pintail.cpp

   1 /*
   2  *  pintail.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 7/9/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "pintail.h"
  11 #include "ignoregaps.h"
  12 #include "eachgapdist.h"
  13
  14 //********************************************************************************************************************
  15 //sorts lowest to highest
  16 inline bool compareQuanMembers(quanMember left, quanMember right){
  17         return (left.score < right.score);
  18 }
  19 //***************************************************************************************************************
  20
  21 Pintail::Pintail(string filename, string temp, bool f, int p, string mask, string cons, string q, int win, int inc, string o) : Chimera() {
  22         try {
  23
  24                 fastafile = filename;
  25                 templateFileName = temp; templateSeqs = readSeqs(temp);
  26                 filter = f;
  27                 processors = p;
  28                 setMask(mask);
  29                 consfile = cons;
  30                 quanfile = q;
  31                 window = win;
  32                 increment = inc;
  33                 outputDir = o;
  34
  35                 distcalculator = new eachGapDist();
  36                 decalc = new DeCalculator();
  37
  38                 doPrep();
  39         }
  40         catch(exception& e) {
  41                 m->errorOut(e, "Pintail", "Pintail");
  42                 exit(1);
  43         }
  44
  45 }
  46 //***************************************************************************************************************
  47
  48 Pintail::~Pintail() {
  49         try {
  50
  51                 delete distcalculator;
  52                 delete decalc;
  53         }
  54         catch(exception& e) {
  55                 m->errorOut(e, "Pintail", "~Pintail");
  56                 exit(1);
  57         }
  58 }
  59 //***************************************************************************************************************
  60 int Pintail::doPrep() {
  61         try {
  62
  63                 mergedFilterString = "";
  64                 windowSizesTemplate.resize(templateSeqs.size(), window);
  65                 quantiles.resize(100);  //one for every percent mismatch
  66                 quantilesMembers.resize(100);  //one for every percent mismatch
  67
  68                 //if the user does not enter a mask then you want to keep all the spots in the alignment
  69                 if (seqMask.length() == 0)      {       decalc->setAlignmentLength(templateSeqs[0]->getAligned().length());     }
  70                 else                                            {       decalc->setAlignmentLength(seqMask.length());                                           }
  71
  72                 decalc->setMask(seqMask);
  73
  74         #ifdef USE_MPI
  75                 //do nothing
  76         #else
  77                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  78                         //find breakup of templatefile for quantiles
  79                         if (processors == 1) {   templateLines.push_back(new linePair(0, templateSeqs.size()));  }
  80                         else {
  81                                 for (int i = 0; i < processors; i++) {
  82                                         templateLines.push_back(new linePair());
  83                                         templateLines[i]->start = int (sqrt(float(i)/float(processors)) * templateSeqs.size());
  84                                         templateLines[i]->end = int (sqrt(float(i+1)/float(processors)) * templateSeqs.size());
  85                                 }
  86                         }
  87                 #else
  88                         templateLines.push_back(new linePair(0, templateSeqs.size()));
  89                 #endif
  90         #endif
  91
  92                 m->mothurOut("Getting conservation... "); cout.flush();
  93                 if (consfile == "") {
  94                         m->mothurOut("Calculating probability of conservation for your template sequences.  This can take a while...  I will output the frequency of the highest base in each position to a .freq file so that you can input them using the conservation parameter next time you run this command.  Providing the .freq file will improve speed.    "); cout.flush();
  95                         probabilityProfile = decalc->calcFreq(templateSeqs, outputDir + getSimpleName(templateFileName));
  96                         if (m->control_pressed) {  return 0;  }
  97                         m->mothurOut("Done."); m->mothurOutEndLine();
  98                 }else                           {   probabilityProfile = readFreq();    m->mothurOut("Done.");            }
  99                 m->mothurOutEndLine();
 100
 101                 //make P into Q
 102                 for (int i = 0; i < probabilityProfile.size(); i++)  { probabilityProfile[i] = 1 - probabilityProfile[i];  }  //
 103
 104                 bool reRead = false;
 105                 //create filter if needed for later
 106                 if (filter) {
 107
 108                         //read in all query seqs
 109                         vector<Sequence*> tempQuerySeqs = readSeqs(fastafile);
 110
 111                         vector<Sequence*> temp;
 112                         //merge query seqs and template seqs
 113                         temp = templateSeqs;
 114                         for (int i = 0; i < tempQuerySeqs.size(); i++) {  temp.push_back(tempQuerySeqs[i]);  }
 115
 116                         if (seqMask != "") {
 117                             reRead = true;
 118                                 //mask templates
 119                                 for (int i = 0; i < temp.size(); i++) {
 120                                         if (m->control_pressed) {
 121                                                 for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i];  }
 122                                                 return 0;
 123                                         }
 124                                         decalc->runMask(temp[i]);
 125                                 }
 126                         }
 127
 128                         mergedFilterString = createFilter(temp, 0.5);
 129
 130                         if (m->control_pressed) {
 131                                 for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i];  }
 132                                 return 0;
 133                         }
 134
 135                         //reread template seqs
 136                         for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i];  }
 137                 }
 138
 139
 140                 //quantiles are used to determine whether the de values found indicate a chimera
 141                 //if you have to calculate them, its time intensive because you are finding the de and deviation values for each
 142                 //combination of sequences in the template
 143                 if (quanfile != "") {
 144                         quantiles = readQuantiles();
 145                 }else {
 146                         if ((!filter) && (seqMask != "")) { //if you didn't filter but you want to mask. if you filtered then you did mask first above.
 147                                 reRead = true;
 148                                 //mask templates
 149                                 for (int i = 0; i < templateSeqs.size(); i++) {
 150                                         if (m->control_pressed) {  return 0;  }
 151                                         decalc->runMask(templateSeqs[i]);
 152                                 }
 153                         }
 154
 155                         if (filter) {
 156                                 reRead = true;
 157                                 for (int i = 0; i < templateSeqs.size(); i++) {
 158                                         if (m->control_pressed) {  return 0;  }
 159                                         runFilter(templateSeqs[i]);
 160                                 }
 161                         }
 162
 163                         m->mothurOut("Calculating quantiles for your template.  This can take a while...  I will output the quantiles to a .quan file that you can input them using the quantiles parameter next time you run this command.  Providing the .quan file will dramatically improve speed.    "); cout.flush();
 164                         if (processors == 1) {
 165                                 quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
 166                         }else {         createProcessesQuan();          }
 167
 168                         if (m->control_pressed) {  return 0;  }
 169
 170                         string noOutliers, outliers;
 171
 172                         if ((!filter) && (seqMask == "")) {
 173                                 noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.quan";
 174                         }else if ((!filter) && (seqMask != "")) {
 175                                 noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.masked.quan";
 176                         }else if ((filter) && (seqMask != "")) {
 177                                 noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.filtered." + getSimpleName(getRootName(fastafile)) + "masked.quan";
 178                         }else if ((filter) && (seqMask == "")) {
 179                                 noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.filtered." + getSimpleName(getRootName(fastafile)) + "quan";
 180                         }
 181
 182                         decalc->removeObviousOutliers(quantilesMembers, templateSeqs.size());
 183
 184                         if (m->control_pressed) {  return 0;  }
 185
 186                         string outputString = "";
 187
 188                         //adjust quantiles
 189                         for (int i = 0; i < quantilesMembers.size(); i++) {
 190                                 vector<float> temp;
 191
 192                                 if (quantilesMembers[i].size() == 0) {
 193                                         //in case this is not a distance found in your template files
 194                                         for (int g = 0; g < 6; g++) {
 195                                                 temp.push_back(0.0);
 196                                         }
 197                                 }else{
 198
 199                                         sort(quantilesMembers[i].begin(), quantilesMembers[i].end());
 200
 201                                         //save 10%
 202                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.10)]);
 203                                         //save 25%
 204                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.25)]);
 205                                         //save 50%
 206                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.5)]);
 207                                         //save 75%
 208                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.75)]);
 209                                         //save 95%
 210                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.95)]);
 211                                         //save 99%
 212                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.99)]);
 213
 214                                 }
 215
 216                                 //output quan value
 217                                 outputString += toString(i+1) + "\t";
 218                                 for (int u = 0; u < temp.size(); u++) {   outputString += toString(temp[u]) + "\t"; }
 219                                 outputString += "\n";
 220
 221                                 quantiles[i] = temp;
 222
 223                         }
 224
 225                         printQuanFile(noOutliers, outputString);
 226
 227                         //free memory
 228                         quantilesMembers.clear();
 229
 230                         m->mothurOut("Done."); m->mothurOutEndLine();
 231                 }
 232
 233                 if (reRead) {
 234                         for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i];  }
 235                         templateSeqs.clear();
 236                         templateSeqs = readSeqs(templateFileName);
 237                 }
 238
 239
 240                 //free memory
 241                 for (int i = 0; i < templateLines.size(); i++) { delete templateLines[i];  }
 242
 243                 return 0;
 244
 245         }
 246         catch(exception& e) {
 247                 m->errorOut(e, "Pintail", "doPrep");
 248                 exit(1);
 249         }
 250 }
 251 //***************************************************************************************************************
 252 int Pintail::print(ostream& out, ostream& outAcc) {
 253         try {
 254                 int index = ceil(deviation);
 255
 256                 //is your DE value higher than the 95%
 257                 string chimera;
 258                 if (index != 0) {  //if index is 0 then its an exact match to a template seq
 259                         if (quantiles[index][4] == 0.0) {
 260                                 chimera = "Your template does not include sequences that provide quantile values at distance " + toString(index);
 261                         }else {
 262                                 if (DE > quantiles[index][4])           {       chimera = "Yes";        }
 263                                 else                                                            {       chimera = "No";         }
 264                         }
 265                 }else{ chimera = "No";          }
 266
 267                 out << querySeq->getName() << '\t' << "div: " << deviation << "\tstDev: " << DE << "\tchimera flag: " << chimera << endl;
 268                 if (chimera == "Yes") {
 269                         m->mothurOut(querySeq->getName() + "\tdiv: " + toString(deviation) + "\tstDev: " + toString(DE) + "\tchimera flag: " + chimera); m->mothurOutEndLine();
 270                         outAcc << querySeq->getName() << endl;
 271                 }
 272                 out << "Observed\t";
 273
 274                 for (int j = 0; j < obsDistance.size(); j++) {  out << obsDistance[j] << '\t';  }
 275                 out << endl;
 276
 277                 out << "Expected\t";
 278
 279                 for (int m = 0; m < expectedDistance.size(); m++) {  out << expectedDistance[m] << '\t';  }
 280                 out << endl;
 281
 282                 return 0;
 283
 284         }
 285         catch(exception& e) {
 286                 m->errorOut(e, "Pintail", "print");
 287                 exit(1);
 288         }
 289 }
 290 #ifdef USE_MPI
 291 //***************************************************************************************************************
 292 int Pintail::print(MPI_File& out, MPI_File& outAcc) {
 293         try {
 294                 bool results = false;
 295                 string outputString = "";
 296                 int index = ceil(deviation);
 297
 298                 //is your DE value higher than the 95%
 299                 string chimera;
 300                 if (index != 0) {  //if index is 0 then its an exact match to a template seq
 301                         if (quantiles[index][4] == 0.0) {
 302                                 chimera = "Your template does not include sequences that provide quantile values at distance " + toString(index);
 303                         }else {
 304                                 if (DE > quantiles[index][4])           {       chimera = "Yes";        }
 305                                 else                                                            {       chimera = "No";         }
 306                         }
 307                 }else{ chimera = "No";          }
 308
 309                 outputString += querySeq->getName() + "\tdiv: " + toString(deviation) + "\tstDev: " + toString(DE) + "\tchimera flag: " + chimera + "\n";
 310                 if (chimera == "Yes") {
 311                         cout << querySeq->getName() << "\tdiv: " << toString(deviation) << "\tstDev: " << toString(DE) << "\tchimera flag: " << chimera << endl;
 312                         string outAccString = querySeq->getName() + "\n";
 313
 314                         MPI_Status statusAcc;
 315                         int length = outAccString.length();
 316                         char* buf = new char[length];
 317                         memcpy(buf, outAccString.c_str(), length);
 318
 319                         MPI_File_write_shared(outAcc, buf, length, MPI_CHAR, &statusAcc);
 320                         delete buf;
 321
 322                         results = true;
 323                 }
 324                 outputString += "Observed\t";
 325
 326                 for (int j = 0; j < obsDistance.size(); j++) {  outputString += toString(obsDistance[j]) + "\t";  }
 327                 outputString += "\n";
 328
 329                 outputString += "Expected\t";
 330
 331                 for (int m = 0; m < expectedDistance.size(); m++) {  outputString += toString(expectedDistance[m]) + "\t";  }
 332                 outputString += "\n";
 333
 334                 MPI_Status status;
 335                 int length = outputString.length();
 336                 char* buf2 = new char[length];
 337                 memcpy(buf2, outputString.c_str(), length);
 338
 339                 MPI_File_write_shared(out, buf2, length, MPI_CHAR, &status);
 340                 delete buf2;
 341
 342                 return results;
 343         }
 344         catch(exception& e) {
 345                 m->errorOut(e, "Pintail", "print");
 346                 exit(1);
 347         }
 348 }
 349 #endif
 350 //***************************************************************************************************************
 351 int Pintail::getChimeras(Sequence* query) {
 352         try {
 353                 querySeq = query;
 354                 trimmed.clear();
 355                 windowSizes = window;
 356
 357                 //find pairs has to be done before a mask
 358                 bestfit = findPairs(query);
 359
 360                 if (m->control_pressed) {  return 0; }
 361
 362                 //if they mask
 363                 if (seqMask != "") {
 364                         decalc->runMask(query);
 365                         decalc->runMask(bestfit);
 366                 }
 367
 368                 if (filter) { //must be done after a mask
 369                         runFilter(query);
 370                         runFilter(bestfit);
 371                 }
 372
 373
 374                 //trim seq
 375                 decalc->trimSeqs(query, bestfit, trimmed);
 376
 377                 //find windows
 378                 it = trimmed.begin();
 379                 windowsForeachQuery = decalc->findWindows(query, it->first, it->second, windowSizes, increment);
 380
 381                 //find observed distance
 382                 obsDistance = decalc->calcObserved(query, bestfit, windowsForeachQuery, windowSizes);
 383
 384                 if (m->control_pressed) {  return 0; }
 385
 386                 Qav = decalc->findQav(windowsForeachQuery, windowSizes, probabilityProfile);
 387
 388                 if (m->control_pressed) {  return 0; }
 389
 390                 //find alpha
 391                 seqCoef = decalc->getCoef(obsDistance, Qav);
 392
 393                 //calculating expected distance
 394                 expectedDistance = decalc->calcExpected(Qav, seqCoef);
 395
 396                 if (m->control_pressed) {  return 0; }
 397
 398                 //finding de
 399                 DE = decalc->calcDE(obsDistance, expectedDistance);
 400
 401                 if (m->control_pressed) {  return 0; }
 402
 403                 //find distance between query and closest match
 404                 it = trimmed.begin();
 405                 deviation = decalc->calcDist(query, bestfit, it->first, it->second);
 406
 407                 delete bestfit;
 408
 409                 return 0;
 410         }
 411         catch(exception& e) {
 412                 m->errorOut(e, "Pintail", "getChimeras");
 413                 exit(1);
 414         }
 415 }
 416
 417 //***************************************************************************************************************
 418
 419 vector<float> Pintail::readFreq() {
 420         try {
 421                 //read in probabilities and store in vector
 422                 int pos; float num;
 423
 424                 vector<float> prob;
 425                 set<int> h = decalc->getPos();  //positions of bases in masking sequence
 426
 427         #ifdef USE_MPI
 428
 429                 MPI_File inMPI;
 430                 MPI_Offset size;
 431                 MPI_Status status;
 432
 433                 //char* inFileName = new char[consfile.length()];
 434                 //memcpy(inFileName, consfile.c_str(), consfile.length());
 435
 436                 char inFileName[1024];
 437                 strcpy(inFileName, consfile.c_str());
 438
 439                 MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 440                 MPI_File_get_size(inMPI, &size);
 441                 //delete inFileName;
 442
 443                 char* buffer = new char[size];
 444                 MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
 445
 446                 string tempBuf = buffer;
 447                 delete buffer;
 448
 449                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 450                 istringstream iss (tempBuf,istringstream::in);
 451
 452                 while(!iss.eof()) {
 453                         iss >> pos >> num;
 454
 455                         if (h.count(pos) > 0) {
 456                                 float Pi;
 457                                 Pi =  (num - 0.25) / 0.75;
 458
 459                                 //cannot have probability less than 0.
 460                                 if (Pi < 0) { Pi = 0.0; }
 461
 462                                 //do you want this spot
 463                                 prob.push_back(Pi);
 464                         }
 465
 466                         gobble(iss);
 467                 }
 468
 469                 MPI_File_close(&inMPI);
 470
 471         #else
 472
 473                 ifstream in;
 474                 openInputFile(consfile, in);
 475
 476                 while(!in.eof()){
 477
 478                         in >> pos >> num;
 479
 480                         if (h.count(pos) > 0) {
 481                                 float Pi;
 482                                 Pi =  (num - 0.25) / 0.75;
 483
 484                                 //cannot have probability less than 0.
 485                                 if (Pi < 0) { Pi = 0.0; }
 486
 487                                 //do you want this spot
 488                                 prob.push_back(Pi);
 489                         }
 490
 491                         gobble(in);
 492                 }
 493                 in.close();
 494
 495         #endif
 496
 497                 return prob;
 498
 499         }
 500         catch(exception& e) {
 501                 m->errorOut(e, "Pintail", "readFreq");
 502                 exit(1);
 503         }
 504 }
 505
 506 //***************************************************************************************************************
 507 //calculate the distances from each query sequence to all sequences in the template to find the closest sequence
 508 Sequence* Pintail::findPairs(Sequence* q) {
 509         try {
 510
 511                 Sequence* seqsMatches;
 512
 513                 seqsMatches = decalc->findClosest(q, templateSeqs);
 514                 return seqsMatches;
 515
 516         }
 517         catch(exception& e) {
 518                 m->errorOut(e, "Pintail", "findPairs");
 519                 exit(1);
 520         }
 521 }
 522 //**************************************************************************************************
 523 void Pintail::createProcessesQuan() {
 524         try {
 525 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 526                 int process = 0;
 527                 vector<int> processIDS;
 528
 529                 //loop through and create all the processes you want
 530                 while (process != processors) {
 531                         int pid = fork();
 532
 533                         if (pid > 0) {
 534                                 processIDS.push_back(pid);
 535                                 process++;
 536                         }else if (pid == 0){
 537
 538                                 quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, templateLines[process]->start, templateLines[process]->end);
 539
 540                                 //write out data to file so parent can read it
 541                                 ofstream out;
 542                                 string s = toString(getpid()) + ".temp";
 543                                 openOutputFile(s, out);
 544
 545
 546                                 //output observed distances
 547                                 for (int i = 0; i < quantilesMembers.size(); i++) {
 548                                         out << quantilesMembers[i].size() << '\t';
 549                                         for (int j = 0; j < quantilesMembers[i].size(); j++) {
 550                                                 out << quantilesMembers[i][j] << '\t';
 551                                         }
 552                                         out << endl;
 553                                 }
 554
 555                                 out.close();
 556
 557                                 exit(0);
 558                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 559                 }
 560
 561                 //force parent to wait until all the processes are done
 562                 for (int i=0;i<processors;i++) {
 563                         int temp = processIDS[i];
 564                         wait(&temp);
 565                 }
 566
 567                 //get data created by processes
 568                 for (int i=0;i<processors;i++) {
 569                         ifstream in;
 570                         string s = toString(processIDS[i]) + ".temp";
 571                         openInputFile(s, in);
 572
 573                         vector< vector<float> > quan;
 574                         quan.resize(100);
 575
 576                         //get quantiles
 577                         for (int h = 0; h < quan.size(); h++) {
 578                                 int num;
 579                                 in >> num;
 580
 581                                 gobble(in);
 582
 583                                 vector<float> q;  float w;
 584                                 for (int j = 0; j < num; j++) {
 585                                         in >> w;
 586                                         q.push_back(w);
 587                                 }
 588
 589                                 quan[h] = q;
 590                                 gobble(in);
 591                         }
 592
 593
 594                         //save quan in quantiles
 595                         for (int j = 0; j < quan.size(); j++) {
 596                                 //put all values of q[i] into quan[i]
 597                                 for (int l = 0; l < quan[j].size(); l++) {  quantilesMembers[j].push_back(quan[j][l]);   }
 598                                 //quantilesMembers[j].insert(quantilesMembers[j].begin(), quan[j].begin(), quan[j].end());
 599                         }
 600
 601                         in.close();
 602                         remove(s.c_str());
 603                 }
 604
 605 #else
 606                 quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
 607 #endif
 608         }
 609         catch(exception& e) {
 610                 m->errorOut(e, "Pintail", "createProcessesQuan");
 611                 exit(1);
 612         }
 613 }
 614 //***************************************************************************************************************
 615 vector< vector<float> > Pintail::readQuantiles() {
 616         try {
 617                 int num;
 618                 float ten, twentyfive, fifty, seventyfive, ninetyfive, ninetynine;
 619
 620                 vector< vector<float> > quan;
 621                 vector <float> temp; temp.resize(6, 0);
 622
 623                 //to fill 0
 624                 quan.push_back(temp);
 625
 626         #ifdef USE_MPI
 627
 628                 MPI_File inMPI;
 629                 MPI_Offset size;
 630                 MPI_Status status;
 631
 632                 //char* inFileName = new char[quanfile.length()];
 633                 //memcpy(inFileName, quanfile.c_str(), quanfile.length());
 634
 635                 char inFileName[1024];
 636                 strcpy(inFileName, quanfile.c_str());
 637
 638                 MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 639                 MPI_File_get_size(inMPI, &size);
 640                 //delete inFileName;
 641
 642
 643                 char* buffer = new char[size];
 644                 MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
 645
 646                 string tempBuf = buffer;
 647                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 648                 istringstream iss (tempBuf,istringstream::in);
 649                 delete buffer;
 650
 651                 while(!iss.eof()) {
 652                         iss >> num >> ten >> twentyfive >> fifty >> seventyfive >> ninetyfive >> ninetynine;
 653
 654                         temp.clear();
 655
 656                         temp.push_back(ten);
 657                         temp.push_back(twentyfive);
 658                         temp.push_back(fifty);
 659                         temp.push_back(seventyfive);
 660                         temp.push_back(ninetyfive);
 661                         temp.push_back(ninetynine);
 662
 663                         quan.push_back(temp);
 664
 665                         gobble(iss);
 666                 }
 667
 668                 MPI_File_close(&inMPI);
 669
 670         #else
 671
 672                 ifstream in;
 673                 openInputFile(quanfile, in);
 674
 675                 while(!in.eof()){
 676
 677                         in >> num >> ten >> twentyfive >> fifty >> seventyfive >> ninetyfive >> ninetynine;
 678
 679                         temp.clear();
 680
 681                         temp.push_back(ten);
 682                         temp.push_back(twentyfive);
 683                         temp.push_back(fifty);
 684                         temp.push_back(seventyfive);
 685                         temp.push_back(ninetyfive);
 686                         temp.push_back(ninetynine);
 687
 688                         quan.push_back(temp);
 689
 690                         gobble(in);
 691                 }
 692                 in.close();
 693         #endif
 694
 695                 return quan;
 696
 697         }
 698         catch(exception& e) {
 699                 m->errorOut(e, "Pintail", "readQuantiles");
 700                 exit(1);
 701         }
 702 }
 703 //***************************************************************************************************************/
 704
 705 void Pintail::printQuanFile(string file, string outputString) {
 706         try {
 707
 708                 #ifdef USE_MPI
 709
 710                         MPI_File outQuan;
 711                         MPI_Status status;
 712
 713                         int pid;
 714                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 715
 716                         int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 717
 718                         //char* FileName = new char[file.length()];
 719                         //memcpy(FileName, file.c_str(), file.length());
 720
 721                         char FileName[1024];
 722                         strcpy(FileName, file.c_str());
 723
 724                         if (pid == 0) {
 725                                 MPI_File_open(MPI_COMM_SELF, FileName, outMode, MPI_INFO_NULL, &outQuan);  //comm, filename, mode, info, filepointer
 726
 727                                 int length = outputString.length();
 728                                 char* buf = new char[length];
 729                                 memcpy(buf, outputString.c_str(), length);
 730
 731                                 MPI_File_write(outQuan, buf, length, MPI_CHAR, &status);
 732                                 delete buf;
 733
 734                                 MPI_File_close(&outQuan);
 735                         }
 736
 737                         //delete FileName;
 738                 #else
 739                         ofstream outQuan;
 740                         openOutputFile(file, outQuan);
 741
 742                         outQuan << outputString;
 743
 744                         outQuan.close();
 745                 #endif
 746         }
 747         catch(exception& e) {
 748                 m->errorOut(e, "Pintail", "printQuanFile");
 749                 exit(1);
 750         }
 751 }
 752
 753 //***************************************************************************************************************/
 754
 755
 756