 exit(1);
 570         }
 571 }
 572
 573 //***************************************************************************************************************
 574
 575 int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 576         try {
 577                 ifstream inputNames;
 578                 m->openInputFile(namefile, inputNames);
 579                 set<string> badSeqGroups;
 580                 string seqName, seqList, group;
 581                 set<string>::iterator it;
 582
 583                 string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
 584                 outputNames.push_back(goodNameFile);  outputTypes["name"].push_back(goodNameFile);
 585
 586                 ofstream goodNameOut;   m->openOutputFile(goodNameFile, goodNameOut);
 587
 588                 while(!inputNames.eof()){
 589                         if (m->control_pressed) { goodNameOut.close();  inputNames.close(); m->mothurRemove(goodNameFile);  return 0; }
 590
 591                         inputNames >> seqName >> seqList;
 592                         it = badSeqNames.find(seqName);
 593
 594                         if(it != badSeqNames.end()){
 595                                 badSeqNames.erase(it);
 596
 597                                 if(namefile != ""){
 598                                         int start = 0;
 599                                         for(int i=0;i<seqList.length();i++){
 600                                                 if(seqList[i] == ','){
 601                                                         badSeqGroups.insert(seqList.substr(start,i-start));
 602                                                         start = i+1;
 603                                                 }
 604                                         }
 605                                         badSeqGroups.insert(seqList.substr(start,seqList.length()-start));
 606                                 }
 607                         }
 608                         else{
 609                                 goodNameOut << seqName << '\t' << seqList << endl;
 610                         }
 611                         m->gobble(inputNames);
 612                 }
 613                 inputNames.close();
 614                 goodNameOut.close();
 615
 616                 //we were unable to remove some of the bad sequences
 617                 if (badSeqNames.size() != 0) {
 618                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 619                                 m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
 620                                 m->mothurOutEndLine();
 621                         }
 622                 }
 623
 624                 if(groupfile != ""){
 625
 626                         ifstream inputGroups;
 627                         m->openInputFile(groupfile, inputGroups);
 628
 629                         string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
 630                         outputNames.push_back(goodGroupFile);   outputTypes["group"].push_back(goodGroupFile);
 631
 632                         ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 633
 634                         while(!inputGroups.eof()){
 635                                 if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodNameFile);  m->mothurRemove(goodGroupFile); return 0; }
 636
 637                                 inputGroups >> seqName >> group;
 638
 639                                 it = badSeqGroups.find(seqName);
 640
 641                                 if(it != badSeqGroups.end()){
 642                                         badSeqGroups.erase(it);
 643                                 }
 644                                 else{
 645                                         goodGroupOut << seqName << '\t' << group << endl;
 646                                 }
 647                                 m->gobble(inputGroups);
 648                         }
 649                         inputGroups.close();
 650                         goodGroupOut.close();
 651
 652                         //we were unable to remove some of the bad sequences
 653                         if (badSeqGroups.size() != 0) {
 654                                 for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
 655                                         m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 656                                         m->mothurOutEndLine();
 657                                 }
 658                         }
 659                 }
 660
 661
 662                 return 0;
 663
 664         }
 665         catch(exception& e) {
 666                 m->errorOut(e, "ScreenSeqsCommand", "screenNameGroupFile");
 667                 exit(1);
 668         }
 669 }
 670 //***************************************************************************************************************
 671 int ScreenSeqsCommand::getSummary(vector<unsigned long long>& positions){
 672         try {
 673
 674                 vector<int> startPosition;
 675                 vector<int> endPosition;
 676                 vector<int> seqLength;
 677                 vector<int> ambigBases;
 678                 vector<int> longHomoPolymer;
 679
 680         vector<unsigned long long> positions;
 681 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 682                 positions = m->divideFile(fastafile, processors);
 683                 for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
 684 #else
 685                 if(processors == 1){ lines.push_back(linePair(0, 1000));  }
 686         else {
 687             int numFastaSeqs = 0;
 688             positions = m->setFilePosFasta(fastafile, numFastaSeqs);
 689             if (positions.size() < processors) { processors = positions.size(); }
 690
 691             //figure out how many sequences you have to process
 692             int numSeqsPerProcessor = numFastaSeqs / processors;
 693             for (int i = 0; i < processors; i++) {
 694                 int startIndex =  i * numSeqsPerProcessor;
 695                 if(i == (processors - 1)){      numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
 696                 lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
 697             }
 698         }
 699 #endif
 700
 701 #ifdef USE_MPI
 702                 int pid;
 703                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 704
 705                 if (pid == 0) {
 706                         driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 707 #else
 708                 int numSeqs = 0;
 709                 //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 710                         if(processors == 1){
 711                                 numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 712                         }else{
 713                                 numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile);
 714                         }
 715
 716                         if (m->control_pressed) {  return 0; }
 717                 //#else
 718                 //      numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 719                 //      if (m->control_pressed) {  return 0; }
 720                 //#endif
 721 #endif
 722                 sort(startPosition.begin(), startPosition.end());
 723                 sort(endPosition.begin(), endPosition.end());
 724                 sort(seqLength.begin(), seqLength.end());
 725                 sort(ambigBases.begin(), ambigBases.end());
 726                 sort(longHomoPolymer.begin(), longHomoPolymer.end());
 727
 728                 //numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs
 729                 int criteriaPercentile  = int(startPosition.size() * (criteria / (float) 100));
 730
 731                 for (int i = 0; i < optimize.size(); i++) {
 732                         if (optimize[i] == "start") { startPos = startPosition[criteriaPercentile]; m->mothurOut("Optimizing start to " + toString(startPos) + "."); m->mothurOutEndLine(); }
 733                         else if (optimize[i] == "end") { int endcriteriaPercentile = int(endPosition.size() * ((100 - criteria) / (float) 100));  endPos = endPosition[endcriteriaPercentile]; m->mothurOut("Optimizing end to " + toString(endPos) + "."); m->mothurOutEndLine();}
 734                         else if (optimize[i] == "maxambig") { maxAmbig = ambigBases[criteriaPercentile]; m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + "."); m->mothurOutEndLine(); }
 735                         else if (optimize[i] == "maxhomop") { maxHomoP = longHomoPolymer[criteriaPercentile]; m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + "."); m->mothurOutEndLine(); }
 736                         else if (optimize[i] == "minlength") { int mincriteriaPercentile = int(seqLength.size() * ((100 - criteria) / (float) 100)); minLength = seqLength[mincriteriaPercentile]; m->mothurOut("Optimizing minlength to " + toString(minLength) + "."); m->mothurOutEndLine(); }
 737                         else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); }
 738                 }
 739
 740 #ifdef USE_MPI
 741                 }
 742
 743                 MPI_Status status;
 744                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 745                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 746
 747                 if (pid == 0) {
 748                         //send file positions to all processes
 749                         for(int i = 1; i < processors; i++) {
 750                                 MPI_Send(&startPos, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 751                                 MPI_Send(&endPos, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 752                                 MPI_Send(&maxAmbig, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 753                                 MPI_Send(&maxHomoP, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 754                                 MPI_Send(&minLength, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 755                                 MPI_Send(&maxLength, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 756                         }
 757                 }else {
 758                         MPI_Recv(&startPos, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 759                         MPI_Recv(&endPos, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 760                         MPI_Recv(&maxAmbig, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 761                         MPI_Recv(&maxHomoP, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 762                         MPI_Recv(&minLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 763                         MPI_Recv(&maxLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 764                 }
 765                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 766 #endif
 767                 return 0;
 768         }
 769         catch(exception& e) {
 770                 m->errorOut(e, "ScreenSeqsCommand", "getSummary");
 771                 exit(1);
 772         }
 773 }
 774 /**************************************************************************************/
 775 int ScreenSeqsCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, linePair filePos) {
 776         try {
 777
 778                 ifstream in;
 779                 m->openInputFile(filename, in);
 780
 781                 in.seekg(filePos.start);
 782
 783                 bool done = false;
 784                 int count = 0;
 785
 786                 while (!done) {
 787
 788                         if (m->control_pressed) { in.close(); return 1; }
 789
 790                         Sequence current(in); m->gobble(in);
 791
 792                         if (current.getName() != "") {
 793                                 int num = 1;
 794                                 if (namefile != "") {
 795                                         //make sure this sequence is in the namefile, else error
 796                                         map<string, int>::iterator it = nameMap.find(current.getName());
 797
 798                                         if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
 799                                         else { num = it->second; }
 800                                 }
 801
 802                                 //for each sequence this sequence represents
 803                                 for (int i = 0; i < num; i++) {
 804                                         startPosition.push_back(current.getStartPos());
 805                                         endPosition.push_back(current.getEndPos());
 806                                         seqLength.push_back(current.getNumBases());
 807                                         ambigBases.push_back(current.getAmbigBases());
 808                                         longHomoPolymer.push_back(current.getLongHomoPolymer());
 809                                 }
 810
 811                                 count++;
 812                         }
 813                         //if((count) % 100 == 0){       m->mothurOut("Optimizing sequence: " + toString(count)); m->mothurOutEndLine();         }
 814                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 815                                 unsigned long long pos = in.tellg();
 816                                 if ((pos == -1) || (pos >= filePos.end)) { break; }
 817                         #else
 818                                 if (in.eof()) { break; }
 819                         #endif
 820
 821                 }
 822
 823                 in.close();
 824
 825                 return count;
 826         }
 827         catch(exception& e) {
 828                 m->errorOut(e, "ScreenSeqsCommand", "driverCreateSummary");
 829                 exit(1);
 830         }
 831 }
 832 /**************************************************************************************************/
 833 int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename) {
 834         try {
 835
 836         int process = 1;
 837                 int num = 0;
 838                 vector<int> processIDS;
 839
 840 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 841
 842                 //loop through and create all the processes you want
 843                 while (process != processors) {
 844                         int pid = fork();
 845
 846                         if (pid > 0) {
 847                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 848                                 process++;
 849                         }else if (pid == 0){
 850                                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[process]);
 851
 852                                 //pass numSeqs to parent
 853                                 ofstream out;
 854                                 string tempFile = fastafile + toString(getpid()) + ".num.temp";
 855                                 m->openOutputFile(tempFile, out);
 856
 857                                 out << num << endl;
 858                                 out << startPosition.size() << endl;
 859                                 for (int k = 0; k < startPosition.size(); k++)          {               out << startPosition[k] << '\t'; }  out << endl;
 860                                 for (int k = 0; k < endPosition.size(); k++)            {               out << endPosition[k] << '\t'; }  out << endl;
 861                                 for (int k = 0; k < seqLength.size(); k++)                      {               out << seqLength[k] << '\t'; }  out << endl;
 862                                 for (int k = 0; k < ambigBases.size(); k++)                     {               out << ambigBases[k] << '\t'; }  out << endl;
 863                                 for (int k = 0; k < longHomoPolymer.size(); k++)        {               out << longHomoPolymer[k] << '\t'; }  out << endl;
 864
 865                                 out.close();
 866
 867                                 exit(0);
 868                         }else {
 869                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 870                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 871                                 exit(0);
 872                         }
 873                 }
 874
 875                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 876
 877                 //force parent to wait until all the processes are done
 878                 for (int i=0;i<processIDS.size();i++) {
 879                         int temp = processIDS[i];
 880                         wait(&temp);
 881                 }
 882
 883                 //parent reads in and combine Filter info
 884                 for (int i = 0; i < processIDS.size(); i++) {
 885                         string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
 886                         ifstream in;
 887                         m->openInputFile(tempFilename, in);
 888
 889                         int temp, tempNum;
 890                         in >> tempNum; m->gobble(in); num += tempNum;
 891                         in >> tempNum; m->gobble(in);
 892                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               m->gobble(in);
 893                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               m->gobble(in);
 894                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               m->gobble(in);
 895                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; ambigBases.push_back(temp);                 }               m->gobble(in);
 896                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; longHomoPolymer.push_back(temp);    }               m->gobble(in);
 897
 898                         in.close();
 899                         m->mothurRemove(tempFilename);
 900                 }
 901
 902
 903 #else
 904         //////////////////////////////////////////////////////////////////////////////////////////////////////
 905                 //Windows version shared memory, so be careful when passing variables through the seqSumData struct.
 906                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 907                 //Taking advantage of shared memory to allow both threads to add info to vectors.
 908                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 909
 910                 vector<sumData*> pDataArray;
 911                 DWORD   dwThreadIdArray[processors-1];
 912                 HANDLE  hThreadArray[processors-1];
 913
 914                 //Create processor worker threads.
 915                 for( int i=0; i<processors-1; i++ ){
 916
 917                         // Allocate memory for thread data.
 918                         sumData* tempSum = new sumData(filename, m, lines[i].start, lines[i].end, namefile, nameMap);
 919                         pDataArray.push_back(tempSum);
 920
 921                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
 922                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 923                         hThreadArray[i] = CreateThread(NULL, 0, MySumThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 924                 }
 925
 926         //do your part
 927                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[processors-1]);
 928
 929                 //Wait until all threads have terminated.
 930                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 931
 932                 //Close all thread handles and free memory allocations.
 933                 for(int i=0; i < pDataArray.size(); i++){
 934                         num += pDataArray[i]->count;
 935             for (int k = 0; k < pDataArray[i]->startPosition.size(); k++) {     startPosition.push_back(pDataArray[i]->startPosition[k]);       }
 936                         for (int k = 0; k < pDataArray[i]->endPosition.size(); k++) {   endPosition.push_back(pDataArray[i]->endPosition[k]);       }
 937             for (int k = 0; k < pDataArray[i]->seqLength.size(); k++) { seqLength.push_back(pDataArray[i]->seqLength[k]);       }
 938             for (int k = 0; k < pDataArray[i]->ambigBases.size(); k++) {        ambigBases.push_back(pDataArray[i]->ambigBases[k]);       }
 939             for (int k = 0; k < pDataArray[i]->longHomoPolymer.size(); k++) {   longHomoPolymer.push_back(pDataArray[i]->longHomoPolymer[k]);       }
 940                         CloseHandle(hThreadArray[i]);
 941                         delete pDataArray[i];
 942                 }
 943
 944 #endif
 945         return num;
 946         }
 947         catch(exception& e) {
 948                 m->errorOut(e, "ScreenSeqsCommand", "createProcessesCreateSummary");
 949                 exit(1);
 950         }
 951 }
 952
 953 //***************************************************************************************************************
 954
 955 int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
 956         try {
 957                 ifstream inputGroups;
 958                 m->openInputFile(groupfile, inputGroups);
 959                 string seqName, group;
 960                 set<string>::iterator it;
 961
 962                 string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
 963         outputNames.push_back(goodGroupFile);  outputTypes["group"].push_back(goodGroupFile);
 964                 ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 965
 966                 while(!inputGroups.eof()){
 967                         if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodGroupFile); return 0; }
 968
 969                         inputGroups >> seqName >> group;
 970                         it = badSeqNames.find(seqName);
 971
 972                         if(it != badSeqNames.end()){
 973                                 badSeqNames.erase(it);
 974                         }
 975                         else{
 976                                 goodGroupOut << seqName << '\t' << group << endl;
 977                         }
 978                         m->gobble(inputGroups);
 979                 }
 980
 981                 if (m->control_pressed) { goodGroupOut.close();  inputGroups.close(); m->mothurRemove(goodGroupFile);  return 0; }
 982
 983                 //we were unable to remove some of the bad sequences
 984                 if (badSeqNames.size() != 0) {
 985                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 986                                 m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 987                                 m->mothurOutEndLine();
 988                         }
 989                 }
 990
 991                 inputGroups.close();
 992                 goodGroupOut.close();
 993
 994                 if (m->control_pressed) { m->mothurRemove(goodGroupFile);   }
 995
 996                 return 0;
 997
 998         }
 999         catch(exception& e) {
1000                 m->errorOut(e, "ScreenSeqsCommand", "screenGroupFile");
1001                 exit(1);
1002         }
1003 }
1004 //***************************************************************************************************************
1005 int ScreenSeqsCommand::screenCountFile(set<string> badSeqNames){
1006         try {
1007                 ifstream in;
1008                 m->openInputFile(countfile, in);
1009                 set<string>::iterator it;
1010
1011                 string goodCountFile = outputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
1012         outputNames.push_back(goodCountFile);  outputTypes["count"].push_back(goodCountFile);
1013                 ofstream goodCountOut;  m->openOutputFile(goodCountFile, goodCountOut);
1014
1015         string headers = m->getline(in); m->gobble(in);
1016         goodCountOut << headers << endl;
1017
1018         string name, rest; int thisTotal;
1019         while (!in.eof()) {
1020
1021                         if (m->control_pressed) { goodCountOut.close(); in.close(); m->mothurRemove(goodCountFile); return 0; }
1022
1023                         in >> name; m->gobble(in);
1024             in >> thisTotal; m->gobble(in);
1025             rest = m->getline(in); m->gobble(in);
1026
1027                         it = badSeqNames.find(name);
1028
1029                         if(it != badSeqNames.end()){
1030                                 badSeqNames.erase(it);
1031                         }
1032                         else{
1033                                 goodCountOut << name << '\t' << thisTotal << '\t' << rest << endl;
1034                         }
1035                 }
1036
1037                 if (m->control_pressed) { goodCountOut.close();  in.close(); m->mothurRemove(goodCountFile);  return 0; }
1038
1039                 //we were unable to remove some of the bad sequences
1040                 if (badSeqNames.size() != 0) {
1041                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
1042                                 m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
1043                                 m->mothurOutEndLine();
1044                         }
1045                 }
1046
1047                 in.close();
1048                 goodCountOut.close();
1049
1050         //check for groups that have been eliminated
1051         CountTable ct;
1052         if (ct.testGroups(goodCountFile)) {
1053             ct.readTable(goodCountFile);
1054             ct.printTable(goodCountFile);
1055         }
1056
1057                 if (m->control_pressed) { m->mothurRemove(goodCountFile);   }
1058
1059                 return 0;
1060
1061         }
1062         catch(exception& e) {
1063                 m->errorOut(e, "ScreenSeqsCommand", "screenCountFile");
1064                 exit(1);
1065         }
1066 }
1067 //***************************************************************************************************************
1068
1069 int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
1070         try {
1071                 ifstream inputAlignReport;
1072                 m->openInputFile(alignreport, inputAlignReport);
1073                 string seqName, group;
1074                 set<string>::iterator it;
1075
1076                 string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + getOutputFileNameTag("alignreport");
1077                 outputNames.push_back(goodAlignReportFile);  outputTypes["alignreport"].push_back(goodAlignReportFile);
1078                 ofstream goodAlignReportOut;    m->openOutputFile(goodAlignReportFile, goodAlignReportOut);
1079
1080                 while (!inputAlignReport.eof()) {               //      need to copy header
1081                         char c = inputAlignReport.get();
1082                         goodAlignReportOut << c;
1083                         if (c == 10 || c == 13){        break;  }
1084                 }
1085
1086                 while(!inputAlignReport.eof()){
1087                         if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); m->mothurRemove(goodAlignReportFile); return 0; }
1088
1089                         inputAlignReport >> seqName;
1090                         it = badSeqNames.find(seqName);
1091                         string line;
1092                         while (!inputAlignReport.eof()) {               //      need to copy header
1093                                 char c = inputAlignReport.get();
1094                                 line += c;
1095                                 if (c == 10 || c == 13){        break;  }
1096                         }
1097
1098                         if(it != badSeqNames.end()){
1099                                 badSeqNames.erase(it);
1100                         }
1101                         else{
1102                                 goodAlignReportOut << seqName << '\t' << line;
1103                         }
1104                         m->gobble(inputAlignReport);
1105                 }
1106
1107                 if (m->control_pressed) { goodAlignReportOut.close();  inputAlignReport.close(); m->mothurRemove(goodAlignReportFile);  return 0; }
1108
1109                 //we were unable to remove some of the bad sequences
1110                 if (badSeqNames.size() != 0) {
1111                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
1112                                 m->mothurOut("Your alignreport file does not include the sequence " + *it + " please correct.");
1113                                 m->mothurOutEndLine();
1114                         }
1115                 }
1116
1117                 inputAlignReport.close();
1118                 goodAlignReportOut.close();
1119
1120                 if (m->control_pressed) {  m->mothurRemove(goodAlignReportFile);  return 0; }
1121
1122                 return 0;
1123
1124         }
1125         catch(exception& e) {
1126                 m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
1127                 exit(1);
1128         }
1129
1130 }
1131 //***************************************************************************************************************
1132
1133 int ScreenSeqsCommand::screenTaxonomy(set<string> badSeqNames){
1134         try {
1135                 ifstream input;
1136                 m->openInputFile(taxonomy, input);
1137                 string seqName, tax;
1138                 set<string>::iterator it;
1139
1140                 string goodTaxFile = outputDir + m->getRootName(m->getSimpleName(taxonomy)) + getOutputFileNameTag("taxonomy", taxonomy);
1141                 outputNames.push_back(goodTaxFile);  outputTypes["taxonomy"].push_back(goodTaxFile);
1142                 ofstream goodTaxOut;    m->openOutputFile(goodTaxFile, goodTaxOut);
1143
1144                 while(!input.eof()){
1145                         if (m->control_pressed) { goodTaxOut.close(); input.close(); m->mothurRemove(goodTaxFile); return 0; }
1146
1147                         input >> seqName >> tax;
1148                         it = badSeqNames.find(seqName);
1149
1150                         if(it != badSeqNames.end()){ badSeqNames.erase(it); }
1151                         else{
1152                                 goodTaxOut << seqName << '\t' << tax << endl;
1153                         }
1154                         m->gobble(input);
1155                 }
1156
1157                 if (m->control_pressed) { goodTaxOut.close(); input.close(); m->mothurRemove(goodTaxFile); return 0; }
1158
1159                 //we were unable to remove some of the bad sequences
1160                 if (badSeqNames.size() != 0) {
1161                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
1162                                 m->mothurOut("Your taxonomy file does not include the sequence " + *it + " please correct.");
1163                                 m->mothurOutEndLine();
1164                         }
1165                 }
1166
1167                 input.close();
1168                 goodTaxOut.close();
1169
1170                 if (m->control_pressed) {  m->mothurRemove(goodTaxFile);  return 0; }
1171
1172                 return 0;
1173
1174         }
1175         catch(exception& e) {
1176                 m->errorOut(e, "ScreenSeqsCommand", "screenTaxonomy");
1177                 exit(1);
1178         }
1179
1180 }
1181 //***************************************************************************************************************
1182
1183 int ScreenSeqsCommand::screenQual(set<string> badSeqNames){
1184         try {
1185                 ifstream in;
1186                 m->openInputFile(qualfile, in);
1187                 set<string>::iterator it;
1188
1189                 string goodQualFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("qfile", qualfile);
1190                 outputNames.push_back(goodQualFile);  outputTypes["qfile"].push_back(goodQualFile);
1191                 ofstream goodQual;      m->openOutputFile(goodQualFile, goodQual);
1192
1193                 while(!in.eof()){
1194
1195                         if (m->control_pressed) { goodQual.close(); in.close(); m->mothurRemove(goodQualFile); return 0; }
1196
1197                         string saveName = "";
1198                         string name = "";
1199                         string scores = "";
1200
1201                         in >> name;
1202
1203                         if (name.length() != 0) {
1204                                 saveName = name.substr(1);
1205                                 while (!in.eof())       {
1206                                         char c = in.get();
1207                                         if (c == 10 || c == 13){        break;  }
1208                                         else { name += c; }
1209                                 }
1210                                 m->gobble(in);
1211                         }
1212
1213                         while(in){
1214                                 char letter= in.get();
1215                                 if(letter == '>'){      in.putback(letter);     break;  }
1216                                 else{ scores += letter; }
1217                         }
1218
1219                         m->gobble(in);
1220
1221                         it = badSeqNames.find(saveName);
1222
1223                         if(it != badSeqNames.end()){
1224                                 badSeqNames.erase(it);
1225                         }else{
1226                                 goodQual << name << endl << scores;
1227                         }
1228
1229                         m->gobble(in);
1230                 }
1231
1232                 in.close();
1233                 goodQual.close();
1234
1235                 //we were unable to remove some of the bad sequences
1236                 if (badSeqNames.size() != 0) {
1237                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
1238                                 m->mothurOut("Your qual file does not include the sequence " + *it + " please correct.");
1239                                 m->mothurOutEndLine();
1240                         }
1241                 }
1242
1243                 if (m->control_pressed) {  m->mothurRemove(goodQualFile);  return 0; }
1244
1245                 return 0;
1246
1247         }
1248         catch(exception& e) {
1249                 m->errorOut(e, "ScreenSeqsCommand", "screenQual");
1250                 exit(1);
1251         }
1252
1253 }
1254 //**********************************************************************************************************************
1255
1256 int ScreenSeqsCommand::driver(linePair filePos, string goodFName, string badAccnosFName, string filename, set<string>& badSeqNames){
1257         try {
1258                 ofstream goodFile;
1259                 m->openOutputFile(goodFName, goodFile);
1260
1261                 ofstream badAccnosFile;
1262                 m->openOutputFile(badAccnosFName, badAccnosFile);
1263
1264                 ifstream inFASTA;
1265                 m->openInputFile(filename, inFASTA);
1266
1267                 inFASTA.seekg(filePos.start);
1268
1269                 bool done = false;
1270                 int count = 0;
1271
1272                 while (!done) {
1273
1274                         if (m->control_pressed) {  return 0; }
1275
1276                         Sequence currSeq(inFASTA); m->gobble(inFASTA);
1277                         if (currSeq.getName() != "") {
1278                                 bool goodSeq = 1;               //      innocent until proven guilty
1279                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
1280                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
1281                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
1282                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
1283                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
1284                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
1285
1286                                 if(goodSeq == 1){
1287                                         currSeq.printSequence(goodFile);
1288                                 }
1289                                 else{
1290                                         badAccnosFile << currSeq.getName() << endl;
1291                                         badSeqNames.insert(currSeq.getName());
1292                                 }
1293                         count++;
1294                         }
1295
1296                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1297                                 unsigned long long pos = inFASTA.tellg();
1298                                 if ((pos == -1) || (pos >= filePos.end)) { break; }
1299                         #else
1300                                 if (inFASTA.eof()) { break; }
1301                         #endif
1302
1303                         //report progress
1304                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1305                 }
1306                 //report progress
1307                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1308
1309
1310                 goodFile.close();
1311                 inFASTA.close();
1312                 badAccnosFile.close();
1313
1314                 return count;
1315         }
1316         catch(exception& e) {
1317                 m->errorOut(e, "ScreenSeqsCommand", "driver");
1318                 exit(1);
1319         }
1320 }
1321 //**********************************************************************************************************************
1322 #ifdef USE_MPI
1323 int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector<unsigned long long>& MPIPos, set<string>& badSeqNames){
1324         try {
1325                 string outputString = "";
1326                 MPI_Status statusGood;
1327                 MPI_Status statusBadAccnos;
1328                 MPI_Status status;
1329                 int pid;
1330                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
1331
1332                 for(int i=0;i<num;i++){
1333
1334                         if (m->control_pressed) {  return 0; }
1335
1336                         //read next sequence
1337                         int length = MPIPos[start+i+1] - MPIPos[start+i];
1338
1339                         char* buf4 = new char[length];
1340
1341                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
1342
1343                         string tempBuf = buf4;  delete buf4;
1344                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
1345                         istringstream iss (tempBuf,istringstream::in);
1346
1347                         Sequence currSeq(iss);
1348
1349                         //process seq
1350                         if (currSeq.getName() != "") {
1351                                 bool goodSeq = 1;               //      innocent until proven guilty
1352                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
1353                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
1354                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
1355                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
1356                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
1357                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
1358
1359                                 if(goodSeq == 1){
1360                                         outputString =  ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
1361
1362                                         //print good seq
1363                                         length = outputString.length();
1364                                         char* buf2 = new char[length];
1365                                         memcpy(buf2, outputString.c_str(), length);
1366
1367                                         MPI_File_write_shared(goodFile, buf2, length, MPI_CHAR, &statusGood);
1368                                         delete buf2;
1369                                 }
1370                                 else{
1371
1372                                         badSeqNames.insert(currSeq.getName());
1373
1374                                         //write to bad accnos file
1375                                         outputString = currSeq.getName() + "\n";
1376
1377                                         length = outputString.length();
1378                                         char* buf3 = new char[length];
1379                                         memcpy(buf3, outputString.c_str(), length);
1380
1381                                         MPI_File_write_shared(badAccnosFile, buf3, length, MPI_CHAR, &statusBadAccnos);
1382                                         delete buf3;
1383                                 }
1384                         }
1385
1386                         //report progress
1387                         if((i) % 100 == 0){     m->mothurOut("Processing sequence: " + toString(i)); m->mothurOutEndLine();             }
1388                 }
1389
1390                 return 1;
1391         }
1392         catch(exception& e) {
1393                 m->errorOut(e, "ScreenSeqsCommand", "driverMPI");
1394                 exit(1);
1395         }
1396 }
1397 #endif
1398 /**************************************************************************************************/
1399
1400 int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, set<string>& badSeqNames) {
1401         try {
1402
1403         vector<int> processIDS;
1404         int process = 1;
1405                 int num = 0;
1406
1407 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1408
1409                 //loop through and create all the processes you want
1410                 while (process != processors) {
1411                         int pid = fork();
1412
1413                         if (pid > 0) {
1414                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1415                                 process++;
1416                         }else if (pid == 0){
1417                                 num = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
1418
1419                                 //pass numSeqs to parent
1420                                 ofstream out;
1421                                 string tempFile = filename + toString(getpid()) + ".num.temp";
1422                                 m->openOutputFile(tempFile, out);
1423                                 out << num << endl;
1424                                 out.close();
1425
1426                                 exit(0);
1427                         }else {
1428                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1429                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1430                                 exit(0);
1431                         }
1432                 }
1433
1434         num = driver(lines[0], goodFileName, badAccnos, filename, badSeqNames);
1435
1436                 //force parent to wait until all the processes are done
1437                 for (int i=0;i<processIDS.size();i++) {
1438                         int temp = processIDS[i];
1439                         wait(&temp);
1440                 }
1441
1442                 for (int i = 0; i < processIDS.size(); i++) {
1443                         ifstream in;
1444                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
1445                         m->openInputFile(tempFile, in);
1446                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
1447                         in.close(); m->mothurRemove(tempFile);
1448
1449             m->appendFiles((goodFileName + toString(processIDS[i]) + ".temp"), goodFileName);
1450             m->mothurRemove((goodFileName + toString(processIDS[i]) + ".temp"));
1451
1452             m->appendFiles((badAccnos + toString(processIDS[i]) + ".temp"), badAccnos);
1453             m->mothurRemove((badAccnos + toString(processIDS[i]) + ".temp"));
1454                 }
1455
1456         //read badSeqs in because root process doesnt know what other "bad" seqs the children found
1457         ifstream inBad;
1458         int ableToOpen = m->openInputFile(badAccnos, inBad, "no error");
1459
1460         if (ableToOpen == 0) {
1461             badSeqNames.clear();
1462             string tempName;
1463             while (!inBad.eof()) {
1464                 inBad >> tempName; m->gobble(inBad);
1465                 badSeqNames.insert(tempName);
1466             }
1467             inBad.close();
1468         }
1469 #else
1470
1471         //////////////////////////////////////////////////////////////////////////////////////////////////////
1472                 //Windows version shared memory, so be careful when passing variables through the sumScreenData struct.
1473                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
1474                 //Taking advantage of shared memory to allow both threads to add info to badSeqNames.
1475                 //////////////////////////////////////////////////////////////////////////////////////////////////////
1476
1477                 vector<sumScreenData*> pDataArray;
1478                 DWORD   dwThreadIdArray[processors-1];
1479                 HANDLE  hThreadArray[processors-1];
1480
1481                 //Create processor worker threads.
1482                 for( int i=0; i<processors-1; i++ ){
1483
1484             string extension = "";
1485             if (i!=0) {extension += toString(i) + ".temp"; processIDS.push_back(i); }
1486
1487                         // Allocate memory for thread data.
1488                         sumScreenData* tempSum = new sumScreenData(startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, filename, m, lines[i].start, lines[i].end,goodFileName+extension, badAccnos+extension);
1489                         pDataArray.push_back(tempSum);
1490
1491                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
1492                         hThreadArray[i] = CreateThread(NULL, 0, MySumScreenThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
1493                 }
1494
1495         //do your part
1496         num = driver(lines[processors-1], (goodFileName+toString(processors-1)+".temp"), (badAccnos+toString(processors-1)+".temp"), filename, badSeqNames);
1497         processIDS.push_back(processors-1);
1498
1499                 //Wait until all threads have terminated.
1500                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
1501
1502                 //Close all thread handles and free memory allocations.
1503                 for(int i=0; i < pDataArray.size(); i++){
1504                         num += pDataArray[i]->count;
1505             for (set<string>::iterator it = pDataArray[i]->badSeqNames.begin(); it != pDataArray[i]->badSeqNames.end(); it++) { badSeqNames.insert(*it);       }
1506                         CloseHandle(hThreadArray[i]);
1507                         delete pDataArray[i];
1508                 }
1509
1510         for (int i = 0; i < processIDS.size(); i++) {
1511             m->appendFiles((goodFileName + toString(processIDS[i]) + ".temp"), goodFileName);
1512             m->mothurRemove((goodFileName + toString(processIDS[i]) + ".temp"));
1513
1514             m->appendFiles((badAccnos + toString(processIDS[i]) + ".temp"), badAccnos);
1515             m->mothurRemove((badAccnos + toString(processIDS[i]) + ".temp"));
1516                 }
1517
1518 #endif
1519
1520         return num;
1521
1522         }
1523         catch(exception& e) {
1524                 m->errorOut(e, "ScreenSeqsCommand", "createProcesses");
1525                 exit(1);
1526         }
1527 }
1528
1529 //***************************************************************************************************************
1530
1531