seqsummarycommand.cpp

   1 /*
   2  *  seqcoordcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 5/30/09.
   6  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "seqsummarycommand.h"
  11 #include "sequence.hpp"
  12
  13 //**********************************************************************************************************************
  14 vector<string> SeqSummaryCommand::getValidParameters(){
  15         try {
  16                 string Array[] =  {"fasta","processors","outputdir","inputdir"};
  17                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  18                 return myArray;
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "SeqSummaryCommand", "getValidParameters");
  22                 exit(1);
  23         }
  24 }
  25 //**********************************************************************************************************************
  26 SeqSummaryCommand::SeqSummaryCommand(){
  27         try {
  28                 //initialize outputTypes
  29                 vector<string> tempOutNames;
  30                 outputTypes["summary"] = tempOutNames;
  31         }
  32         catch(exception& e) {
  33                 m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
  34                 exit(1);
  35         }
  36 }
  37 //**********************************************************************************************************************
  38 vector<string> SeqSummaryCommand::getRequiredParameters(){
  39         try {
  40                 string Array[] =  {"fasta"};
  41                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  42                 return myArray;
  43         }
  44         catch(exception& e) {
  45                 m->errorOut(e, "SeqSummaryCommand", "getRequiredParameters");
  46                 exit(1);
  47         }
  48 }
  49 //**********************************************************************************************************************
  50 vector<string> SeqSummaryCommand::getRequiredFiles(){
  51         try {
  52                 vector<string> myArray;
  53                 return myArray;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "SeqSummaryCommand", "getRequiredFiles");
  57                 exit(1);
  58         }
  59 }
  60 //***************************************************************************************************************
  61
  62 SeqSummaryCommand::SeqSummaryCommand(string option)  {
  63         try {
  64                 abort = false;
  65
  66                 //allow user to run help
  67                 if(option == "help") { help(); abort = true; }
  68
  69                 else {
  70                         //valid paramters for this command
  71                         string Array[] =  {"fasta","processors","outputdir","inputdir"};
  72                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  73
  74                         OptionParser parser(option);
  75                         map<string,string> parameters = parser.getParameters();
  76
  77                         ValidParameters validParameter("summary.seqs");
  78                         map<string,string>::iterator it;
  79
  80                         //check to make sure all parameters are valid for command
  81                         for (it = parameters.begin(); it != parameters.end(); it++) {
  82                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  83                         }
  84
  85                         //if the user changes the input directory command factory will send this info to us in the output parameter
  86                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  87                         if (inputDir == "not found"){   inputDir = "";          }
  88                         else {
  89                                 string path;
  90                                 it = parameters.find("fasta");
  91                                 //user has given a template file
  92                                 if(it != parameters.end()){
  93                                         path = m->hasPath(it->second);
  94                                         //if the user has not given a path then, add inputdir. else leave path alone.
  95                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  96                                 }
  97                         }
  98
  99                         //initialize outputTypes
 100                         vector<string> tempOutNames;
 101                         outputTypes["summary"] = tempOutNames;
 102
 103                         //check for required parameters
 104                         fastafile = validParameter.validFile(parameters, "fasta", true);
 105                         if (fastafile == "not open") { abort = true; }
 106                         else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the summary.seqs command."); m->mothurOutEndLine(); abort = true;  }
 107
 108                         //if the user changes the output directory command factory will send this info to us in the output parameter
 109                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 110                                 outputDir = "";
 111                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 112                         }
 113
 114                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = "1";                             }
 115                         convert(temp, processors);
 116
 117
 118                 }
 119         }
 120         catch(exception& e) {
 121                 m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
 122                 exit(1);
 123         }
 124 }
 125 //**********************************************************************************************************************
 126
 127 void SeqSummaryCommand::help(){
 128         try {
 129                 m->mothurOut("The summary.seqs command reads a fastafile and summarizes the sequences.\n");
 130                 m->mothurOut("The summary.seqs command parameters are fasta and processors, fasta is required.\n");
 131                 m->mothurOut("The summary.seqs command should be in the following format: \n");
 132                 m->mothurOut("summary.seqs(fasta=yourFastaFile, processors=2) \n");
 133                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 134         }
 135         catch(exception& e) {
 136                 m->errorOut(e, "SeqSummaryCommand", "help");
 137                 exit(1);
 138         }
 139 }
 140
 141 //***************************************************************************************************************
 142
 143 SeqSummaryCommand::~SeqSummaryCommand(){        /*      do nothing      */      }
 144
 145 //***************************************************************************************************************
 146
 147 int SeqSummaryCommand::execute(){
 148         try{
 149
 150                 if (abort == true) { return 0; }
 151
 152                 string summaryFile = outputDir + m->getSimpleName(fastafile) + ".summary";
 153
 154                 int numSeqs = 0;
 155
 156                 vector<int> startPosition;
 157                 vector<int> endPosition;
 158                 vector<int> seqLength;
 159                 vector<int> ambigBases;
 160                 vector<int> longHomoPolymer;
 161
 162 #ifdef USE_MPI
 163                                 int pid, numSeqsPerProcessor;
 164                                 int tag = 2001;
 165                                 int startTag = 1; int endTag = 2; int lengthTag = 3; int baseTag = 4; int lhomoTag = 5;
 166                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 167                                 vector<unsigned long int> MPIPos;
 168
 169                                 MPI_Status status;
 170                                 MPI_Status statusOut;
 171                                 MPI_File inMPI;
 172                                 MPI_File outMPI;
 173                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 174                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 175
 176                                 char tempFileName[1024];
 177                                 strcpy(tempFileName, fastafile.c_str());
 178
 179                                 char sumFileName[1024];
 180                                 strcpy(sumFileName, summaryFile.c_str());
 181
 182                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 183                                 MPI_File_open(MPI_COMM_WORLD, sumFileName, outMode, MPI_INFO_NULL, &outMPI);
 184
 185                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); return 0;  }
 186
 187                                 if (pid == 0) { //you are the root process
 188                                                 //print header
 189                                                 string outputString = "seqname\tstart\tend\tnbases\tambigs\tpolymer\n";
 190                                                 int length = outputString.length();
 191                                                 char* buf2 = new char[length];
 192                                                 memcpy(buf2, outputString.c_str(), length);
 193
 194                                                 MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &statusOut);
 195                                                 delete buf2;
 196
 197                                                 MPIPos = m->setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
 198
 199                                                 for(int i = 1; i < processors; i++) {
 200                                                         MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 201                                                         MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 202                                                 }
 203
 204                                                 //figure out how many sequences you have to do
 205                                                 numSeqsPerProcessor = numSeqs / processors;
 206                                                 int startIndex =  pid * numSeqsPerProcessor;
 207                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 208
 209                                                 //do your part
 210                                                 MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
 211
 212                                 }else { //i am the child process
 213
 214                                         MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 215                                         MPIPos.resize(numSeqs+1);
 216                                         MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 217
 218                                         //figure out how many sequences you have to align
 219                                         numSeqsPerProcessor = numSeqs / processors;
 220                                         int startIndex =  pid * numSeqsPerProcessor;
 221                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 222
 223                                         //do your part
 224                                         MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
 225                                 }
 226
 227                                 MPI_File_close(&inMPI);
 228                                 MPI_File_close(&outMPI);
 229                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 230
 231                                 if (pid == 0) {
 232                                         //get the info from the child processes
 233                                         for(int i = 1; i < processors; i++) {
 234                                                 int size;
 235                                                 MPI_Recv(&size, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 236
 237                                                 vector<int> temp; temp.resize(size+1);
 238
 239                                                 for(int j = 0; j < 5; j++) {
 240
 241                                                         MPI_Recv(&temp[0], (size+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 242                                                         int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what count this is for
 243
 244                                                         if (receiveTag == startTag) {
 245                                                                 for (int k = 0; k < size; k++) {                startPosition.push_back(temp[k]);       }
 246                                                         }else if (receiveTag == endTag) {
 247                                                                 for (int k = 0; k < size; k++) {                endPosition.push_back(temp[k]); }
 248                                                         }else if (receiveTag == lengthTag) {
 249                                                                 for (int k = 0; k < size; k++) {                seqLength.push_back(temp[k]);   }
 250                                                         }else if (receiveTag == baseTag) {
 251                                                                 for (int k = 0; k < size; k++) {                ambigBases.push_back(temp[k]);  }
 252                                                         }else if (receiveTag == lhomoTag) {
 253                                                                 for (int k = 0; k < size; k++) {                longHomoPolymer.push_back(temp[k]);     }
 254                                                         }
 255                                                 }
 256                                         }
 257
 258                                 }else{
 259
 260                                         //send my counts
 261                                         int size = startPosition.size();
 262                                         MPI_Send(&size, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 263
 264                                         startPosition.push_back(startTag);
 265                                         int ierr = MPI_Send(&(startPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 266                                         endPosition.push_back(endTag);
 267                                         ierr = MPI_Send (&(endPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 268                                         seqLength.push_back(lengthTag);
 269                                         ierr = MPI_Send(&(seqLength[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 270                                         ambigBases.push_back(baseTag);
 271                                         ierr = MPI_Send(&(ambigBases[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 272                                         longHomoPolymer.push_back(lhomoTag);
 273                                         ierr = MPI_Send(&(longHomoPolymer[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 274                                 }
 275
 276                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 277 #else
 278                         vector<unsigned long int> positions = m->divideFile(fastafile, processors);
 279
 280                         for (int i = 0; i < (positions.size()-1); i++) {
 281                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 282                         }
 283
 284                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 285                                 if(processors == 1){
 286                                         numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
 287                                 }else{
 288                                         numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile);
 289
 290                                         rename((summaryFile + toString(processIDS[0]) + ".temp").c_str(), summaryFile.c_str());
 291                                         //append files
 292                                         for(int i=1;i<processors;i++){
 293                                                 m->appendFiles((summaryFile + toString(processIDS[i]) + ".temp"), summaryFile);
 294                                                 remove((summaryFile + toString(processIDS[i]) + ".temp").c_str());
 295                                         }
 296                                 }
 297
 298                                 if (m->control_pressed) {  return 0; }
 299                 #else
 300                                 numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
 301                                 if (m->control_pressed) {  return 0; }
 302                 #endif
 303 #endif
 304
 305                 #ifdef USE_MPI
 306                         if (pid == 0) {
 307                 #endif
 308
 309                 sort(startPosition.begin(), startPosition.end());
 310                 sort(endPosition.begin(), endPosition.end());
 311                 sort(seqLength.begin(), seqLength.end());
 312                 sort(ambigBases.begin(), ambigBases.end());
 313                 sort(longHomoPolymer.begin(), longHomoPolymer.end());
 314
 315                 int ptile0_25   = int(numSeqs * 0.025);
 316                 int ptile25             = int(numSeqs * 0.250);
 317                 int ptile50             = int(numSeqs * 0.500);
 318                 int ptile75             = int(numSeqs * 0.750);
 319                 int ptile97_5   = int(numSeqs * 0.975);
 320                 int ptile100    = numSeqs - 1;
 321
 322                 //to compensate for blank sequences that would result in startPosition and endPostion equalling -1
 323                 if (startPosition[0] == -1) {  startPosition[0] = 0;    }
 324                 if (endPosition[0] == -1)       {  endPosition[0] = 0;          }
 325
 326                 if (m->control_pressed) {  remove(summaryFile.c_str()); return 0; }
 327
 328                 m->mothurOutEndLine();
 329                 m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer"); m->mothurOutEndLine();
 330                 m->mothurOut("Minimum:\t" + toString(startPosition[0]) + "\t" + toString(endPosition[0]) + "\t" + toString(seqLength[0]) + "\t" + toString(ambigBases[0]) + "\t" + toString(longHomoPolymer[0])); m->mothurOutEndLine();
 331                 m->mothurOut("2.5%-tile:\t" + toString(startPosition[ptile0_25]) + "\t" + toString(endPosition[ptile0_25]) + "\t" + toString(seqLength[ptile0_25]) + "\t" + toString(ambigBases[ptile0_25]) + "\t"+ toString(longHomoPolymer[ptile0_25])); m->mothurOutEndLine();
 332                 m->mothurOut("25%-tile:\t" + toString(startPosition[ptile25]) + "\t" + toString(endPosition[ptile25]) + "\t" + toString(seqLength[ptile25]) + "\t" + toString(ambigBases[ptile25]) + "\t" + toString(longHomoPolymer[ptile25])); m->mothurOutEndLine();
 333                 m->mothurOut("Median: \t" + toString(startPosition[ptile50]) + "\t" + toString(endPosition[ptile50]) + "\t" + toString(seqLength[ptile50]) + "\t" + toString(ambigBases[ptile50]) + "\t" + toString(longHomoPolymer[ptile50])); m->mothurOutEndLine();
 334                 m->mothurOut("75%-tile:\t" + toString(startPosition[ptile75]) + "\t" + toString(endPosition[ptile75]) + "\t" + toString(seqLength[ptile75]) + "\t" + toString(ambigBases[ptile75]) + "\t" + toString(longHomoPolymer[ptile75])); m->mothurOutEndLine();
 335                 m->mothurOut("97.5%-tile:\t" + toString(startPosition[ptile97_5]) + "\t" + toString(endPosition[ptile97_5]) + "\t" + toString(seqLength[ptile97_5]) + "\t" + toString(ambigBases[ptile97_5]) + "\t" + toString(longHomoPolymer[ptile97_5])); m->mothurOutEndLine();
 336                 m->mothurOut("Maximum:\t" + toString(startPosition[ptile100]) + "\t" + toString(endPosition[ptile100]) + "\t" + toString(seqLength[ptile100]) + "\t" + toString(ambigBases[ptile100]) + "\t" + toString(longHomoPolymer[ptile100])); m->mothurOutEndLine();
 337                 m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine();
 338
 339                 if (m->control_pressed) {  remove(summaryFile.c_str()); return 0; }
 340
 341                 m->mothurOutEndLine();
 342                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 343                 m->mothurOut(summaryFile); m->mothurOutEndLine();       outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile);
 344                 m->mothurOutEndLine();
 345
 346                 #ifdef USE_MPI
 347                         }
 348                 #endif
 349
 350                 return 0;
 351         }
 352         catch(exception& e) {
 353                 m->errorOut(e, "SeqSummaryCommand", "execute");
 354                 exit(1);
 355         }
 356 }
 357 /**************************************************************************************/
 358 int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile, linePair* filePos) {
 359         try {
 360
 361                 ofstream outSummary;
 362                 m->openOutputFile(sumFile, outSummary);
 363
 364                 //print header if you are process 0
 365                 if (filePos->start == 0) {
 366                         outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer" << endl;
 367                 }
 368
 369                 ifstream in;
 370                 m->openInputFile(filename, in);
 371
 372                 in.seekg(filePos->start);
 373
 374                 bool done = false;
 375                 int count = 0;
 376
 377                 while (!done) {
 378
 379                         if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
 380
 381                         Sequence current(in); m->gobble(in);
 382
 383                         if (current.getName() != "") {
 384                                 startPosition.push_back(current.getStartPos());
 385                                 endPosition.push_back(current.getEndPos());
 386                                 seqLength.push_back(current.getNumBases());
 387                                 ambigBases.push_back(current.getAmbigBases());
 388                                 longHomoPolymer.push_back(current.getLongHomoPolymer());
 389
 390                                 outSummary << current.getName() << '\t';
 391                                 outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
 392                                 outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
 393                                 outSummary << current.getLongHomoPolymer() << endl;
 394                                 count++;
 395                         }
 396
 397                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 398                                 unsigned long int pos = in.tellg();
 399                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 400                         #else
 401                                 if (in.eof()) { break; }
 402                         #endif
 403
 404                         //report progress
 405                         //if((count) % 100 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 406                 }
 407                 //report progress
 408                 //if((count) % 100 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 409
 410                 in.close();
 411
 412                 return count;
 413         }
 414         catch(exception& e) {
 415                 m->errorOut(e, "SeqSummaryCommand", "driverCreateSummary");
 416                 exit(1);
 417         }
 418 }
 419 #ifdef USE_MPI
 420 /**************************************************************************************/
 421 int SeqSummaryCommand::MPICreateSummary(int start, int num, vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos) {
 422         try {
 423
 424                 int pid;
 425                 MPI_Status status;
 426                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 427
 428
 429                 for(int i=0;i<num;i++){
 430
 431                         if (m->control_pressed) { return 0; }
 432
 433                         //read next sequence
 434                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 435
 436                         char* buf4 = new char[length];
 437                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 438
 439                         string tempBuf = buf4;
 440                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 441                         istringstream iss (tempBuf,istringstream::in);
 442                         delete buf4;
 443
 444                         Sequence current(iss);
 445
 446                         if (current.getName() != "") {
 447                                 startPosition.push_back(current.getStartPos());
 448                                 endPosition.push_back(current.getEndPos());
 449                                 seqLength.push_back(current.getNumBases());
 450                                 ambigBases.push_back(current.getAmbigBases());
 451                                 longHomoPolymer.push_back(current.getLongHomoPolymer());
 452
 453                                 string outputString = current.getName() + "\t" + toString(current.getStartPos()) + "\t" + toString(current.getEndPos()) + "\t";
 454                                 outputString += toString(current.getNumBases()) + "\t" + toString(current.getAmbigBases()) + "\t" + toString(current.getLongHomoPolymer()) + "\n";
 455
 456                                 //output to file
 457                                 length = outputString.length();
 458                                 char* buf3 = new char[length];
 459                                 memcpy(buf3, outputString.c_str(), length);
 460
 461                                 MPI_File_write_shared(outMPI, buf3, length, MPI_CHAR, &status);
 462                                 delete buf3;
 463                         }
 464                 }
 465
 466                 return 0;
 467         }
 468         catch(exception& e) {
 469                 m->errorOut(e, "SeqSummaryCommand", "MPICreateSummary");
 470                 exit(1);
 471         }
 472 }
 473 #endif
 474 /**************************************************************************************************/
 475 int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile) {
 476         try {
 477 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 478                 int process = 0;
 479                 int num = 0;
 480                 processIDS.clear();
 481
 482                 //loop through and create all the processes you want
 483                 while (process != processors) {
 484                         int pid = fork();
 485
 486                         if (pid > 0) {
 487                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 488                                 process++;
 489                         }else if (pid == 0){
 490                                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile + toString(getpid()) + ".temp", lines[process]);
 491
 492                                 //pass numSeqs to parent
 493                                 ofstream out;
 494                                 string tempFile = fastafile + toString(getpid()) + ".num.temp";
 495                                 m->openOutputFile(tempFile, out);
 496
 497                                 out << num << endl;
 498                                 for (int k = 0; k < startPosition.size(); k++)          {               out << startPosition[k] << '\t'; }  out << endl;
 499                                 for (int k = 0; k < endPosition.size(); k++)            {               out << endPosition[k] << '\t'; }  out << endl;
 500                                 for (int k = 0; k < seqLength.size(); k++)                      {               out << seqLength[k] << '\t'; }  out << endl;
 501                                 for (int k = 0; k < ambigBases.size(); k++)                     {               out << ambigBases[k] << '\t'; }  out << endl;
 502                                 for (int k = 0; k < longHomoPolymer.size(); k++)        {               out << longHomoPolymer[k] << '\t'; }  out << endl;
 503
 504                                 out.close();
 505
 506                                 exit(0);
 507                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 508                 }
 509
 510                 //force parent to wait until all the processes are done
 511                 for (int i=0;i<processors;i++) {
 512                         int temp = processIDS[i];
 513                         wait(&temp);
 514                 }
 515
 516                 //parent reads in and combine Filter info
 517                 for (int i = 0; i < processIDS.size(); i++) {
 518                         string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
 519                         ifstream in;
 520                         m->openInputFile(tempFilename, in);
 521
 522                         int temp, tempNum;
 523                         in >> tempNum; m->gobble(in); num += tempNum;
 524                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               m->gobble(in);
 525                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               m->gobble(in);
 526                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               m->gobble(in);
 527                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; ambigBases.push_back(temp);                 }               m->gobble(in);
 528                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; longHomoPolymer.push_back(temp);    }               m->gobble(in);
 529
 530                         in.close();
 531                         remove(tempFilename.c_str());
 532                 }
 533
 534                 return num;
 535 #endif
 536         }
 537         catch(exception& e) {
 538                 m->errorOut(e, "SeqSummaryCommand", "createProcessesCreateSummary");
 539                 exit(1);
 540         }
 541 }
 542 //***************************************************************************************************************
 543
 544