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