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(), compareQuanMembers);
 200
 201                                         //save 10%
 202                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.10)].score);
 203                                         //save 25%
 204                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.25)].score);
 205                                         //save 50%
 206                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.5)].score);
 207                                         //save 75%
 208                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.75)].score);
 209                                         //save 95%
 210                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.95)].score);
 211                                         //save 99%
 212                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.99)].score);
 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                         m->mothurOut("Done."); m->mothurOutEndLine();
 228                 }
 229
 230                 if (reRead) {
 231                         for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i];  }
 232                         templateSeqs.clear();
 233                         templateSeqs = readSeqs(templateFileName);
 234                 }
 235
 236
 237                 //free memory
 238                 for (int i = 0; i < templateLines.size(); i++) { delete templateLines[i];  }
 239
 240                 return 0;
 241
 242         }
 243         catch(exception& e) {
 244                 m->errorOut(e, "Pintail", "doPrep");
 245                 exit(1);
 246         }
 247 }
 248 //***************************************************************************************************************
 249 int Pintail::print(ostream& out, ostream& outAcc) {
 250         try {
 251                 int index = ceil(deviation);
 252
 253                 //is your DE value higher than the 95%
 254                 string chimera;
 255                 if (index != 0) {  //if index is 0 then its an exact match to a template seq
 256                         if (quantiles[index][4] == 0.0) {
 257                                 chimera = "Your template does not include sequences that provide quantile values at distance " + toString(index);
 258                         }else {
 259                                 if (DE > quantiles[index][4])           {       chimera = "Yes";        }
 260                                 else                                                            {       chimera = "No";         }
 261                         }
 262                 }else{ chimera = "No";          }
 263
 264                 out << querySeq->getName() << '\t' << "div: " << deviation << "\tstDev: " << DE << "\tchimera flag: " << chimera << endl;
 265                 if (chimera == "Yes") {
 266                         m->mothurOut(querySeq->getName() + "\tdiv: " + toString(deviation) + "\tstDev: " + toString(DE) + "\tchimera flag: " + chimera); m->mothurOutEndLine();
 267                         outAcc << querySeq->getName() << endl;
 268                 }
 269                 out << "Observed\t";
 270
 271                 for (int j = 0; j < obsDistance.size(); j++) {  out << obsDistance[j] << '\t';  }
 272                 out << endl;
 273
 274                 out << "Expected\t";
 275
 276                 for (int m = 0; m < expectedDistance.size(); m++) {  out << expectedDistance[m] << '\t';  }
 277                 out << endl;
 278
 279                 return 0;
 280
 281         }
 282         catch(exception& e) {
 283                 m->errorOut(e, "Pintail", "print");
 284                 exit(1);
 285         }
 286 }
 287 #ifdef USE_MPI
 288 //***************************************************************************************************************
 289 int Pintail::print(MPI_File& out, MPI_File& outAcc) {
 290         try {
 291                 bool results = false;
 292                 string outputString = "";
 293                 int index = ceil(deviation);
 294
 295                 //is your DE value higher than the 95%
 296                 string chimera;
 297                 if (index != 0) {  //if index is 0 then its an exact match to a template seq
 298                         if (quantiles[index][4] == 0.0) {
 299                                 chimera = "Your template does not include sequences that provide quantile values at distance " + toString(index);
 300                         }else {
 301                                 if (DE > quantiles[index][4])           {       chimera = "Yes";        }
 302                                 else                                                            {       chimera = "No";         }
 303                         }
 304                 }else{ chimera = "No";          }
 305
 306                 outputString += querySeq->getName() + "\tdiv: " + toString(deviation) + "\tstDev: " + toString(DE) + "\tchimera flag: " + chimera + "\n";
 307                 if (chimera == "Yes") {
 308                         cout << querySeq->getName() << "\tdiv: " << toString(deviation) << "\tstDev: " << toString(DE) << "\tchimera flag: " << chimera << endl;
 309                         string outAccString = querySeq->getName() + "\n";
 310
 311                         MPI_Status statusAcc;
 312                         int length = outAccString.length();
 313                         char* buf = new char[length];
 314                         memcpy(buf, outAccString.c_str(), length);
 315
 316                         MPI_File_write_shared(outAcc, buf, length, MPI_CHAR, &statusAcc);
 317                         delete buf;
 318
 319                         results = true;
 320                 }
 321                 outputString += "Observed\t";
 322
 323                 for (int j = 0; j < obsDistance.size(); j++) {  outputString += toString(obsDistance[j]) + "\t";  }
 324                 outputString += "\n";
 325
 326                 outputString += "Expected\t";
 327
 328                 for (int m = 0; m < expectedDistance.size(); m++) {  outputString += toString(expectedDistance[m]) + "\t";  }
 329                 outputString += "\n";
 330
 331                 MPI_Status status;
 332                 int length = outputString.length();
 333                 char* buf2 = new char[length];
 334                 memcpy(buf2, outputString.c_str(), length);
 335
 336                 MPI_File_write_shared(out, buf2, length, MPI_CHAR, &status);
 337                 delete buf2;
 338
 339                 return results;
 340         }
 341         catch(exception& e) {
 342                 m->errorOut(e, "Pintail", "print");
 343                 exit(1);
 344         }
 345 }
 346 #endif
 347 //***************************************************************************************************************
 348 int Pintail::getChimeras(Sequence* query) {
 349         try {
 350                 querySeq = query;
 351                 trimmed.clear();
 352                 windowSizes = window;
 353
 354                 //find pairs has to be done before a mask
 355                 bestfit = findPairs(query);
 356
 357                 if (m->control_pressed) {  return 0; }
 358
 359                 //if they mask
 360                 if (seqMask != "") {
 361                         decalc->runMask(query);
 362                         decalc->runMask(bestfit);
 363                 }
 364
 365                 if (filter) { //must be done after a mask
 366                         runFilter(query);
 367                         runFilter(bestfit);
 368                 }
 369
 370
 371                 //trim seq
 372                 decalc->trimSeqs(query, bestfit, trimmed);
 373
 374                 //find windows
 375                 it = trimmed.begin();
 376                 windowsForeachQuery = decalc->findWindows(query, it->first, it->second, windowSizes, increment);
 377
 378                 //find observed distance
 379                 obsDistance = decalc->calcObserved(query, bestfit, windowsForeachQuery, windowSizes);
 380
 381                 if (m->control_pressed) {  return 0; }
 382
 383                 Qav = decalc->findQav(windowsForeachQuery, windowSizes, probabilityProfile);
 384
 385                 if (m->control_pressed) {  return 0; }
 386
 387                 //find alpha
 388                 seqCoef = decalc->getCoef(obsDistance, Qav);
 389
 390                 //calculating expected distance
 391                 expectedDistance = decalc->calcExpected(Qav, seqCoef);
 392
 393                 if (m->control_pressed) {  return 0; }
 394
 395                 //finding de
 396                 DE = decalc->calcDE(obsDistance, expectedDistance);
 397
 398                 if (m->control_pressed) {  return 0; }
 399
 400                 //find distance between query and closest match
 401                 it = trimmed.begin();
 402                 deviation = decalc->calcDist(query, bestfit, it->first, it->second);
 403
 404                 delete bestfit;
 405
 406                 return 0;
 407         }
 408         catch(exception& e) {
 409                 m->errorOut(e, "Pintail", "getChimeras");
 410                 exit(1);
 411         }
 412 }
 413
 414 //***************************************************************************************************************
 415
 416 vector<float> Pintail::readFreq() {
 417         try {
 418                 //read in probabilities and store in vector
 419                 int pos; float num;
 420
 421                 vector<float> prob;
 422                 set<int> h = decalc->getPos();  //positions of bases in masking sequence
 423
 424         #ifdef USE_MPI
 425
 426                 MPI_File inMPI;
 427                 MPI_Offset size;
 428                 MPI_Status status;
 429
 430                 //char* inFileName = new char[consfile.length()];
 431                 //memcpy(inFileName, consfile.c_str(), consfile.length());
 432
 433                 char inFileName[1024];
 434                 strcpy(inFileName, consfile.c_str());
 435
 436                 MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 437                 MPI_File_get_size(inMPI, &size);
 438                 //delete inFileName;
 439
 440                 char* buffer = new char[size];
 441                 MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
 442
 443                 string tempBuf = buffer;
 444                 delete buffer;
 445
 446                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 447                 istringstream iss (tempBuf,istringstream::in);
 448
 449                 while(!iss.eof()) {
 450                         iss >> pos >> num;
 451
 452                         if (h.count(pos) > 0) {
 453                                 float Pi;
 454                                 Pi =  (num - 0.25) / 0.75;
 455
 456                                 //cannot have probability less than 0.
 457                                 if (Pi < 0) { Pi = 0.0; }
 458
 459                                 //do you want this spot
 460                                 prob.push_back(Pi);
 461                         }
 462
 463                         gobble(iss);
 464                 }
 465
 466                 MPI_File_close(&inMPI);
 467
 468         #else
 469
 470                 ifstream in;
 471                 openInputFile(consfile, in);
 472
 473                 while(!in.eof()){
 474
 475                         in >> pos >> num;
 476
 477                         if (h.count(pos) > 0) {
 478                                 float Pi;
 479                                 Pi =  (num - 0.25) / 0.75;
 480
 481                                 //cannot have probability less than 0.
 482                                 if (Pi < 0) { Pi = 0.0; }
 483
 484                                 //do you want this spot
 485                                 prob.push_back(Pi);
 486                         }
 487
 488                         gobble(in);
 489                 }
 490                 in.close();
 491
 492         #endif
 493
 494                 return prob;
 495
 496         }
 497         catch(exception& e) {
 498                 m->errorOut(e, "Pintail", "readFreq");
 499                 exit(1);
 500         }
 501 }
 502
 503 //***************************************************************************************************************
 504 //calculate the distances from each query sequence to all sequences in the template to find the closest sequence
 505 Sequence* Pintail::findPairs(Sequence* q) {
 506         try {
 507
 508                 Sequence* seqsMatches;
 509
 510                 seqsMatches = decalc->findClosest(q, templateSeqs);
 511                 return seqsMatches;
 512
 513         }
 514         catch(exception& e) {
 515                 m->errorOut(e, "Pintail", "findPairs");
 516                 exit(1);
 517         }
 518 }
 519 //**************************************************************************************************
 520 void Pintail::createProcessesQuan() {
 521         try {
 522 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 523                 int process = 0;
 524                 vector<int> processIDS;
 525
 526                 //loop through and create all the processes you want
 527                 while (process != processors) {
 528                         int pid = fork();
 529
 530                         if (pid > 0) {
 531                                 processIDS.push_back(pid);
 532                                 process++;
 533                         }else if (pid == 0){
 534
 535                                 quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, templateLines[process]->start, templateLines[process]->end);
 536
 537                                 //write out data to file so parent can read it
 538                                 ofstream out;
 539                                 string s = toString(getpid()) + ".temp";
 540                                 openOutputFile(s, out);
 541
 542
 543                                 //output observed distances
 544                                 for (int i = 0; i < quantilesMembers.size(); i++) {
 545                                         out << quantilesMembers[i].size() << '\t';
 546                                         for (int j = 0; j < quantilesMembers[i].size(); j++) {
 547                                                 out << quantilesMembers[i][j].score << '\t' << quantilesMembers[i][j].member1 << '\t' << quantilesMembers[i][j].member2 << '\t';
 548                                         }
 549                                         out << endl;
 550                                 }
 551
 552                                 out.close();
 553
 554                                 exit(0);
 555                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 556                 }
 557
 558                 //force parent to wait until all the processes are done
 559                 for (int i=0;i<processors;i++) {
 560                         int temp = processIDS[i];
 561                         wait(&temp);
 562                 }
 563
 564                 //get data created by processes
 565                 for (int i=0;i<processors;i++) {
 566                         ifstream in;
 567                         string s = toString(processIDS[i]) + ".temp";
 568                         openInputFile(s, in);
 569
 570                         vector< vector<quanMember> > quan;
 571                         quan.resize(100);
 572
 573                         //get quantiles
 574                         for (int m = 0; m < quan.size(); m++) {
 575                                 int num;
 576                                 in >> num;
 577
 578                                 gobble(in);
 579
 580                                 vector<quanMember> q;  float w; int b, n;
 581                                 for (int j = 0; j < num; j++) {
 582                                         in >> w >> b >> n;
 583
 584                                         quanMember newMember(w, b, n);
 585                                         q.push_back(newMember);
 586                                 }
 587
 588                                 quan[m] = q;
 589                                 gobble(in);
 590                         }
 591
 592
 593                         //save quan in quantiles
 594                         for (int j = 0; j < quan.size(); j++) {
 595                                 //put all values of q[i] into quan[i]
 596                                 for (int l = 0; l < quan[j].size(); l++) {  quantilesMembers[j].push_back(quan[j][l]);   }
 597                                 //quantilesMembers[j].insert(quantilesMembers[j].begin(), quan[j].begin(), quan[j].end());
 598                         }
 599
 600                         in.close();
 601                         remove(s.c_str());
 602                 }
 603
 604 #else
 605                 quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
 606 #endif
 607         }
 608         catch(exception& e) {
 609                 m->errorOut(e, "Pintail", "createProcessesQuan");
 610                 exit(1);
 611         }
 612 }
 613 //***************************************************************************************************************
 614 vector< vector<float> > Pintail::readQuantiles() {
 615         try {
 616                 int num;
 617                 float ten, twentyfive, fifty, seventyfive, ninetyfive, ninetynine;
 618
 619                 vector< vector<float> > quan;
 620                 vector <float> temp; temp.resize(6, 0);
 621
 622                 //to fill 0
 623                 quan.push_back(temp);
 624
 625         #ifdef USE_MPI
 626
 627                 MPI_File inMPI;
 628                 MPI_Offset size;
 629                 MPI_Status status;
 630
 631                 //char* inFileName = new char[quanfile.length()];
 632                 //memcpy(inFileName, quanfile.c_str(), quanfile.length());
 633
 634                 char inFileName[1024];
 635                 strcpy(inFileName, quanfile.c_str());
 636
 637                 MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 638                 MPI_File_get_size(inMPI, &size);
 639                 //delete inFileName;
 640
 641
 642                 char* buffer = new char[size];
 643                 MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
 644
 645                 string tempBuf = buffer;
 646                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 647                 istringstream iss (tempBuf,istringstream::in);
 648                 delete buffer;
 649
 650                 while(!iss.eof()) {
 651                         iss >> num >> ten >> twentyfive >> fifty >> seventyfive >> ninetyfive >> ninetynine;
 652
 653                         temp.clear();
 654
 655                         temp.push_back(ten);
 656                         temp.push_back(twentyfive);
 657                         temp.push_back(fifty);
 658                         temp.push_back(seventyfive);
 659                         temp.push_back(ninetyfive);
 660                         temp.push_back(ninetynine);
 661
 662                         quan.push_back(temp);
 663
 664                         gobble(iss);
 665                 }
 666
 667                 MPI_File_close(&inMPI);
 668
 669         #else
 670
 671                 ifstream in;
 672                 openInputFile(quanfile, in);
 673
 674                 while(!in.eof()){
 675
 676                         in >> num >> ten >> twentyfive >> fifty >> seventyfive >> ninetyfive >> ninetynine;
 677
 678                         temp.clear();
 679
 680                         temp.push_back(ten);
 681                         temp.push_back(twentyfive);
 682                         temp.push_back(fifty);
 683                         temp.push_back(seventyfive);
 684                         temp.push_back(ninetyfive);
 685                         temp.push_back(ninetynine);
 686
 687                         quan.push_back(temp);
 688
 689                         gobble(in);
 690                 }
 691                 in.close();
 692         #endif
 693
 694                 return quan;
 695
 696         }
 697         catch(exception& e) {
 698                 m->errorOut(e, "Pintail", "readQuantiles");
 699                 exit(1);
 700         }
 701 }
 702 //***************************************************************************************************************/
 703
 704 void Pintail::printQuanFile(string file, string outputString) {
 705         try {
 706
 707                 #ifdef USE_MPI
 708
 709                         MPI_File outQuan;
 710                         MPI_Status status;
 711
 712                         int pid;
 713                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 714
 715                         int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 716
 717                         //char* FileName = new char[file.length()];
 718                         //memcpy(FileName, file.c_str(), file.length());
 719
 720                         char FileName[1024];
 721                         strcpy(FileName, file.c_str());
 722
 723                         if (pid == 0) {
 724                                 MPI_File_open(MPI_COMM_SELF, FileName, outMode, MPI_INFO_NULL, &outQuan);  //comm, filename, mode, info, filepointer
 725
 726                                 int length = outputString.length();
 727                                 char* buf = new char[length];
 728                                 memcpy(buf, outputString.c_str(), length);
 729
 730                                 MPI_File_write(outQuan, buf, length, MPI_CHAR, &status);
 731                                 delete buf;
 732
 733                                 MPI_File_close(&outQuan);
 734                         }
 735
 736                         //delete FileName;
 737                 #else
 738                         ofstream outQuan;
 739                         openOutputFile(file, outQuan);
 740
 741                         outQuan << outputString;
 742
 743                         outQuan.close();
 744                 #endif
 745         }
 746         catch(exception& e) {
 747                 m->errorOut(e, "Pintail", "printQuanFile");
 748                 exit(1);
 749         }
 750 }
 751
 752 //***************************************************************************************************************/
 753
 754
 755