filterseqscommand.cpp

   1 /*
   2  *  filterseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 5/4/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "filterseqscommand.h"
  11 #include "sequence.hpp"
  12
  13
  14 //**********************************************************************************************************************
  15 vector<string> FilterSeqsCommand::setParameters(){
  16         try {
  17                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-filter",false,true, true); parameters.push_back(pfasta);
  18                 CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(phard);
  19                 CommandParameter ptrump("trump", "String", "", "*", "", "", "","",false,false, true); parameters.push_back(ptrump);
  20                 CommandParameter psoft("soft", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psoft);
  21                 CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "","",false,false, true); parameters.push_back(pvertical);
  22                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false, true); parameters.push_back(pprocessors);
  23                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  24                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  25
  26                 vector<string> myArray;
  27                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  28                 return myArray;
  29         }
  30         catch(exception& e) {
  31                 m->errorOut(e, "FilterSeqsCommand", "setParameters");
  32                 exit(1);
  33         }
  34 }
  35 //**********************************************************************************************************************
  36 string FilterSeqsCommand::getHelpString(){
  37         try {
  38                 string helpString = "";
  39                 helpString += "The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n";
  40                 helpString += "The filter.seqs command parameters are fasta, trump, soft, hard, processors and vertical. \n";
  41                 helpString += "The fasta parameter is required, unless you have a valid current fasta file. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n";
  42                 helpString += "For example: fasta=abrecovery.fasta-amazon.fasta \n";
  43                 helpString += "The trump option will remove a column if the trump character is found at that position in any sequence of the alignment. Default=*, meaning no trump. \n";
  44                 helpString += "A soft mask removes any column where the dominant base (i.e. A, T, G, C, or U) does not occur in at least a designated percentage of sequences. Default=0.\n";
  45                 helpString += "The hard parameter allows you to enter a file containing the filter you want to use.\n";
  46                 helpString += "The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n";
  47                 helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
  48                 helpString += "The filter.seqs command should be in the following format: \n";
  49                 helpString += "filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n";
  50                 helpString += "Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n";
  51                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  52                 return helpString;
  53         }
  54         catch(exception& e) {
  55                 m->errorOut(e, "FilterSeqsCommand", "getHelpString");
  56                 exit(1);
  57         }
  58 }
  59 //**********************************************************************************************************************
  60 string FilterSeqsCommand::getOutputPattern(string type) {
  61     try {
  62         string pattern = "";
  63
  64         if (type == "fasta") {  pattern = "[filename],filter.fasta"; }
  65         else if (type == "filter") {  pattern =  "[filename],filter"; }
  66         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  67
  68         return pattern;
  69     }
  70     catch(exception& e) {
  71         m->errorOut(e, "FilterSeqsCommand", "getOutputPattern");
  72         exit(1);
  73     }
  74 }
  75 //**********************************************************************************************************************
  76 FilterSeqsCommand::FilterSeqsCommand(){
  77         try {
  78                 abort = true; calledHelp = true;
  79                 setParameters();
  80                 vector<string> tempOutNames;
  81                 outputTypes["fasta"] = tempOutNames;
  82                 outputTypes["filter"] = tempOutNames;
  83         }
  84         catch(exception& e) {
  85                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
  86                 exit(1);
  87         }
  88 }
  89 /**************************************************************************************/
  90 FilterSeqsCommand::FilterSeqsCommand(string option)  {
  91         try {
  92                 abort = false; calledHelp = false;
  93                 filterFileName = "";
  94
  95                 //allow user to run help
  96                 if(option == "help") { help(); abort = true; calledHelp = true; }
  97                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  98
  99                 else {
 100                         vector<string> myArray = setParameters();
 101
 102                         OptionParser parser(option);
 103                         map<string,string> parameters = parser.getParameters();
 104
 105                         ValidParameters validParameter("filter.seqs");
 106                         map<string,string>::iterator it;
 107
 108                         //check to make sure all parameters are valid for command
 109                         for (it = parameters.begin(); it != parameters.end(); it++) {
 110                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 111                         }
 112
 113                         //initialize outputTypes
 114                         vector<string> tempOutNames;
 115                         outputTypes["fasta"] = tempOutNames;
 116                         outputTypes["filter"] = tempOutNames;
 117
 118                         //if the user changes the input directory command factory will send this info to us in the output parameter
 119                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 120                         if (inputDir == "not found"){   inputDir = "";          }
 121                         else {
 122                                 string path;
 123                                 it = parameters.find("fasta");
 124                                 //user has given a template file
 125                                 if(it != parameters.end()){
 126                                         path = m->hasPath(it->second);
 127                                         //if the user has not given a path then, add inputdir. else leave path alone.
 128                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 129                                 }
 130
 131                                 it = parameters.find("hard");
 132                                 //user has given a template file
 133                                 if(it != parameters.end()){
 134                                         path = m->hasPath(it->second);
 135                                         //if the user has not given a path then, add inputdir. else leave path alone.
 136                                         if (path == "") {       parameters["hard"] = inputDir + it->second;             }
 137                                 }
 138                         }
 139
 140                         //check for required parameters
 141                         fasta = validParameter.validFile(parameters, "fasta", false);
 142                         if (fasta == "not found") {
 143                                 fasta = m->getFastaFile();
 144                                 if (fasta != "") {
 145                     fastafileNames.push_back(fasta);
 146                     m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine();
 147                     string simpleName = m->getSimpleName(fasta);
 148                     filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
 149                 }
 150                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 151                         }
 152                         else {
 153                                 m->splitAtDash(fasta, fastafileNames);
 154
 155                                 //go through files and make sure they are good, if not, then disregard them
 156                                 for (int i = 0; i < fastafileNames.size(); i++) {
 157
 158                                         bool ignore = false;
 159                                         if (fastafileNames[i] == "current") {
 160                                                 fastafileNames[i] = m->getFastaFile();
 161                                                 if (fastafileNames[i] != "") {  m->mothurOut("Using " + fastafileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 162                                                 else {
 163                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 164                                                         //erase from file list
 165                                                         fastafileNames.erase(fastafileNames.begin()+i);
 166                                                         i--;
 167                                                 }
 168                                         }
 169
 170                                         if (!ignore) {
 171                                                 if (inputDir != "") {
 172                                                         string path = m->hasPath(fastafileNames[i]);
 173                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 174                                                         if (path == "") {       fastafileNames[i] = inputDir + fastafileNames[i];               }
 175                                                 }
 176
 177                                                 ifstream in;
 178                                                 int ableToOpen = m->openInputFile(fastafileNames[i], in, "noerror");
 179
 180                                                 //if you can't open it, try default location
 181                                                 if (ableToOpen == 1) {
 182                                                         if (m->getDefaultPath() != "") { //default path is set
 183                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(fastafileNames[i]);
 184                                                                 m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 185                                                                 ifstream in2;
 186                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 187                                                                 in2.close();
 188                                                                 fastafileNames[i] = tryPath;
 189                                                         }
 190                                                 }
 191
 192                                                 //if you can't open it, try default location
 193                                                 if (ableToOpen == 1) {
 194                                                         if (m->getOutputDir() != "") { //default path is set
 195                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(fastafileNames[i]);
 196                                                                 m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 197                                                                 ifstream in2;
 198                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 199                                                                 in2.close();
 200                                                                 fastafileNames[i] = tryPath;
 201                                                         }
 202                                                 }
 203
 204                                                 in.close();
 205
 206                                                 if (ableToOpen == 1) {
 207                                                         m->mothurOut("Unable to open " + fastafileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 208                                                         //erase from file list
 209                                                         fastafileNames.erase(fastafileNames.begin()+i);
 210                                                         i--;
 211                                                 }else{
 212                                                         string simpleName = m->getSimpleName(fastafileNames[i]);
 213                                                         filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
 214                                                         m->setFastaFile(fastafileNames[i]);
 215                                                 }
 216                                                 in.close();
 217                                         }
 218                                 }
 219
 220                                 //make sure there is at least one valid file left
 221                                 if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 222                         }
 223
 224                         if (!abort) {
 225                                 //if the user changes the output directory command factory will send this info to us in the output parameter
 226                                 outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 227                                         outputDir = "";
 228                                         outputDir += m->hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
 229                                 }
 230                         }
 231                         //check for optional parameter and set defaults
 232                         // ...at some point should added some additional type checking...
 233
 234                         string temp;
 235                         hard = validParameter.validFile(parameters, "hard", true);                              if (hard == "not found") { hard = ""; }
 236                         else if (hard == "not open") { hard = ""; abort = true; }
 237
 238                         temp = validParameter.validFile(parameters, "trump", false);                    if (temp == "not found") { temp = "*"; }
 239                         trump = temp[0];
 240
 241                         temp = validParameter.validFile(parameters, "soft", false);                             if (temp == "not found") { soft = 0; }
 242                         else {  soft = (float)atoi(temp.c_str()) / 100.0;  }
 243
 244                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 245                         m->setProcessors(temp);
 246                         m->mothurConvert(temp, processors);
 247
 248                         vertical = validParameter.validFile(parameters, "vertical", false);
 249                         if (vertical == "not found") {
 250                                 if ((hard == "") && (trump == '*') && (soft == 0)) { vertical = "T"; } //you have not given a hard file or set the trump char.
 251                                 else { vertical = "F";  }
 252                         }
 253
 254                         numSeqs = 0;
 255                 }
 256
 257         }
 258         catch(exception& e) {
 259                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
 260                 exit(1);
 261         }
 262 }
 263 /**************************************************************************************/
 264
 265 int FilterSeqsCommand::execute() {
 266         try {
 267
 268                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 269
 270                 ifstream inFASTA;
 271                 m->openInputFile(fastafileNames[0], inFASTA);
 272
 273                 Sequence testSeq(inFASTA);
 274                 alignmentLength = testSeq.getAlignLength();
 275                 inFASTA.close();
 276
 277                 ////////////create filter/////////////////
 278                 m->mothurOut("Creating Filter... "); m->mothurOutEndLine();
 279
 280                 filter = createFilter();
 281
 282                 m->mothurOutEndLine();  m->mothurOutEndLine();
 283
 284                 if (m->control_pressed) { outputTypes.clear(); return 0; }
 285
 286                 #ifdef USE_MPI
 287                         int pid;
 288                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 289
 290                         if (pid == 0) { //only one process should output the filter
 291                 #endif
 292
 293                 ofstream outFilter;
 294
 295                 //prevent giantic file name
 296         map<string, string> variables;
 297         variables["[filename]"] = outputDir + filterFileName + ".";
 298                 if (fastafileNames.size() > 3) { variables["[filename]"] = outputDir + "merge."; }
 299                 string filterFile = getOutputFileName("filter", variables);
 300
 301                 m->openOutputFile(filterFile, outFilter);
 302                 outFilter << filter << endl;
 303                 outFilter.close();
 304                 outputNames.push_back(filterFile); outputTypes["filter"].push_back(filterFile);
 305
 306                 #ifdef USE_MPI
 307                         }
 308                 #endif
 309
 310                 ////////////run filter/////////////////
 311
 312                 m->mothurOut("Running Filter... "); m->mothurOutEndLine();
 313
 314                 filterSequences();
 315
 316                 m->mothurOutEndLine();  m->mothurOutEndLine();
 317
 318                 int filteredLength = 0;
 319                 for(int i=0;i<alignmentLength;i++){
 320                         if(filter[i] == '1'){   filteredLength++;       }
 321                 }
 322
 323                 if (m->control_pressed) {  outputTypes.clear(); for(int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }  return 0; }
 324
 325
 326                 m->mothurOutEndLine();
 327                 m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
 328                 m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
 329                 m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
 330                 m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
 331
 332                 //set fasta file as new current fastafile
 333                 string current = "";
 334                 itTypes = outputTypes.find("fasta");
 335                 if (itTypes != outputTypes.end()) {
 336                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 337                 }
 338
 339                 m->mothurOutEndLine();
 340                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 341                 for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }
 342                 m->mothurOutEndLine();
 343
 344                 return 0;
 345
 346         }
 347         catch(exception& e) {
 348                 m->errorOut(e, "FilterSeqsCommand", "execute");
 349                 exit(1);
 350         }
 351 }
 352 /**************************************************************************************/
 353 int FilterSeqsCommand::filterSequences() {
 354         try {
 355
 356                 numSeqs = 0;
 357
 358                 for (int s = 0; s < fastafileNames.size(); s++) {
 359
 360                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 361
 362                 map<string, string> variables;
 363                 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s]));
 364                                 string filteredFasta = getOutputFileName("fasta", variables);
 365 #ifdef USE_MPI
 366                                 int pid, numSeqsPerProcessor, num;
 367                                 int tag = 2001;
 368                                 vector<unsigned long long>MPIPos;
 369
 370                                 MPI_Status status;
 371                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 372                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 373
 374                                 MPI_File outMPI;
 375                                 MPI_File inMPI;
 376                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 377                                 int inMode=MPI_MODE_RDONLY;
 378
 379                                 char outFilename[1024];
 380                                 strcpy(outFilename, filteredFasta.c_str());
 381
 382                                 char inFileName[1024];
 383                                 strcpy(inFileName, fastafileNames[s].c_str());
 384
 385                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 386                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 387
 388                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 389
 390                                 if (pid == 0) { //you are the root process
 391
 392                                         MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 393                                         numSeqs += num;
 394
 395                                         //send file positions to all processes
 396                                         for(int i = 1; i < processors; i++) {
 397                                                 MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 398                                                 MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 399                                         }
 400
 401                                         //figure out how many sequences you have to do
 402                                         numSeqsPerProcessor = num / processors;
 403                                         int startIndex =  pid * numSeqsPerProcessor;
 404                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 405
 406
 407                                         //do your part
 408                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 409
 410                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 411
 412                                         //wait on chidren
 413                                         for(int i = 1; i < processors; i++) {
 414                                                 char buf[5];
 415                                                 MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 416                                         }
 417
 418                                 }else { //you are a child process
 419                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 420                                         MPIPos.resize(num+1);
 421                                         numSeqs += num;
 422                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 423
 424                                         //figure out how many sequences you have to align
 425                                         numSeqsPerProcessor = num / processors;
 426                                         int startIndex =  pid * numSeqsPerProcessor;
 427                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 428
 429
 430                                         //align your part
 431                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 432
 433                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 434
 435                                         char buf[5];
 436                                         strcpy(buf, "done");
 437
 438                                         //tell parent you are done.
 439                                         MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 440                                 }
 441
 442                                 MPI_File_close(&outMPI);
 443                                 MPI_File_close(&inMPI);
 444                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 445
 446 #else
 447
 448             vector<unsigned long long> positions;
 449             if (savedPositions.size() != 0) { positions = savedPositions[s]; }
 450             else {
 451 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 452                                 positions = m->divideFile(fastafileNames[s], processors);
 453 #else
 454                 if(processors != 1){
 455                     int numFastaSeqs = 0;
 456                     positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs);
 457                     if (positions.size() < processors) { processors = positions.size(); }
 458                 }
 459 #endif
 460             }
 461                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 462                         //vector<unsigned long long> positions = m->divideFile(fastafileNames[s], processors);
 463
 464                         for (int i = 0; i < (positions.size()-1); i++) {
 465                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 466                         }
 467
 468                                 if(processors == 1){
 469                                         int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 470                                         numSeqs += numFastaSeqs;
 471                                 }else{
 472                                         int numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s], filteredFasta);
 473                                         numSeqs += numFastaSeqs;
 474                                 }
 475
 476                                 if (m->control_pressed) {  return 1; }
 477                 #else
 478             if(processors == 1){
 479                 lines.push_back(new linePair(0, 1000));
 480                                 int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 481                                 numSeqs += numFastaSeqs;
 482             }else {
 483                 int numFastaSeqs = positions.size()-1;
 484                 //positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs);
 485
 486                 //figure out how many sequences you have to process
 487                 int numSeqsPerProcessor = numFastaSeqs / processors;
 488                 for (int i = 0; i < processors; i++) {
 489                     int startIndex =  i * numSeqsPerProcessor;
 490                     if(i == (processors - 1)){  numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
 491                     lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
 492                 }
 493
 494                 numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s], filteredFasta);
 495                 numSeqs += numFastaSeqs;
 496             }
 497
 498                                 if (m->control_pressed) {  return 1; }
 499                 #endif
 500 #endif
 501                         outputNames.push_back(filteredFasta); outputTypes["fasta"].push_back(filteredFasta);
 502                 }
 503
 504                 return 0;
 505         }
 506         catch(exception& e) {
 507                 m->errorOut(e, "FilterSeqsCommand", "filterSequences");
 508                 exit(1);
 509         }
 510 }
 511 #ifdef USE_MPI
 512 /**************************************************************************************/
 513 int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long long>& MPIPos) {
 514         try {
 515                 string outputString = "";
 516                 int count = 0;
 517                 MPI_Status status;
 518
 519                 for(int i=0;i<num;i++){
 520
 521                         if (m->control_pressed) { return 0; }
 522
 523                         //read next sequence
 524                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 525                         char* buf4 = new char[length];
 526                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 527
 528                         string tempBuf = buf4;
 529                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 530                         istringstream iss (tempBuf,istringstream::in);
 531                         delete buf4;
 532
 533                         Sequence seq(iss);  m->gobble(iss);
 534
 535                         if (seq.getName() != "") {
 536                                 string align = seq.getAligned();
 537                                 string filterSeq = "";
 538
 539                                 for(int j=0;j<alignmentLength;j++){
 540                                         if(filter[j] == '1'){
 541                                                 filterSeq += align[j];
 542                                         }
 543                                 }
 544
 545                                 count++;
 546                                 outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
 547
 548                                 if(count % 10 == 0){ //output to file
 549                                         //send results to parent
 550                                         int length = outputString.length();
 551                                         char* buf = new char[length];
 552                                         memcpy(buf, outputString.c_str(), length);
 553
 554                                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 555                                         outputString = "";
 556                                         delete buf;
 557                                 }
 558
 559                         }
 560
 561                         if((i+1) % 100 == 0){   cout << (i+1) << endl;          }
 562                 }
 563
 564                 if(outputString != ""){ //output to file
 565                         //send results to parent
 566                         int length = outputString.length();
 567                         char* buf = new char[length];
 568                         memcpy(buf, outputString.c_str(), length);
 569
 570                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 571                         outputString = "";
 572                         delete buf;
 573                 }
 574
 575                 if((num) % 100 != 0){   cout << (num) << endl;          }
 576
 577                 return 0;
 578         }
 579         catch(exception& e) {
 580                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 581                 exit(1);
 582         }
 583 }
 584 #endif
 585 /**************************************************************************************/
 586 int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* filePos) {
 587         try {
 588                 ofstream out;
 589                 m->openOutputFile(outputFilename, out);
 590
 591                 ifstream in;
 592                 m->openInputFile(inputFilename, in);
 593
 594                 in.seekg(filePos->start);
 595
 596                 bool done = false;
 597                 int count = 0;
 598
 599                 while (!done) {
 600
 601                                 if (m->control_pressed) { in.close(); out.close(); return 0; }
 602
 603                                 Sequence seq(in); m->gobble(in);
 604                                 if (seq.getName() != "") {
 605                                         string align = seq.getAligned();
 606                                         string filterSeq = "";
 607
 608                                         for(int j=0;j<alignmentLength;j++){
 609                                                 if(filter[j] == '1'){
 610                                                         filterSeq += align[j];
 611                                                 }
 612                                         }
 613
 614                                         out << '>' << seq.getName() << endl << filterSeq << endl;
 615                                 count++;
 616                         }
 617
 618                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 619                                 unsigned long long pos = in.tellg();
 620                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 621                         #else
 622                                 if (in.eof()) { break; }
 623                         #endif
 624
 625                         //report progress
 626                         if((count) % 100 == 0){ m->mothurOutJustToScreen(toString(count)+"\n");         }
 627                 }
 628                 //report progress
 629                 if((count) % 100 != 0){ m->mothurOutJustToScreen(toString(count)+"\n");                 }
 630
 631
 632                 out.close();
 633                 in.close();
 634
 635                 return count;
 636         }
 637         catch(exception& e) {
 638                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 639                 exit(1);
 640         }
 641 }
 642 /**************************************************************************************************/
 643
 644 int FilterSeqsCommand::createProcessesRunFilter(string F, string filename, string filteredFastaName) {
 645         try {
 646
 647         int process = 1;
 648                 int num = 0;
 649                 processIDS.clear();
 650
 651 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 652
 653
 654                 //loop through and create all the processes you want
 655                 while (process != processors) {
 656                         int pid = fork();
 657
 658                         if (pid > 0) {
 659                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 660                                 process++;
 661                         }else if (pid == 0){
 662                                 string filteredFasta = filename + toString(getpid()) + ".temp";
 663                                 num = driverRunFilter(F, filteredFasta, filename, lines[process]);
 664
 665                                 //pass numSeqs to parent
 666                                 ofstream out;
 667                                 string tempFile = filename +  toString(getpid()) + ".num.temp";
 668                                 m->openOutputFile(tempFile, out);
 669                                 out << num << endl;
 670                                 out.close();
 671
 672                                 exit(0);
 673                         }else {
 674                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 675                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 676                                 exit(0);
 677                         }
 678                 }
 679
 680         num = driverRunFilter(F, filteredFastaName, filename, lines[0]);
 681
 682                 //force parent to wait until all the processes are done
 683                 for (int i=0;i<processIDS.size();i++) {
 684                         int temp = processIDS[i];
 685                         wait(&temp);
 686                 }
 687
 688                 for (int i = 0; i < processIDS.size(); i++) {
 689                         ifstream in;
 690                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
 691                         m->openInputFile(tempFile, in);
 692                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 693                         in.close(); m->mothurRemove(tempFile);
 694
 695             m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filteredFastaName);
 696             m->mothurRemove((filename + toString(processIDS[i]) + ".temp"));
 697                 }
 698
 699 #else
 700
 701         //////////////////////////////////////////////////////////////////////////////////////////////////////
 702                 //Windows version shared memory, so be careful when passing variables through the filterData struct.
 703                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 704                 //Taking advantage of shared memory to allow both threads to add info to F.
 705                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 706
 707                 vector<filterRunData*> pDataArray;
 708                 DWORD   dwThreadIdArray[processors-1];
 709                 HANDLE  hThreadArray[processors-1];
 710
 711                 //Create processor worker threads.
 712                 for( int i=0; i<processors-1; i++){
 713
 714             string extension = "";
 715                         if (i != 0) { extension = toString(i) + ".temp"; }
 716
 717                         filterRunData* tempFilter = new filterRunData(filter, filename, (filteredFastaName + extension), m, lines[i]->start, lines[i]->end, alignmentLength, i);
 718                         pDataArray.push_back(tempFilter);
 719                         processIDS.push_back(i);
 720
 721                         hThreadArray[i] = CreateThread(NULL, 0, MyRunFilterThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 722                 }
 723
 724         num = driverRunFilter(F, (filteredFastaName + toString(processors-1) + ".temp"), filename, lines[processors-1]);
 725
 726                 //Wait until all threads have terminated.
 727                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 728
 729                 //Close all thread handles and free memory allocations.
 730                 for(int i=0; i < pDataArray.size(); i++){
 731                         num += pDataArray[i]->count;
 732             if (pDataArray[i]->count != pDataArray[i]->end) {
 733                 m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
 734             }
 735             CloseHandle(hThreadArray[i]);
 736                         delete pDataArray[i];
 737                 }
 738
 739         for (int i = 1; i < processors; i++) {
 740             m->appendFiles((filteredFastaName + toString(i) + ".temp"), filteredFastaName);
 741             m->mothurRemove((filteredFastaName + toString(i) + ".temp"));
 742                 }
 743 #endif
 744
 745         return num;
 746
 747         }
 748         catch(exception& e) {
 749                 m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
 750                 exit(1);
 751         }
 752 }
 753 /**************************************************************************************/
 754 string FilterSeqsCommand::createFilter() {
 755         try {
 756                 string filterString = "";
 757                 Filters F;
 758
 759                 if (soft != 0)                  {  F.setSoft(soft);             }
 760                 if (trump != '*')               {  F.setTrump(trump);   }
 761
 762                 F.setLength(alignmentLength);
 763
 764                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 765                         F.initialize();
 766                 }
 767
 768                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 769                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 770
 771                 numSeqs = 0;
 772                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 773                         for (int s = 0; s < fastafileNames.size(); s++) {
 774
 775                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 776
 777 #ifdef USE_MPI
 778                                 int pid, numSeqsPerProcessor, num;
 779                                 int tag = 2001;
 780                                 vector<unsigned long long> MPIPos;
 781
 782                                 MPI_Status status;
 783                                 MPI_File inMPI;
 784                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 785                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 786
 787                                 //char* tempFileName = new char(fastafileNames[s].length());
 788                                 //tempFileName = &(fastafileNames[s][0]);
 789
 790                                 char tempFileName[1024];
 791                                 strcpy(tempFileName, fastafileNames[s].c_str());
 792
 793                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 794
 795                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 796
 797                                 if (pid == 0) { //you are the root process
 798                                                 MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 799                                                 numSeqs += num;
 800
 801                                                 //send file positions to all processes
 802                                                 for(int i = 1; i < processors; i++) {
 803                                                         MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 804                                                         MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 805                                                 }
 806
 807                                                 //figure out how many sequences you have to do
 808                                                 numSeqsPerProcessor = num / processors;
 809                                                 int startIndex =  pid * numSeqsPerProcessor;
 810                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 811
 812
 813                                                 //do your part
 814                                                 MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
 815
 816                                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 817
 818                                 }else { //i am the child process
 819                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 820                                         MPIPos.resize(num+1);
 821                                         numSeqs += num;
 822                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 823
 824                                         //figure out how many sequences you have to align
 825                                         numSeqsPerProcessor = num / processors;
 826                                         int startIndex =  pid * numSeqsPerProcessor;
 827                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 828
 829
 830                                         //do your part
 831                                         MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI,  MPIPos);
 832
 833                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 834                                 }
 835
 836                                 MPI_File_close(&inMPI);
 837                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 838
 839 #else
 840
 841                 vector<unsigned long long> positions;
 842                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 843                                 positions = m->divideFile(fastafileNames[s], processors);
 844                                 for (int i = 0; i < (positions.size()-1); i++) {
 845                                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 846                                 }
 847
 848                                 if(processors == 1){
 849                                         int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 850                                         numSeqs += numFastaSeqs;
 851                                 }else{
 852                                         int numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
 853                                         numSeqs += numFastaSeqs;
 854                                 }
 855                 #else
 856                 if(processors == 1){
 857                     lines.push_back(new linePair(0, 1000));
 858                     int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 859                     numSeqs += numFastaSeqs;
 860                                 }else {
 861                     int numFastaSeqs = 0;
 862                     positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs);
 863                     if (positions.size() < processors) { processors = positions.size(); }
 864
 865                     //figure out how many sequences you have to process
 866                     int numSeqsPerProcessor = numFastaSeqs / processors;
 867                     for (int i = 0; i < processors; i++) {
 868                         int startIndex =  i * numSeqsPerProcessor;
 869                         if(i == (processors - 1)){      numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
 870                         lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
 871                     }
 872
 873                     numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
 874                                         numSeqs += numFastaSeqs;
 875                 }
 876                 #endif
 877                 //save the file positions so we can reuse them in the runFilter function
 878                 savedPositions[s] = positions;
 879
 880                                 if (m->control_pressed) {  return filterString; }
 881 #endif
 882
 883                         }
 884                 }
 885
 886
 887 #ifdef USE_MPI
 888                 int pid;
 889                 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
 890                 MPI_Status status;
 891
 892                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 893
 894                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 895
 896                         if (pid == 0) { //only one process should output the filter
 897
 898                                 vector<int> temp; temp.resize(alignmentLength+1);
 899
 900                                 //get the frequencies from the child processes
 901                                 for(int i = 1; i < processors; i++) {
 902
 903                                         for (int j = 0; j < 5; j++) {
 904
 905                                                 MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 906                                                 int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
 907
 908                                                 if (receiveTag == Atag) { //you are recieveing the A frequencies
 909                                                         for (int k = 0; k < alignmentLength; k++) {             F.a[k] += temp[k];      }
 910                                                 }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
 911                                                         for (int k = 0; k < alignmentLength; k++) {             F.t[k] += temp[k];      }
 912                                                 }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
 913                                                         for (int k = 0; k < alignmentLength; k++) {             F.c[k] += temp[k];      }
 914                                                 }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
 915                                                         for (int k = 0; k < alignmentLength; k++) {             F.g[k] += temp[k];      }
 916                                                 }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
 917                                                         for (int k = 0; k < alignmentLength; k++) {             F.gap[k] += temp[k];    }
 918                                                 }
 919                                         }
 920                                 }
 921                         }else{
 922
 923                                 //send my fequency counts
 924                                 F.a.push_back(Atag);
 925                                 int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 926                                 F.t.push_back(Ttag);
 927                                 ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 928                                 F.c.push_back(Ctag);
 929                                 ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 930                                 F.g.push_back(Gtag);
 931                                 ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 932                                 F.gap.push_back(Gaptag);
 933                                 ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 934                         }
 935
 936                 }
 937
 938                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 939
 940                 if (pid == 0) { //only one process should output the filter
 941 #endif
 942
 943                 F.setNumSeqs(numSeqs);
 944                 if(m->isTrue(vertical) == 1)    {       F.doVertical(); }
 945                 if(soft != 0)                           {       F.doSoft();             }
 946                 filterString = F.getFilter();
 947
 948 #ifdef USE_MPI
 949                 //send filter string to kids
 950                 //for(int i = 1; i < processors; i++) {
 951                 //      MPI_Send(&filterString[0], alignmentLength, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 952                 //}
 953                 MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 954         }else{
 955                 //recieve filterString
 956                 char* tempBuf = new char[alignmentLength];
 957                 //MPI_Recv(&tempBuf[0], alignmentLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 958                 MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 959
 960                 filterString = tempBuf;
 961                 if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength);  }
 962                 delete tempBuf;
 963         }
 964
 965         MPI_Barrier(MPI_COMM_WORLD);
 966 #endif
 967
 968                 return filterString;
 969         }
 970         catch(exception& e) {
 971                 m->errorOut(e, "FilterSeqsCommand", "createFilter");
 972                 exit(1);
 973         }
 974 }
 975 /**************************************************************************************/
 976 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* filePos) {
 977         try {
 978
 979                 ifstream in;
 980                 m->openInputFile(filename, in);
 981
 982                 in.seekg(filePos->start);
 983
 984                 bool done = false;
 985                 int count = 0;
 986
 987                 while (!done) {
 988
 989                         if (m->control_pressed) { in.close(); return 1; }
 990
 991                         Sequence seq(in); m->gobble(in);
 992                         if (seq.getName() != "") {
 993                                         if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 994
 995                                         if(trump != '*')                        {       F.doTrump(seq);         }
 996                                         if(m->isTrue(vertical) || soft != 0)    {       F.getFreqs(seq);        }
 997                                         cout.flush();
 998                                         count++;
 999                         }
1000
1001                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1002                                 unsigned long long pos = in.tellg();
1003                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
1004                         #else
1005                                 if (in.eof()) { break; }
1006                         #endif
1007
1008                         //report progress
1009                         if((count) % 100 == 0){ m->mothurOutJustToScreen(toString(count)+"\n");                 }
1010                 }
1011                 //report progress
1012                 if((count) % 100 != 0){ m->mothurOutJustToScreen(toString(count)+"\n");         }
1013                 in.close();
1014
1015                 return count;
1016         }
1017         catch(exception& e) {
1018                 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
1019                 exit(1);
1020         }
1021 }
1022 #ifdef USE_MPI
1023 /**************************************************************************************/
1024 int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long long>& MPIPos) {
1025         try {
1026
1027                 MPI_Status status;
1028                 int pid;
1029                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
1030
1031                 for(int i=0;i<num;i++){
1032
1033                         if (m->control_pressed) { return 0; }
1034
1035                         //read next sequence
1036                         int length = MPIPos[start+i+1] - MPIPos[start+i];
1037
1038                         char* buf4 = new char[length];
1039                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
1040
1041                         string tempBuf = buf4;
1042                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
1043                         istringstream iss (tempBuf,istringstream::in);
1044                         delete buf4;
1045
1046                         Sequence seq(iss);
1047
1048                         if (seq.getAligned().length() != alignmentLength) {  cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1);  }
1049
1050                         if(trump != '*'){       F.doTrump(seq); }
1051                         if(m->isTrue(vertical) || soft != 0){   F.getFreqs(seq);        }
1052                         cout.flush();
1053
1054                         //report progress
1055                         if((i+1) % 100 == 0){   cout << (i+1) << endl;          }
1056                 }
1057
1058                 //report progress
1059                 if((num) % 100 != 0){   cout << num << endl;    }
1060
1061                 return 0;
1062         }
1063         catch(exception& e) {
1064                 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
1065                 exit(1);
1066         }
1067 }
1068 #endif
1069 /**************************************************************************************************/
1070
1071 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
1072         try {
1073         int process = 1;
1074                 int num = 0;
1075                 processIDS.clear();
1076
1077 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1078
1079                 //loop through and create all the processes you want
1080                 while (process != processors) {
1081                         int pid = fork();
1082
1083                         if (pid > 0) {
1084                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1085                                 process++;
1086                         }else if (pid == 0){
1087                                 //reset child's filter counts to 0;
1088                                 F.a.clear(); F.a.resize(alignmentLength, 0);
1089                                 F.t.clear(); F.t.resize(alignmentLength, 0);
1090                                 F.g.clear(); F.g.resize(alignmentLength, 0);
1091                                 F.c.clear(); F.c.resize(alignmentLength, 0);
1092                                 F.gap.clear(); F.gap.resize(alignmentLength, 0);
1093
1094                                 num = driverCreateFilter(F, filename, lines[process]);
1095
1096                                 //write out filter counts to file
1097                                 filename += toString(getpid()) + "filterValues.temp";
1098                                 ofstream out;
1099                                 m->openOutputFile(filename, out);
1100
1101                                 out << num << endl;
1102                                 out << F.getFilter() << endl;
1103                                 for (int k = 0; k < alignmentLength; k++) {             out << F.a[k] << '\t'; }  out << endl;
1104                                 for (int k = 0; k < alignmentLength; k++) {             out << F.t[k] << '\t'; }  out << endl;
1105                                 for (int k = 0; k < alignmentLength; k++) {             out << F.g[k] << '\t'; }  out << endl;
1106                                 for (int k = 0; k < alignmentLength; k++) {             out << F.c[k] << '\t'; }  out << endl;
1107                                 for (int k = 0; k < alignmentLength; k++) {             out << F.gap[k] << '\t'; }  out << endl;
1108
1109                                 //cout << F.getFilter() << endl;
1110                                 out.close();
1111
1112                                 exit(0);
1113                         }else {
1114                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1115                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1116                                 exit(0);
1117                         }
1118                 }
1119
1120                 //parent do your part
1121                 num = driverCreateFilter(F, filename, lines[0]);
1122
1123                 //force parent to wait until all the processes are done
1124                 for (int i=0;i<(processors-1);i++) {
1125                         int temp = processIDS[i];
1126                         wait(&temp);
1127                 }
1128
1129                 //parent reads in and combines Filter info
1130                 for (int i = 0; i < processIDS.size(); i++) {
1131                         string tempFilename = filename + toString(processIDS[i]) + "filterValues.temp";
1132                         ifstream in;
1133                         m->openInputFile(tempFilename, in);
1134
1135                         int temp, tempNum;
1136                         string tempFilterString;
1137
1138                         in >> tempNum; m->gobble(in); num += tempNum;
1139
1140                         in >> tempFilterString;
1141                         F.mergeFilter(tempFilterString);
1142
1143                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.a[k] += temp; }           m->gobble(in);
1144                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.t[k] += temp; }           m->gobble(in);
1145                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.g[k] += temp; }           m->gobble(in);
1146                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.c[k] += temp; }           m->gobble(in);
1147                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.gap[k] += temp; } m->gobble(in);
1148
1149                         in.close();
1150                         m->mothurRemove(tempFilename);
1151                 }
1152
1153
1154 #else
1155
1156         //////////////////////////////////////////////////////////////////////////////////////////////////////
1157                 //Windows version shared memory, so be careful when passing variables through the filterData struct.
1158                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
1159                 //Taking advantage of shared memory to allow both threads to add info to F.
1160                 //////////////////////////////////////////////////////////////////////////////////////////////////////
1161
1162                 vector<filterData*> pDataArray;
1163                 DWORD   dwThreadIdArray[processors];
1164                 HANDLE  hThreadArray[processors];
1165
1166                 //Create processor worker threads.
1167                 for( int i=0; i<processors; i++ ){
1168
1169                         filterData* tempFilter = new filterData(filename, m, lines[i]->start, lines[i]->end, alignmentLength, trump, vertical, soft, hard, i);
1170                         pDataArray.push_back(tempFilter);
1171                         processIDS.push_back(i);
1172
1173                         hThreadArray[i] = CreateThread(NULL, 0, MyCreateFilterThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
1174                 }
1175
1176                 //Wait until all threads have terminated.
1177                 WaitForMultipleObjects(processors, hThreadArray, TRUE, INFINITE);
1178
1179                 //Close all thread handles and free memory allocations.
1180                 for(int i=0; i < pDataArray.size(); i++){
1181                         num += pDataArray[i]->count;
1182             if (pDataArray[i]->count != pDataArray[i]->end) {
1183                 m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
1184             }
1185             F.mergeFilter(pDataArray[i]->F.getFilter());
1186
1187                         for (int k = 0; k < alignmentLength; k++) {      F.a[k] += pDataArray[i]->F.a[k];       }
1188                         for (int k = 0; k < alignmentLength; k++) {      F.t[k] += pDataArray[i]->F.t[k];       }
1189                         for (int k = 0; k < alignmentLength; k++) {      F.g[k] += pDataArray[i]->F.g[k];       }
1190                         for (int k = 0; k < alignmentLength; k++) {      F.c[k] += pDataArray[i]->F.c[k];       }
1191                         for (int k = 0; k < alignmentLength; k++) {      F.gap[k] += pDataArray[i]->F.gap[k];   }
1192
1193                         CloseHandle(hThreadArray[i]);
1194                         delete pDataArray[i];
1195                 }
1196
1197 #endif
1198         return num;
1199
1200         }
1201         catch(exception& e) {
1202                 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
1203                 exit(1);
1204         }
1205 }
1206 /**************************************************************************************/