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