segment.cpp 29.6 KB
Newer Older
Mikaël Salson's avatar
Mikaël Salson committed
1
/*
2
  This file is part of Vidjil <http://www.vidjil.org>
3
  Copyright (C) 2011, 2012, 2013, 2014, 2015, 2016 by Bonsai bioinformatics
4 5 6 7 8
  at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
  Contributors: 
      Mathieu Giraud <mathieu.giraud@vidjil.org>
      Mikaël Salson <mikael.salson@vidjil.org>
      Marc Duez <marc.duez@vidjil.org>
Mikaël Salson's avatar
Mikaël Salson committed
9 10 11 12 13 14 15 16 17 18 19 20 21 22

  "Vidjil" is free software: you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation, either version 3 of the License, or
  (at your option) any later version.

  "Vidjil" is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with "Vidjil". If not, see <http://www.gnu.org/licenses/>
*/
Mikaël Salson's avatar
Mikaël Salson committed
23
#include <algorithm>    // std::sort
Mikaël Salson's avatar
Mikaël Salson committed
24 25 26 27
#include <cassert>
#include "segment.h"
#include "tools.h"
#include "affectanalyser.h"
Mikaël Salson's avatar
Mikaël Salson committed
28
#include <sstream>
29
#include <cstring>
Marc Duez's avatar
Marc Duez committed
30
#include <string>
Mikaël Salson's avatar
Mikaël Salson committed
31

32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48

AlignBox::AlignBox() {
  del_left = 0 ;
  start = 0 ;
  end = 0 ;
  del_right = 0 ;

  ref_nb = 0 ;
  ref = "";
  ref_label = "";
}

string AlignBox::getSequence(string sequence) {
  return sequence.substr(start, end-start+1);
}


49 50 51 52 53 54 55 56 57 58 59
ostream &operator<<(ostream &out, const AlignBox &box)
{
  out << "[/" << box.del_left << " " ;
  out << "@" << box.start << " " ;
  out << box.ref_label << "(" << box.ref_nb << ") " ;
  out << "@" << box.end << " " ;
  out << box.del_right << "/]" ;

  return out ;
}

60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79
string codeFromBoxes(vector <AlignBox*> boxes, string sequence)
{
  string code = "";

  int n = boxes.size();

  for (int i=0; i<n; i++) {

    if (i>0) {
      code += " " + string_of_int(boxes[i-1]->del_right) + "/"
        // From box_left->end + 1 to box_right->start - 1
        + sequence.substr(boxes[i-1]->end + 1, boxes[i]->start - boxes[i-1]->end - 1)
        + "/" + string_of_int(boxes[i]->del_left) + " " ;
    }

    code += boxes[i]->ref_label ;
  }

  return code;
}
80

81

Mathieu Giraud's avatar
Mathieu Giraud committed
82
Segmenter::~Segmenter() {}
Mikaël Salson's avatar
Mikaël Salson committed
83

Mathieu Giraud's avatar
Mathieu Giraud committed
84
Sequence Segmenter::getSequence() const {
Mikaël Salson's avatar
Mikaël Salson committed
85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104
  Sequence s ;
  s.label_full = info ;
  s.label = label + " " + (reversed ? "-" : "+");
  s.sequence = revcomp(sequence, reversed);

  return s ;
}

string Segmenter::getJunction(int l) const {
  assert(isSegmented());

  int start = (getLeft() + getRight())/2 - l/2;
  
  if (start < 0 or start + l > (int)sequence.size())  // TODO: +l ou +l-1 ?
    return "" ;

  return getSequence().sequence.substr(start, l);
}

int Segmenter::getLeft() const {
105
  return box_V->end;
Mikaël Salson's avatar
Mikaël Salson committed
106 107 108
}
  
int Segmenter::getRight() const {
109
  return box_J->start;
Mikaël Salson's avatar
Mikaël Salson committed
110 111 112
}

int Segmenter::getLeftD() const {
113
  return box_D->start;
Mikaël Salson's avatar
Mikaël Salson committed
114 115 116
}
  
int Segmenter::getRightD() const {
117
  return box_D->end;
Mikaël Salson's avatar
Mikaël Salson committed
118 119 120 121 122 123 124 125 126 127 128 129 130 131
}

bool Segmenter::isReverse() const {
  return reversed;
}

bool Segmenter::isSegmented() const {
  return segmented;
}

bool Segmenter::isDSegmented() const {
  return dSegmented;
}

132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150

// E-values

void Segmenter::checkLeftRightEvaluesThreshold(double threshold, int strand)
{
  if (threshold == NO_LIMIT_VALUE)
    return ;

  if (evalue_left >= threshold && evalue_right >= threshold)
    because = UNSEG_TOO_FEW_ZERO ;
  else if ((strand == 1 ? evalue_left : evalue_right) >= threshold)
    because = UNSEG_TOO_FEW_V ;
  else if ((strand == 1 ? evalue_right : evalue_left) >= threshold)
    because = UNSEG_TOO_FEW_J ;
  else if (evalue >= threshold) // left and right are <= threshold, but their sum is > threshold
    because = UNSEG_TOO_FEW_ZERO ;
}


Mikaël Salson's avatar
Mikaël Salson committed
151 152 153 154 155 156 157 158
// Chevauchement

string Segmenter::removeChevauchement()
{
  assert(isSegmented());
  
  string chevauchement = "" ;

159
  if (box_V->end >= box_J->start)
Mikaël Salson's avatar
Mikaël Salson committed
160
    {
161 162 163 164
      int middle = (box_V->end + box_J->start) / 2 ;
      chevauchement = " !ov " + string_of_int (box_V->end - box_J->start + 1);
      box_V->end = middle ;
      box_J->start = middle+1 ;
Mikaël Salson's avatar
Mikaël Salson committed
165 166 167 168 169 170 171 172 173 174 175 176 177 178
    }

  return chevauchement ;
}

// Prettyprint


bool Segmenter::finishSegmentation() 
{
  assert(isSegmented());
  
  string seq = getSequence().sequence;
    
179 180 181 182 183
  seg_V = seq.substr(0, box_V->end+1) ;
  seg_N = seq.substr(box_V->end+1, box_J->start-box_V->end-1) ;  // Twice computed for FineSegmenter, but only once in KmerSegmenter !
  seg_J = seq.substr(box_J->start) ;
  box_D->start=0;
  box_D->end=0;
Mikaël Salson's avatar
Mikaël Salson committed
184 185 186 187 188 189 190 191 192 193 194 195 196

  info = "VJ \t" + string_of_int(FIRST_POS) + " " + info + " " + string_of_int(seq.size() - 1 + FIRST_POS) ;
  info += "\t" + code ;

  info = (reversed ? "- " : "+ ") + info ;

  return true ;
}

bool Segmenter::finishSegmentationD() 
{
  string seq = getSequence().sequence;

197 198 199 200
  seg_V = seq.substr(0, box_V->end+1) ; // From pos. 0 to box_V->end
  seg_J = seq.substr(box_J->start) ;
  seg_N = seq.substr(box_V->end+1, box_J->start-box_V->end-1) ;  // Twice computed for FineSegmenter, but only once in KmerSegmenter !
  seg_D  = seq.substr(box_D->start, box_D->end-box_D->start+1) ; // From Dstart to Dend
Mikaël Salson's avatar
Mikaël Salson committed
201
  
202 203 204 205
  info = "VDJ \t0 " + string_of_int(box_V->end) +
                " " + string_of_int(box_D->start) +
		" " + string_of_int(box_D->end) +
		" " + string_of_int(box_J->start) +
Mikaël Salson's avatar
Mikaël Salson committed
206 207 208 209 210 211 212 213 214
		" " + string_of_int(seq.size()-1+FIRST_POS) ;
		
  info += "\t" + code ;
  
  info = (reversed ? "- " : "+ ") + info ;

  return true ;
}

215 216
string Segmenter::getInfoLine() const
{
217
  string s = "" ;
218 219 220 221 222

  s += (segmented ? "" : "! ") + info ;
  s += " " + info_extra ;
  s += " " + segmented_germline->code ;
  s += " " + string(segmented_mesg[because]) ;
223 224 225 226

  if (evalue > NO_LIMIT_VALUE)
    s += " " + scientific_string_of_double(evalue);

227 228 229 230 231
  if (evalue_left > NO_LIMIT_VALUE)
    s += " " + scientific_string_of_double(evalue_left);
  if (evalue_right > NO_LIMIT_VALUE)
    s += "/" + scientific_string_of_double(evalue_right);

232 233 234
  return s ;
}

235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250
string KmerSegmenter::getInfoLineWithAffects() const
{
   stringstream ss;

   ss << "# "
      << right << setw(3) << score << " "
      << left << setw(30)
      << getInfoLine() ;

   if (getSegmentationStatus() != UNSEG_TOO_SHORT)
     ss << getKmerAffectAnalyser()->toString();

   return ss.str();
}


Mikaël Salson's avatar
Mikaël Salson committed
251 252
ostream &operator<<(ostream &out, const Segmenter &s)
{
253
  out << ">" << s.label << " " ;
254
  out << s.getInfoLine() << endl;
Mikaël Salson's avatar
Mikaël Salson committed
255 256 257 258 259 260 261 262 263

  if (s.segmented)
    {
      out << s.seg_V << endl ;
      out << s.seg_N << endl ;
      out << s.seg_J << endl ;
    }
  else
    {
264
      out << s.getSequence().sequence << endl ;
Mikaël Salson's avatar
Mikaël Salson committed
265 266 267 268 269 270 271 272
    }

  return out ;
}


// KmerSegmenter (Cheap)

273 274
KmerSegmenter::KmerSegmenter() { kaa = 0 ; }

275
KmerSegmenter::KmerSegmenter(Sequence seq, Germline *germline, double threshold, int multiplier)
Mikaël Salson's avatar
Mikaël Salson committed
276
{
277 278 279 280
  box_V = new AlignBox();
  box_D = new AlignBox();
  box_J = new AlignBox();

Mikaël Salson's avatar
Mikaël Salson committed
281 282 283
  label = seq.label ;
  sequence = seq.sequence ;
  info = "" ;
284
  info_extra = "seed";
Mikaël Salson's avatar
Mikaël Salson committed
285
  segmented = false;
286
  segmented_germline = germline ;
287
  system = germline->code; // useful ?
288
  reversed = false;
289
  because = NOT_PROCESSED ; // Cause of unsegmentation
290
  score = 0 ;
291
  evalue = NO_LIMIT_VALUE;
292 293
  evalue_left = NO_LIMIT_VALUE;
  evalue_right = NO_LIMIT_VALUE;
294

295
  int s = (size_t)germline->index->getS() ;
Mikaël Salson's avatar
Mikaël Salson committed
296
  int length = sequence.length() ;
Mikaël Salson's avatar
Mikaël Salson committed
297

298
  if (length < s) 
Mikaël Salson's avatar
Mikaël Salson committed
299
    {
Mathieu Giraud's avatar
Mathieu Giraud committed
300 301
      because = UNSEG_TOO_SHORT;
      kaa = NULL;
302
      return ;
Mikaël Salson's avatar
Mikaël Salson committed
303 304
    }
 
305
  kaa = new KmerAffectAnalyser(*(germline->index), sequence);
Mikaël Salson's avatar
Mikaël Salson committed
306 307
  
  // Check strand consistency among the affectations.
Mikaël Salson's avatar
Mikaël Salson committed
308 309 310 311 312 313 314 315 316
  int strand;
  int nb_strand[2] = {0,0};     // In cell 0 we'll put the number of negative
                                // strand, while in cell 1 we'll put the
                                // positives
  for (int i = 0; i < kaa->count(); i++) { 
    KmerAffect it = kaa->getAffectation(i);
    if (! it.isAmbiguous() && ! it.isUnknown()) {
      strand = affect_strand(it.affect);
      nb_strand[(strand + 1) / 2] ++; // (strand+1) / 2 → 0 if strand == -1; 1 if strand == 1
Mikaël Salson's avatar
Mikaël Salson committed
317 318 319
    }
  }

320 321
  score = nb_strand[0] + nb_strand[1] ; // Used only for non-segmented germlines

322 323
  reversed = (nb_strand[0] > nb_strand[1]) ;

324 325
  if ((germline->seg_method == SEG_METHOD_MAX12)
      || (germline->seg_method == SEG_METHOD_MAX1U))
326 327 328 329
    { // Pseudo-germline, MAX12 and MAX1U
      pair <KmerAffect, KmerAffect> max12 ;
      CountKmerAffectAnalyser ckaa(*(germline->index), sequence);

330 331 332 333 334

      set<KmerAffect> forbidden;
      forbidden.insert(KmerAffect::getAmbiguous());
      forbidden.insert(KmerAffect::getUnknown());

335
      if (germline->seg_method == SEG_METHOD_MAX12)
336 337 338
        // MAX12: two maximum k-mers (no unknown)
        {
          max12 = ckaa.max12(forbidden);
339

340 341 342 343 344 345
          if (max12.first.isUnknown() || max12.second.isUnknown())
            {
              because = UNSEG_TOO_FEW_ZERO ;
              return ;
            }
        }
346

347 348
      else
        // MAX1U: the maximum k-mers (no unknown) + unknown
349
        {
350 351 352 353 354 355 356 357 358
          CountKmerAffectAnalyser ckaa(*(germline->index), sequence);
          KmerAffect max = ckaa.max(forbidden);

          if (max.isUnknown())
            {
              because = UNSEG_TOO_FEW_ZERO ;
              return ;
            }
          max12 = make_pair(max, KmerAffect::getUnknown());
359 360
        }

361 362 363 364 365
      pair <KmerAffect, KmerAffect> before_after =  ckaa.sortLeftRight(max12);

      before = before_after.first ;
      after = before_after.second ;

366 367 368
      // This strand computation is only a heuristic, especially for chimera +/- reads
      // Anyway, it allows to gather such reads and their reverse complement into a unique window...
      // ... except when the read is quite different outside the window
369
      strand = reversed ? -1 : 1 ;
370 371 372 373 374
    }

  else
    { // Regular germline

375
  // Test on which strand we are, select the before and after KmerAffects
Mikaël Salson's avatar
Mikaël Salson committed
376
  if (nb_strand[0] == 0 && nb_strand[1] == 0) {
377
    because = UNSEG_TOO_FEW_ZERO ;
378
    return ;
Mikaël Salson's avatar
Mikaël Salson committed
379 380
  } else if (nb_strand[0] > RATIO_STRAND * nb_strand[1]) {
    strand = -1;
381 382
    before = KmerAffect(germline->affect_3, -1); 
    after = KmerAffect(germline->affect_5, -1);
Mikaël Salson's avatar
Mikaël Salson committed
383 384
  } else if (nb_strand[1] > RATIO_STRAND * nb_strand[0]) {
    strand = 1;
385 386
    before = KmerAffect(germline->affect_5, 1); 
    after = KmerAffect(germline->affect_3, 1);    
Mikaël Salson's avatar
Mikaël Salson committed
387 388
  } else {
    // Ambiguous information: we have positive and negative strands
389 390 391 392 393
    // and there is not enough difference to put them apart.
    if (nb_strand[0] + nb_strand[1] >= DETECT_THRESHOLD_STRAND)
      because = UNSEG_STRAND_NOT_CONSISTENT ;
    else
      because = UNSEG_TOO_FEW_ZERO ;
394
    return ;
Mikaël Salson's avatar
Mikaël Salson committed
395 396
  }

397
    } // endif Pseudo-germline
398
 
399
  computeSegmentation(strand, before, after, threshold, multiplier);
Mathieu Giraud's avatar
Mathieu Giraud committed
400
}
Mikaël Salson's avatar
Mikaël Salson committed
401

Mathieu Giraud's avatar
Mathieu Giraud committed
402
KmerSegmenter::~KmerSegmenter() {
403 404
  if (kaa)
    delete kaa;
405 406 407 408

  delete box_V;
  delete box_D;
  delete box_J;
409 410
}

411 412
KmerMultiSegmenter::KmerMultiSegmenter(Sequence seq, MultiGermline *multigermline, ostream *out_unsegmented,
                                       double threshold, int nb_reads_for_evalue)
413
{
414 415
  bool found_seg = false ; // Found a segmentation
  double best_evalue_seg = NO_LIMIT_VALUE ; // Best evalue, segmented sequences
416
  int best_score_unseg = 0 ; // Best score, unsegmented sequences
417
  the_kseg = NULL;
418
  multi_germline = multigermline;
419
  threshold_nb_expected = threshold;
420 421 422

  // E-value multiplier
  int multiplier = multi_germline->germlines.size() * nb_reads_for_evalue;
423
  
424 425 426 427 428
  // Iterate over the germlines
  for (list<Germline*>::const_iterator it = multigermline->germlines.begin(); it != multigermline->germlines.end(); ++it)
    {
      Germline *germline = *it ;

429
      KmerSegmenter *kseg = new KmerSegmenter(seq, germline, threshold, multiplier);
430
      bool keep_seg = false;
431

432 433 434
      if (out_unsegmented)
        {
          // Debug, display k-mer affectation and segmentation result for this germline
435
          *out_unsegmented << kseg->getInfoLineWithAffects() << endl ;
436 437
        }

438 439
      // Always remember the first kseg
      if (the_kseg == NULL)
440
        keep_seg = true;
441
      
442
      if (kseg->isSegmented())
443 444
        {
          // Yes, it is segmented
445
          // Should we keep the kseg ?
446
          if (!found_seg || (kseg->evalue < best_evalue_seg))
447
            {
448
              keep_seg = true;
449 450 451
              best_evalue_seg = kseg->evalue ;

              found_seg = true;
452
            }
453
        }
454 455 456 457 458 459 460
      else
        {
          // It is not segmented
          // Should we keep the kseg (with the unsegmentation cause) ?
            if (kseg->score > best_score_unseg)
            {              
              best_score_unseg = kseg->score ;
461
              if (!found_seg)
462 463 464 465
                keep_seg = true;
            }
        }
      
466
      if (keep_seg) {
467 468
        if (the_kseg)
          delete the_kseg;
469 470 471 472
        the_kseg = kseg;
      } else {
        delete kseg;
      }
473 474 475
    } // end for (Germlines)
}

476
KmerMultiSegmenter::~KmerMultiSegmenter() {
477 478
  if (the_kseg)
    delete the_kseg;
Mathieu Giraud's avatar
Mathieu Giraud committed
479 480
}

481 482
void KmerSegmenter::computeSegmentation(int strand, KmerAffect before, KmerAffect after,
                                        double threshold, int multiplier) {
483
  // Try to segment, computing 'box_V->end' and 'box_J->start'
484 485
  // If not segmented, put the cause of unsegmentation in 'because'

486
  affect_infos max;
487
  max = kaa->getMaximum(before, after);
Mikaël Salson's avatar
Mikaël Salson committed
488

489 490 491
  // We did not find a good segmentation point
  if (!max.max_found) {
    // We labeled it detected if there were both enough affect_5 and enough affect_3
492 493 494 495 496 497 498 499 500
    bool detected_before = (max.nb_before_left + max.nb_before_right >= DETECT_THRESHOLD);
    bool detected_after = (max.nb_after_left + max.nb_after_right >= DETECT_THRESHOLD);

    if (detected_before && detected_after)
      because = UNSEG_AMBIGUOUS ;
    else if ((strand == 1 && detected_before) || (strand == -1 && detected_after))
      because = UNSEG_TOO_FEW_J ;
    else if ((strand == 1 && detected_after) || (strand == -1 && detected_before))
      because = UNSEG_TOO_FEW_V ;
501
    else
502
      because = UNSEG_TOO_FEW_ZERO ;
503 504 505 506 507

    return ;
  }


508
  // E-values
509 510 511
  pair <double, double> pvalues = kaa->getLeftRightProbabilityAtLeastOrAbove();
  evalue_left = pvalues.first * multiplier ;
  evalue_right = pvalues.second * multiplier ;
512
  evalue = evalue_left + evalue_right ;
513

514
  checkLeftRightEvaluesThreshold(threshold, strand);
515

516
  if (because != NOT_PROCESSED)
517 518
    return ;

519 520
   // There was a good segmentation point

521 522
   box_V->end = max.first_pos_max;
   box_J->start = max.last_pos_max + 1;
523
   if (strand == -1) {
524 525 526
     int tmp = sequence.size() - box_V->end - 1;
     box_V->end = sequence.size() - box_J->start - 1;
     box_J->start = tmp;
527 528 529 530 531 532
   }

  // Yes, it is segmented
  segmented = true;
  because = reversed ? SEG_MINUS : SEG_PLUS ;

533
  info = string_of_int(box_V->end + FIRST_POS) + " " + string_of_int(box_J->start + FIRST_POS)  ;
534 535 536 537 538 539

  // removeChevauchement is called once info was already computed: it is only to output info_extra
  info_extra += removeChevauchement();
  finishSegmentation();

  return ;
Mathieu Giraud's avatar
Mathieu Giraud committed
540
}
Mikaël Salson's avatar
Mikaël Salson committed
541

542
KmerAffectAnalyser *KmerSegmenter::getKmerAffectAnalyser() const {
Mathieu Giraud's avatar
Mathieu Giraud committed
543 544
  return kaa;
}
Mikaël Salson's avatar
Mikaël Salson committed
545

546
int Segmenter::getSegmentationStatus() const {
Mathieu Giraud's avatar
Mathieu Giraud committed
547
  return because;
Mikaël Salson's avatar
Mikaël Salson committed
548 549
}

550 551 552 553 554
void Segmenter::setSegmentationStatus(int status) {
  because = status;
  segmented = (status == SEG_PLUS || status == SEG_MINUS);
}

Mikaël Salson's avatar
Mikaël Salson committed
555 556
// FineSegmenter

557

558
string check_and_resolve_overlap(string seq, int seq_begin, int seq_end,
559 560
                                 AlignBox *box_left, AlignBox *box_right,
                                 Cost segment_cost)
Mikaël Salson's avatar
Mikaël Salson committed
561
{
562
  // Overlap size
563
  int overlap = box_left->end - box_right->start + 1;
564 565 566

  if (overlap > 0)
    {
567 568
      string seq_left = seq.substr(seq_begin, box_left->end - seq_begin + 1);
      string seq_right = seq.substr(box_right->start, seq_end - box_right->start + 1);
569

Mikaël Salson's avatar
Mikaël Salson committed
570 571 572 573
      int score_r[overlap+1];
      int score_l[overlap+1];
      
      //LEFT
574
      DynProg dp_l = DynProg(seq_left, box_left->ref,
Mikaël Salson's avatar
Mikaël Salson committed
575
			   DynProg::Local, segment_cost);
576
      score_l[0] = dp_l.compute();
577

Mikaël Salson's avatar
Mikaël Salson committed
578 579
      
      //RIGHT
580
      // reverse right sequence
581
      string ref_right=string(box_right->ref.rbegin(), box_right->ref.rend());
582 583 584
      seq_right=string(seq_right.rbegin(), seq_right.rend());


585
      DynProg dp_r = DynProg(seq_right, ref_right,
Mikaël Salson's avatar
Mikaël Salson committed
586
			   DynProg::Local, segment_cost);
587
      score_r[0] = dp_r.compute();
588 589 590 591 592 593 594 595 596



      int trim_l[overlap+1];
      int trim_r[overlap+1];

      for(int i=0; i<=overlap; i++) {
        score_l[i] = i < seq_left.size()  ? dp_l.best_score_on_i(seq_left.size()  - i, trim_l + i) : MINUS_INF ;
        score_r[i] = i < seq_right.size() ? dp_r.best_score_on_i(seq_right.size() - i, trim_r + i) : MINUS_INF ;
Mikaël Salson's avatar
Mikaël Salson committed
597
      }
598

599 600 601 602 603 604

// #define DEBUG_OVERLAP
#ifdef DEBUG_OVERLAP
      cout << dp_l ;
      cout << dp_r ;

605 606
      cout << "seq:" << seq_left << "\t\t" << seq_right << endl;
      cout << "ref:" << ref_left << "\t\t" << ref_right << endl;
607 608 609 610 611 612 613 614
      for(int i=0; i<=overlap; i++)
        cout << i << "  left: " << score_l[i] << "/" << trim_l[i] << "     right: " << score_r[i] << "/" << trim_r[i] << endl;
#endif

      int score = MINUS_INF;
      int best_i = 0 ;
      int best_j = 0 ;

Mikaël Salson's avatar
Mikaël Salson committed
615

616
      // Find (i, j), with i+j >= overlap,
617
      // maximizing score_l[j] + score_r[i]
Mikaël Salson's avatar
Mikaël Salson committed
618 619
      for (int i=0; i<=overlap; i++){
	for (int j=overlap-i; j<=overlap; j++){
620
          int score_ij = score_l[i] + score_r[j];
621

622 623 624
	  if (score_ij > score) {
            best_i = i ;
            best_j = j ;
625 626
            box_left->del_right = box_left->ref.size() - trim_l[i];
	    box_right->del_left = box_right->ref.size() - trim_r[j];
627
	    score = score_ij;
Mikaël Salson's avatar
Mikaël Salson committed
628 629 630
	  }
	}
      }
631

632 633
      box_left->end -= best_i ;
      box_right->start += best_j ;
634 635

#ifdef DEBUG_OVERLAP
636
      cout << "overlap: " << overlap << ", " << "best_overlap_split: " << score
637 638
           << "    left: " << best_i << "-" << box_left->del_right << " @" << box_left->end
           << "    right:" << best_j << "-" << box_right->del_left << " @" << box_right->start
639
           << endl;
640
#endif
641 642
    } // end if (overlap > 0)

643 644
  // From box_left->end + 1 to box_right->start - 1
  return seq.substr(box_left->end + 1, box_right->start - box_left->end - 1);
Mikaël Salson's avatar
Mikaël Salson committed
645 646
}

Mikaël Salson's avatar
Mikaël Salson committed
647 648 649 650 651
bool comp_pair (pair<int,int> i,pair<int,int> j)
{
  return ( i.first > j.first);
}

652 653 654 655 656

/**
 * Align a read against a collection of sequences, maximizing the alignment 'score'
 * @param read:         the read
 * @param rep:          a collection of reference sequences
657
 * @param reverse_ref:  if true, reverse the reference sequences (VkVk)
658
 * @param reverse_both: if true, reverse both the read and the reference sequences (J segment)
659
 * @param local:        if true, Local alignment (D segment), otherwise LocalEndWithSomeDeletions and onlyBottomTriangle (V and J segments)
660
 * @param box:          the AligBox to fill
661
 * @param segment_cost: the cost used by the dynamic programing
662
 * @post  box is filled
663 664
 */

665
void align_against_collection(string &read, Fasta &rep, bool reverse_ref, bool reverse_both, bool local,
666
                             AlignBox *box, Cost segment_cost)
Mikaël Salson's avatar
Mikaël Salson committed
667 668 669
{
  
  int best_score = MINUS_INF ;
670
  box->ref_nb = MINUS_INF ;
Mikaël Salson's avatar
Mikaël Salson committed
671 672 673 674
  int best_best_i = (int) string::npos ;
  int best_best_j = (int) string::npos ;
  int best_first_i = (int) string::npos ;
  int best_first_j = (int) string::npos ;
675

Mikaël Salson's avatar
Mikaël Salson committed
676
  vector<pair<int, int> > score_r;
Mikaël Salson's avatar
Mikaël Salson committed
677 678 679

  DynProg::DynProgMode dpMode = DynProg::LocalEndWithSomeDeletions;
  if (local==true) dpMode = DynProg::Local;
680 681 682

  // With reverse_ref, the read is reversed to prevent calling revcomp on each reference sequence
  string sequence_or_rc = revcomp(read, reverse_ref);
Mikaël Salson's avatar
Mikaël Salson committed
683 684 685
  
  for (int r = 0 ; r < rep.size() ; r++)
    {
686
      DynProg dp = DynProg(sequence_or_rc, rep.sequence(r),
Mikaël Salson's avatar
Mikaël Salson committed
687 688 689
			   dpMode, // DynProg::SemiGlobalTrans, 
			   segment_cost, // DNA
			   reverse_both, reverse_both);
690 691 692

      bool onlyBottomTriangle = !local ;
      int score = dp.compute(onlyBottomTriangle, BOTTOM_TRIANGLE_SHIFT);
Mikaël Salson's avatar
Mikaël Salson committed
693
      
Mikaël Salson's avatar
Mikaël Salson committed
694 695 696 697 698 699 700 701 702 703 704
      if (local==true){ 
	dp.backtrack();
      }
      
      if (score > best_score)
	{
	  best_score = score ;
	  best_best_i = dp.best_i ;
	  best_best_j = dp.best_j ;
	  best_first_i = dp.first_i ;
	  best_first_j = dp.first_j ;
705 706
	  box->ref_nb = r ;
	  box->ref_label = rep.label(r) ;
Mikaël Salson's avatar
Mikaël Salson committed
707
	}
Mikaël Salson's avatar
Mikaël Salson committed
708 709
	
	score_r.push_back(make_pair(score, r));
Mathieu Giraud's avatar
Mathieu Giraud committed
710 711 712 713 714 715

	// #define DEBUG_SEGMENT      

#ifdef DEBUG_SEGMENT	
	cout << rep.label(r) << " " << score << " " << dp.best_i << endl ;
#endif
Mikaël Salson's avatar
Mikaël Salson committed
716 717

    }
Mikaël Salson's avatar
Mikaël Salson committed
718
    sort(score_r.begin(),score_r.end(),comp_pair);
Mikaël Salson's avatar
Mikaël Salson committed
719

720 721 722 723
  box->ref = rep.sequence(box->ref_nb);
  box->del_right = reverse_both ? best_best_j : box->ref.size() - best_best_j - 1;
  box->del_left = best_first_j;
  box->start = best_first_i;
Mikaël Salson's avatar
Mikaël Salson committed
724
  
725
  box->score = score_r;
Mathieu Giraud's avatar
Mathieu Giraud committed
726 727 728

#ifdef DEBUG_SEGMENT	
  cout << "best: " << best_labels << " " << best_score ;
729
  cout << "del/del2/begin:" << (box->del_right) << "/" << (box->del_left) << "/" << (box->start) << endl;
Mathieu Giraud's avatar
Mathieu Giraud committed
730 731
  cout << endl;
#endif
732 733 734 735

  if (reverse_ref)
    // Why -1 here and +1 in dynprog.cpp /// best_i = m - best_i + 1 ;
    best_best_i = read.length() - best_best_i - 1 ;
736 737

  box->end = best_best_i ;
Mikaël Salson's avatar
Mikaël Salson committed
738 739 740 741 742 743 744
}

string format_del(int deletions)
{
  return deletions ? *"(" + string_of_int(deletions) + " del)" : "" ;
}

745
FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c,  double threshold, int multiplier)
Mikaël Salson's avatar
Mikaël Salson committed
746
{
747 748 749 750
  box_V = new AlignBox();
  box_D = new AlignBox();
  box_J = new AlignBox();

751 752
  segmented = false;
  dSegmented = false;
753
  because = NOT_PROCESSED ;
754
  segmented_germline = germline ;
755
  info_extra = "" ;
Mikaël Salson's avatar
Mikaël Salson committed
756 757 758
  label = seq.label ;
  sequence = seq.sequence ;
  segment_cost=segment_c;
759
  evalue = NO_LIMIT_VALUE;
760 761
  evalue_left = NO_LIMIT_VALUE;
  evalue_right = NO_LIMIT_VALUE;
Mikaël Salson's avatar
Mikaël Salson committed
762

763 764
  CDR3start = -1;
  CDR3end = -1;
765

766 767 768
  bool reverse_V = false ;
  bool reverse_J = false ;

769
  if ((germline->seg_method == SEG_METHOD_MAX12) || (germline->seg_method == SEG_METHOD_MAX1U))
770
    {
771
      // We check whether this sequence is segmented with MAX12 or MAX1U (with default e-value parameters)
772
      KmerSegmenter *kseg = new KmerSegmenter(seq, germline, THRESHOLD_NB_EXPECTED, 1);
773
      if (kseg->isSegmented())
774
        {
775 776 777 778 779
          reversed = kseg->isReverse();

          KmerAffect left = reversed ? KmerAffect(kseg->after, true) : kseg->before ;
          KmerAffect right = reversed ? KmerAffect(kseg->before, true) : kseg->after ;

780 781
          delete kseg ;

782 783 784
          reverse_V = (left.getStrand() == -1);
          reverse_J = (right.getStrand() == -1);

785
          code = "Unexpected ";
786

787 788 789 790
          code += left.toStringSigns() + germline->index->getLabel(left).name;
          code += "/";
          code += right.toStringSigns() + germline->index->getLabel(right).name;
          info_extra += " " + left.toString() + "/" + right.toString() + " (" + code + ")";
791 792 793 794 795

          if (germline->seg_method == SEG_METHOD_MAX1U)
            return ;

          germline->override_rep5_rep3_from_labels(left, right);
796
        }
797
      else
798 799 800 801
        {
          delete kseg ;
          return ;
        }
802
    }
803

804 805 806 807 808 809 810
  // Strand determination, with KmerSegmenter (with default e-value parameters)
  // Note that we use only the 'strand' component
  // When the KmerSegmenter fails, continue with positive strand
  // TODO: flag to force a strand / to test both strands ?

  KmerSegmenter *kseg = new KmerSegmenter(seq, germline, THRESHOLD_NB_EXPECTED, 1);
  reversed = kseg->isReverse();
811
  delete kseg ;
Mikaël Salson's avatar
Mikaël Salson committed
812
  
813
  sequence_or_rc = revcomp(sequence, reversed); // sequence, possibly reversed
814

Mathieu Giraud's avatar
Mathieu Giraud committed
815 816

  /* Segmentation */
817
  align_against_collection(sequence_or_rc, germline->rep_5, reverse_V, reverse_V, false,
818
                                        box_V, segment_cost);
819

820
  align_against_collection(sequence_or_rc, germline->rep_3, reverse_J, !reverse_J, false,
821
                                          box_J, segment_cost);
822 823 824 825 826

  // J was run with '!reverseJ', we copy the box informations from right to left
  // Should this directly be handled in align_against_collection() ?
  box_J->start = box_J->end ;
  box_J->del_left = box_J->del_right;
827

828
  /* E-values */
829 830
  evalue_left  = multiplier * sequence.size() * germline->rep_5.totalSize() * segment_cost.toPValue(box_V->score[0].first);
  evalue_right = multiplier * sequence.size() * germline->rep_3.totalSize() * segment_cost.toPValue(box_J->score[0].first);
831
  evalue = evalue_left + evalue_right ;
832 833

  /* Unsegmentation causes */
834
  if (box_V->end == (int) string::npos)
835
    {
836
      evalue_left = BAD_EVALUE ;
837
    }
838
      
839
  if (box_J->start == (int) string::npos)
840
    {
841
      evalue_right = BAD_EVALUE ;
842 843
    }

844 845
  checkLeftRightEvaluesThreshold(threshold, reversed ? -1 : 1);

846 847 848
  if (because != NOT_PROCESSED)
    {
      segmented = false;
849
      info = " @" + string_of_int (box_V->end + FIRST_POS) + "  @" + string_of_int(box_J->start + FIRST_POS) ;
Mikaël Salson's avatar
Mikaël Salson committed
850 851
      return ;
    }
852 853 854 855

  /* The sequence is segmented */
  segmented = true ;
  because = reversed ? SEG_MINUS : SEG_PLUS ;
856

Mikaël Salson's avatar
Mikaël Salson committed
857
    //overlap VJ
858
  seg_N = check_and_resolve_overlap(sequence_or_rc, 0, sequence_or_rc.length(),
859
                                    box_V, box_J, segment_cost);
860

861
  // Why could this happen ?
862 863
      if (box_J->start>=(int) sequence.length())
	  box_J->start=sequence.length()-1;
Mikaël Salson's avatar
Mikaël Salson committed
864

865
  // seg_N will be recomputed in finishSegmentation()
Mikaël Salson's avatar
Mikaël Salson committed
866

867 868 869
  vector <AlignBox*> boxes ;
  boxes.push_back(box_V);
  boxes.push_back(box_J);
870
  code = codeFromBoxes(boxes, sequence_or_rc);
Mikaël Salson's avatar
Mikaël Salson committed
871

872
  info = string_of_int(box_V->end + FIRST_POS) + " " + string_of_int(box_J->start + FIRST_POS) ;
Mikaël Salson's avatar
Mikaël Salson committed
873 874 875
  finishSegmentation();
}

876
bool FineSegmenter::FineSegmentD(Germline *germline,
877
                                 AlignBox *box_Y, AlignBox *box_DD, AlignBox *box_Z,
878
                                 double evalue_threshold, int multiplier){
879

Mikaël Salson's avatar
Mikaël Salson committed
880
    // Create a zone where to look for D, adding at most EXTEND_D_ZONE nucleotides at each side
881
    int l = box_Y->end - EXTEND_D_ZONE;
Mikaël Salson's avatar
Mikaël Salson committed
882 883 884
    if (l<0) 
      l=0 ;

885
    int r = box_Z->start + EXTEND_D_ZONE;
Mikaël Salson's avatar
Mikaël Salson committed
886

887 888 889 890
    string seq = getSequence().sequence; // segmented sequence, possibly rev-comped

    if (r > (int) seq.length())
      r = seq.length();
Mikaël Salson's avatar
Mikaël Salson committed
891
      
892
    string str = seq.substr(l, r-l);
Mikaël Salson's avatar
Mikaël Salson committed
893 894

    // Align
895
    align_against_collection(str, germline->rep_4, false, false, true,
896
                                           box_DD, segment_cost);
897

898 899 900 901
    box_DD->start += l ;
    box_DD->end += l ;

    float evalue_D = multiplier * (r-l) * germline->rep_4.totalSize() * segment_cost.toPValue(box_DD->score[0].first);
902

903
    if (evalue_D > evalue_threshold)
904
      return false;
Mikaël Salson's avatar
Mikaël Salson committed
905 906
    
    //overlap VD
907 908
    seg_N1 = check_and_resolve_overlap(seq, 0, box_DD->end,
                                       box_Y, box_DD, segment_cost);
Mikaël Salson's avatar
Mikaël Salson committed
909 910
    
    //overlap DJ
911 912
    seg_N2 = check_and_resolve_overlap(seq, box_DD->start, seq.length(),
                                       box_DD, box_Z, segment_cost);
913 914 915 916 917 918 919 920 921

    return true;
}

void FineSegmenter::FineSegmentD(Germline *germline, double evalue_threshold, int multiplier){

  if (segmented){

    dSegmented = FineSegmentD(germline,
922
                              box_V, box_D, box_J,
923 924 925 926
                              evalue_threshold, multiplier);

    if (!dSegmented)
      return ;
927

928 929 930 931
    vector <AlignBox*> boxes ;
    boxes.push_back(box_V);
    boxes.push_back(box_D);
    boxes.push_back(box_J);
Mathieu Giraud's avatar