segment.cpp 19 KB
Newer Older
Mikaël Salson's avatar
Mikaël Salson committed
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
/*
  This file is part of "Vidjil" <http://bioinfo.lifl.fr/vidjil>
  Copyright (C) 2011, 2012, 2013 by Bonsai bioinformatics at LIFL (UMR CNRS 8022, Université Lille) and Inria Lille
  Contributors: Mathieu Giraud <mathieu.giraud@lifl.fr>, Mikaël Salson <mikael.salson@lifl.fr>, Marc Duez

  "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
19
#include <algorithm>    // std::sort
Mikaël Salson's avatar
Mikaël Salson committed
20 21 22 23
#include <cassert>
#include "segment.h"
#include "tools.h"
#include "affectanalyser.h"
Mikaël Salson's avatar
Mikaël Salson committed
24
#include <sstream>
Mikaël Salson's avatar
Mikaël Salson committed
25

Mathieu Giraud's avatar
Mathieu Giraud committed
26
Segmenter::~Segmenter() {}
Mikaël Salson's avatar
Mikaël Salson committed
27

Mathieu Giraud's avatar
Mathieu Giraud committed
28
Sequence Segmenter::getSequence() const {
Mikaël Salson's avatar
Mikaël Salson committed
29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48
  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 {
Mathieu Giraud's avatar
Mathieu Giraud committed
49
  return Vend;
Mikaël Salson's avatar
Mikaël Salson committed
50 51 52
}
  
int Segmenter::getRight() const {
Mathieu Giraud's avatar
Mathieu Giraud committed
53
  return Jstart;
Mikaël Salson's avatar
Mikaël Salson committed
54 55 56
}

int Segmenter::getLeftD() const {
Mathieu Giraud's avatar
Mathieu Giraud committed
57
  return Dstart;
Mikaël Salson's avatar
Mikaël Salson committed
58 59 60
}
  
int Segmenter::getRightD() const {
Mathieu Giraud's avatar
Mathieu Giraud committed
61
  return Dend;
Mikaël Salson's avatar
Mikaël Salson committed
62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83
}

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

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

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

// Chevauchement

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

Mathieu Giraud's avatar
Mathieu Giraud committed
84
  if (Vend >= Jstart)
Mikaël Salson's avatar
Mikaël Salson committed
85
    {
Mathieu Giraud's avatar
Mathieu Giraud committed
86
      int middle = (Vend + Jstart) / 2 ;
87
      chevauchement = " !ov " + string_of_int (Vend - Jstart + 1);
Mathieu Giraud's avatar
Mathieu Giraud committed
88 89
      Vend = middle ;
      Jstart = middle+1 ;
Mikaël Salson's avatar
Mikaël Salson committed
90 91 92 93 94 95 96 97 98 99 100 101 102 103
    }

  return chevauchement ;
}

// Prettyprint


bool Segmenter::finishSegmentation() 
{
  assert(isSegmented());
  
  string seq = getSequence().sequence;
    
Mathieu Giraud's avatar
Mathieu Giraud committed
104 105 106 107 108
  seg_V = seq.substr(0, Vend+1) ;
  seg_N = seq.substr(Vend+1, Jstart-Vend-1) ;  // Twice computed for FineSegmenter, but only once in KmerSegmenter !
  seg_J = seq.substr(Jstart) ;
  Dstart=0;
  Dend=0;
Mikaël Salson's avatar
Mikaël Salson committed
109 110 111 112 113 114 115 116 117 118 119 120 121

  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;

Mathieu Giraud's avatar
Mathieu Giraud committed
122 123
  seg_V = seq.substr(0, Vend+1) ; // From pos. 0 to Vend
  seg_J = seq.substr(Jstart) ;
Mikaël Salson's avatar
Mikaël Salson committed
124
  
Mathieu Giraud's avatar
Mathieu Giraud committed
125
  seg_D  = seq.substr(Dstart, Dend-Dstart+1) ; // From Dstart to Dend
Mikaël Salson's avatar
Mikaël Salson committed
126
  
Mathieu Giraud's avatar
Mathieu Giraud committed
127 128 129 130
  info = "VDJ \t0 " + string_of_int(Vend) +
		" " + string_of_int(Dstart) + 
		" " + string_of_int(Dend) +
		" " + string_of_int(Jstart) +
Mikaël Salson's avatar
Mikaël Salson committed
131 132 133 134 135 136 137 138 139 140 141 142 143
		" " + string_of_int(seq.size()-1+FIRST_POS) ;
		
  info += "\t" + code ;
  
  info = (reversed ? "- " : "+ ") + info ;

  return true ;
}

ostream &operator<<(ostream &out, const Segmenter &s)
{
  out << ">" << s.label << " " ;
  out << (s.segmented ? "" : "! ") << s.info ;
144
  out << " " << s.info_extra ;
Mikaël Salson's avatar
Mikaël Salson committed
145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163
  out << endl ;

  if (s.segmented)
    {
      out << s.seg_V << endl ;
      out << s.seg_N << endl ;
      out << s.seg_J << endl ;
    }
  else
    {
      out << s.sequence << endl ;
    }

  return out ;
}


// KmerSegmenter (Cheap)

164
KmerSegmenter::KmerSegmenter(Sequence seq, MultiGermline *multigermline)
Mikaël Salson's avatar
Mikaël Salson committed
165 166 167 168
{
  label = seq.label ;
  sequence = seq.sequence ;
  info = "" ;
169
  info_extra = "seed";
Mikaël Salson's avatar
Mikaël Salson committed
170
  segmented = false;
171
  segmented_germline = 0;
172
  reversed = false;
Mathieu Giraud's avatar
Mathieu Giraud committed
173
  Dend=0;
Mikaël Salson's avatar
Mikaël Salson committed
174
  
175 176 177
  // Now we just take one germline
  Germline *germline = multigermline->germlines.back(); 
  int s = (size_t)germline->index->getS() ;
Mikaël Salson's avatar
Mikaël Salson committed
178
  int length = sequence.length() ;
Mikaël Salson's avatar
Mikaël Salson committed
179

180
  if (length < s) 
Mikaël Salson's avatar
Mikaël Salson committed
181
    {
Mathieu Giraud's avatar
Mathieu Giraud committed
182 183
      because = UNSEG_TOO_SHORT;
      kaa = NULL;
Mikaël Salson's avatar
Mikaël Salson committed
184 185 186
      return ;
    }
 
187
  kaa = new KmerAffectAnalyser<KmerAffect>(*(germline->index), sequence);
Mikaël Salson's avatar
Mikaël Salson committed
188 189
  
  // Check strand consistency among the affectations.
Mikaël Salson's avatar
Mikaël Salson committed
190 191 192 193 194 195 196 197 198
  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
199 200 201
    }
  }

Mikaël Salson's avatar
Mikaël Salson committed
202 203 204 205 206 207 208 209 210 211 212 213 214
  // Test on which strand we are.
  if (nb_strand[0] == 0 && nb_strand[1] == 0) {
    strand = 0;                 // No info
  } else if (nb_strand[0] > RATIO_STRAND * nb_strand[1]) {
    strand = -1;
  } else if (nb_strand[1] > RATIO_STRAND * nb_strand[0]) {
    strand = 1;
  } else {
    // Ambiguous information: we have positive and negative strands
    // and there is not enough difference to put them aparat.
    strand = 2;
  }

215
  computeSegmentation(strand, germline->delta_min, germline->delta_max, s);
Mathieu Giraud's avatar
Mathieu Giraud committed
216 217 218 219

  if (segmented)
    {
      // Yes, it is segmented
220
      segmented_germline = germline;
Mathieu Giraud's avatar
Mathieu Giraud committed
221 222 223 224 225

      reversed = (strand == -1); 
      because = reversed ? SEG_MINUS : SEG_PLUS ;

      info = string_of_int(Vend + FIRST_POS) + " " + string_of_int(Jstart + FIRST_POS)  ;
226 227
      // removeChevauchement is called once info was already computed: it is only to output info_extra
      info_extra += removeChevauchement();
Mathieu Giraud's avatar
Mathieu Giraud committed
228 229 230
      finishSegmentation();
    } 
}
Mikaël Salson's avatar
Mikaël Salson committed
231

Mathieu Giraud's avatar
Mathieu Giraud committed
232 233 234 235 236
KmerSegmenter::~KmerSegmenter() {
  if (kaa)
    delete kaa;
}

237 238 239 240
void KmerSegmenter::computeSegmentation(int strand, int delta_min, int delta_max, int s) {
  // Try to segment, computing 'Vend' and 'Jstart', and 'segmented'
  // If not segmented, put the cause of unsegmentation in 'because'

Mikaël Salson's avatar
Mikaël Salson committed
241
  segmented = true ;
Mathieu Giraud's avatar
Mathieu Giraud committed
242
  because = 0 ; // Cause of unsegmentation
Mikaël Salson's avatar
Mikaël Salson committed
243 244 245 246

  // Zero information
  if (strand == 0)
    {
Mikaël Salson's avatar
Mikaël Salson committed
247
      because = UNSEG_TOO_FEW_ZERO ;
Mathieu Giraud's avatar
Mathieu Giraud committed
248 249
    } 
  else if (strand == 2) // Ambiguous
Mikaël Salson's avatar
Mikaël Salson committed
250
    {
Mikaël Salson's avatar
Mikaël Salson committed
251
      because = UNSEG_STRAND_NOT_CONSISTENT ;
Mathieu Giraud's avatar
Mathieu Giraud committed
252
    } 
253
  else
Mikaël Salson's avatar
Mikaël Salson committed
254 255
    {
      // Strand +
256 257 258 259 260 261 262
      affect_infos max;
      if (strand == 1)
        max = kaa->getMaximum(AFFECT_V, AFFECT_J);
      else
        max = kaa->getMaximum(AFFECT_J_BWD, AFFECT_V_BWD);

      if (! max.max_found) {
263 264
        if ((strand == 1 && max.nb_before_left == 0)
            || (strand == -1 && max.nb_after_right == 0)) 
265
          because = UNSEG_TOO_FEW_V ;
266 267
        else if ((strand == 1 && max.nb_after_right == 0)
                 || (strand == -1 && max.nb_before_left == 0))
Mikaël Salson's avatar
Mikaël Salson committed
268
	{
Mikaël Salson's avatar
Mikaël Salson committed
269
	  because = UNSEG_TOO_FEW_J ;
270
	} else 
271 272 273 274 275 276 277 278 279 280
          because = UNSEG_AMBIGUOUS; 
      } else {
        Vend = max.first_pos_max;
        Jstart = max.last_pos_max + 1;
        if (strand == -1) {
          int tmp = sequence.size() - Vend - 1;
          Vend = sequence.size() - Jstart - 1;
          Jstart = tmp;
        }
      }
Mikaël Salson's avatar
Mikaël Salson committed
281 282
    } 
  
Mathieu Giraud's avatar
Mathieu Giraud committed
283
  if (! because)
Mikaël Salson's avatar
Mikaël Salson committed
284
    {
Mathieu Giraud's avatar
Mathieu Giraud committed
285
      // Now we check the delta between Vend and right
Mikaël Salson's avatar
Mikaël Salson committed
286
   
Mathieu Giraud's avatar
Mathieu Giraud committed
287
      if (Jstart - Vend < delta_min)
Mikaël Salson's avatar
Mikaël Salson committed
288 289 290
	{
	  because = UNSEG_BAD_DELTA_MIN ;
	}
Mikaël Salson's avatar
Mikaël Salson committed
291

Mathieu Giraud's avatar
Mathieu Giraud committed
292
      if (Jstart - Vend > delta_max)
Mikaël Salson's avatar
Mikaël Salson committed
293 294 295
	{
	  because = UNSEG_BAD_DELTA_MAX ;
	}
Mathieu Giraud's avatar
Mathieu Giraud committed
296 297 298 299
    } 
  if (because)
    segmented = false;
}
Mikaël Salson's avatar
Mikaël Salson committed
300

301
KmerAffectAnalyser<KmerAffect> *KmerSegmenter::getKmerAffectAnalyser() const {
Mathieu Giraud's avatar
Mathieu Giraud committed
302 303
  return kaa;
}
Mikaël Salson's avatar
Mikaël Salson committed
304

Mathieu Giraud's avatar
Mathieu Giraud committed
305 306
int KmerSegmenter::getSegmentationStatus() const {
  return because;
Mikaël Salson's avatar
Mikaël Salson committed
307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363
}

// FineSegmenter

void best_align(int overlap, string seq_left, string seq_right,
		string ref_left ,string ref_right, int *b_r, int *b_l, Cost segment_cost)
{
      int score_r[overlap+1];
      int score_l[overlap+1];
      
      //LEFT
      ref_left=string(ref_left.rbegin(), ref_left.rend());
      seq_left=string(seq_left.rbegin(), seq_left.rend()); 
      
      DynProg dp1 = DynProg(seq_left, ref_left,
			   DynProg::Local, segment_cost);
      score_l[0] = dp1.compute();
      dp1.backtrack();
      
      //RIGHT
      DynProg dp = DynProg(seq_right, ref_right,
			   DynProg::Local, segment_cost);
      score_r[0] = dp.compute();
      dp.backtrack();    
      
      for(int i=1; i<=overlap; i++){
	if(dp.best_i-i >0)
	score_r[i] = dp.S[dp.best_i-i][dp.best_j];
	else
	score_r[i] =0;
	if(dp1.best_i-i >0)
	score_l[i] = dp1.S[dp1.best_i-i][dp1.best_j];	
	else
	score_l[i] =0;
      }
      int score=-1000000;
      int best_r=0;
      int best_l=0;

      for (int i=0; i<=overlap; i++){
	for (int j=overlap-i; j<=overlap; j++){
	  if ( ((score_r[i]+score_l[j]) == score) && (i+j < best_r+best_l )){
	    best_r=i;
	    best_l=j;
	    score=(score_r[i]+score_l[j]) ;
	  }
	  if ( (score_r[i]+score_l[j]) > score){
	    best_r=i;
	    best_l=j;
	    score=(score_r[i]+score_l[j]) ;
	  }
	}
      }
      *b_r=best_r;
      *b_l=best_l;
}

Mikaël Salson's avatar
Mikaël Salson committed
364 365 366 367 368
bool comp_pair (pair<int,int> i,pair<int,int> j)
{
  return ( i.first > j.first);
}

Mathieu Giraud's avatar
Mathieu Giraud committed
369
int align_against_collection(string &read, Fasta &rep, bool reverse_both, bool local, int *tag, 
Mikaël Salson's avatar
Mikaël Salson committed
370
			     int *del, int *del2, int *begin, int *length, vector<pair<int, int> > *score
Mikaël Salson's avatar
Mikaël Salson committed
371 372 373 374 375 376 377 378 379 380
			    , Cost segment_cost)
{
  
  int best_score = MINUS_INF ;
  int best_r = MINUS_INF ;
  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 ;
  string best_label = "" ;
Mikaël Salson's avatar
Mikaël Salson committed
381
  vector<pair<int, int> > score_r;
Mikaël Salson's avatar
Mikaël Salson committed
382 383 384 385 386 387 388 389 390 391 392

  DynProg::DynProgMode dpMode = DynProg::LocalEndWithSomeDeletions;
  if (local==true) dpMode = DynProg::Local;
  
  for (int r = 0 ; r < rep.size() ; r++)
    {
      DynProg dp = DynProg(read, rep.sequence(r),
			   dpMode, // DynProg::SemiGlobalTrans, 
			   segment_cost, // DNA
			   reverse_both, reverse_both);
      int score = dp.compute();
Mikaël Salson's avatar
Mikaël Salson committed
393
      
Mikaël Salson's avatar
Mikaël Salson committed
394 395 396 397 398 399 400 401 402 403 404 405 406 407
      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 ;
	  best_r = r ;
	  best_label = rep.label(r) ;
	}
Mikaël Salson's avatar
Mikaël Salson committed
408 409
	
	score_r.push_back(make_pair(score, r));
Mathieu Giraud's avatar
Mathieu Giraud committed
410 411 412 413 414 415

	// #define DEBUG_SEGMENT      

#ifdef DEBUG_SEGMENT	
	cout << rep.label(r) << " " << score << " " << dp.best_i << endl ;
#endif
Mikaël Salson's avatar
Mikaël Salson committed
416 417

    }
Mikaël Salson's avatar
Mikaël Salson committed
418
    sort(score_r.begin(),score_r.end(),comp_pair);
Mikaël Salson's avatar
Mikaël Salson committed
419 420 421 422

  *del = reverse_both ? best_best_j : rep.sequence(best_r).size() - best_best_j - 1;
  *del2 = best_first_j;
  *begin = best_first_i;
Mathieu Giraud's avatar
Mathieu Giraud committed
423
  *tag = best_r ; 
Mikaël Salson's avatar
Mikaël Salson committed
424 425
  
  *length -= *del ;
Mikaël Salson's avatar
Mikaël Salson committed
426 427
  
  *score=score_r;
Mathieu Giraud's avatar
Mathieu Giraud committed
428 429 430 431 432 433

#ifdef DEBUG_SEGMENT	
  cout << "best: " << best_labels << " " << best_score ;
  cout << "del/del2/begin:" << (*del) << "/" << (*del2) << "/" << (*begin) << endl;
  cout << endl;
#endif
Mikaël Salson's avatar
Mikaël Salson committed
434 435 436 437 438 439 440 441 442
  
  return best_best_i ;
}

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

443
FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c)
Mikaël Salson's avatar
Mikaël Salson committed
444 445
{

446
  info_extra = "" ;
Mikaël Salson's avatar
Mikaël Salson committed
447 448
  label = seq.label ;
  sequence = seq.sequence ;
Mathieu Giraud's avatar
Mathieu Giraud committed
449
  Dend=0;
Mikaël Salson's avatar
Mikaël Salson committed
450 451 452 453 454 455 456
  segment_cost=segment_c;

  // TODO: factoriser tout cela, peut-etre en lancant deux segmenteurs, un +, un -, puis un qui chapote
  
  // Strand +
  
  int plus_score = 0 ;
Mathieu Giraud's avatar
Mathieu Giraud committed
457
  int tag_plus_V, tag_plus_J;
Mikaël Salson's avatar
Mikaël Salson committed
458 459 460 461
  int plus_length = 0 ;
  int del_plus_V, del_plus_J ;
  int del2=0;
  int beg=0;
Mikaël Salson's avatar
Mikaël Salson committed
462 463 464 465
  
  vector<pair<int, int> > score_plus_V;
  vector<pair<int, int> > score_plus_J;
  
466
  int plus_left = align_against_collection(sequence, germline->rep_5, false, false, &tag_plus_V, &del_plus_V, &del2, &beg, 
Mikaël Salson's avatar
Mikaël Salson committed
467 468
					   &plus_length, &score_plus_V
					   , segment_cost);
469
  int plus_right = align_against_collection(sequence, germline->rep_3, true, false, &tag_plus_J, &del_plus_J, &del2, &beg,
Mikaël Salson's avatar
Mikaël Salson committed
470 471
					    &plus_length, &score_plus_J
					    , segment_cost);
Mikaël Salson's avatar
Mikaël Salson committed
472 473
  plus_length += plus_right - plus_left ;

Mikaël Salson's avatar
Mikaël Salson committed
474 475
  plus_score=score_plus_V[0].first + score_plus_J[0].first ;
  
Mikaël Salson's avatar
Mikaël Salson committed
476 477 478
  // Strand -
  string rc = revcomp(sequence) ;
  int minus_score = 0 ;
Mathieu Giraud's avatar
Mathieu Giraud committed
479
  int tag_minus_V, tag_minus_J;
Mikaël Salson's avatar
Mikaël Salson committed
480 481
  int minus_length = 0 ;
  int del_minus_V, del_minus_J ;
Mikaël Salson's avatar
Mikaël Salson committed
482 483 484 485
  
  vector<pair<int, int> > score_minus_V;
  vector<pair<int, int> > score_minus_J;
  
486
  int minus_left = align_against_collection(rc, germline->rep_5, false, false, &tag_minus_V, &del_minus_V, &del2, &beg,
Mikaël Salson's avatar
Mikaël Salson committed
487 488
					    &minus_length, &score_minus_V
					    ,  segment_cost);
489
  int minus_right = align_against_collection(rc, germline->rep_3, true, false, &tag_minus_J, &del_minus_J, &del2, &beg,
Mikaël Salson's avatar
Mikaël Salson committed
490 491
					     &minus_length, &score_minus_J
					     , segment_cost);
Mikaël Salson's avatar
Mikaël Salson committed
492 493
  minus_length += minus_right - minus_left ;

Mikaël Salson's avatar
Mikaël Salson committed
494 495
  minus_score=score_minus_V[0].first + score_minus_J[0].first ;
  
Mikaël Salson's avatar
Mikaël Salson committed
496 497 498 499
  reversed = (minus_score > plus_score) ;

  if (!reversed)
    {
Mathieu Giraud's avatar
Mathieu Giraud committed
500 501 502 503
      Vend = plus_left ;
      Jstart = plus_right ;
      best_V = tag_plus_V ;
      best_J = tag_plus_J ;
Mikaël Salson's avatar
Mikaël Salson committed
504 505
      del_V = del_plus_V ;
      del_J = del_plus_J ;
Mikaël Salson's avatar
Mikaël Salson committed
506 507
      score_V=score_plus_V;
      score_J=score_plus_J;
Mikaël Salson's avatar
Mikaël Salson committed
508 509 510
    }
  else
    {
Mathieu Giraud's avatar
Mathieu Giraud committed
511 512 513 514
      Vend = minus_left ;
      Jstart = minus_right ;
      best_V = tag_minus_V ;
      best_J = tag_minus_J ;
Mikaël Salson's avatar
Mikaël Salson committed
515 516
      del_V = del_minus_V ;
      del_J = del_minus_J ;
Mikaël Salson's avatar
Mikaël Salson committed
517 518
      score_V=score_minus_V;
      score_J=score_minus_J;
Mikaël Salson's avatar
Mikaël Salson committed
519 520
    }

Mathieu Giraud's avatar
Mathieu Giraud committed
521
  segmented = (Vend != (int) string::npos) && (Jstart != (int) string::npos) && 
522
    (Jstart - Vend >= germline->delta_min) && (Jstart - Vend <= germline->delta_max);
Mikaël Salson's avatar
Mikaël Salson committed
523 524 525 526 527
    
  dSegmented=false;

  if (!segmented)
    {
528
      because = DONT_KNOW;
Mathieu Giraud's avatar
Mathieu Giraud committed
529
      info = " @" + string_of_int (Vend + FIRST_POS) + "  @" + string_of_int(Jstart + FIRST_POS) ;
530
      
531
      if (Jstart - Vend < germline->delta_min)
532 533 534 535
        {
          because = UNSEG_BAD_DELTA_MIN  ;
        }

536
      if (Jstart - Vend > germline->delta_max)
537 538 539 540 541 542 543 544 545 546 547 548 549 550
        {
          because = UNSEG_BAD_DELTA_MAX  ;
        }
        
      if (Vend == (int) string::npos) 
        {
          because = UNSEG_TOO_FEW_V ;
        }
      
      if (Jstart == (int) string::npos)
        {
          because = UNSEG_TOO_FEW_J ;
        }
      
Mikaël Salson's avatar
Mikaël Salson committed
551 552 553
      return ;
    }
    
554 555
    because = reversed ? SEG_MINUS : SEG_PLUS ;
    
Mikaël Salson's avatar
Mikaël Salson committed
556
    //overlap VJ
Mathieu Giraud's avatar
Mathieu Giraud committed
557
    if(Jstart-Vend <=0){
Mikaël Salson's avatar
Mikaël Salson committed
558
      int b_r, b_l;
Mathieu Giraud's avatar
Mathieu Giraud committed
559
      int overlap=Vend-Jstart+1;
Mikaël Salson's avatar
Mikaël Salson committed
560
      
Mathieu Giraud's avatar
Mathieu Giraud committed
561 562
      string seq_left = sequence.substr(0, Vend+1);
      string seq_right = sequence.substr(Jstart);
Mikaël Salson's avatar
Mikaël Salson committed
563 564

      best_align(overlap, seq_left, seq_right, 
565
		 germline->rep_5.sequence(best_V), germline->rep_3.sequence(best_J), &b_r,&b_l, segment_cost);
Mikaël Salson's avatar
Mikaël Salson committed
566
      // Trim V
Mathieu Giraud's avatar
Mathieu Giraud committed
567
      Vend -= b_l;
Mikaël Salson's avatar
Mikaël Salson committed
568 569 570
      del_V += b_l;

      // Trim J
Mathieu Giraud's avatar
Mathieu Giraud committed
571
      Jstart += b_r;
Mikaël Salson's avatar
Mikaël Salson committed
572
      del_J += b_r;
573
      if (Jstart>=(int) sequence.length())
Mathieu Giraud's avatar
Mathieu Giraud committed
574
	  Jstart=sequence.length()-1;
Mikaël Salson's avatar
Mikaël Salson committed
575 576 577
    }

    // string chevauchement = removeChevauchement();
Mikaël Salson's avatar
Mikaël Salson committed
578 579

    /// used only below, then recomputed in finishSegmentation() ;
Mathieu Giraud's avatar
Mathieu Giraud committed
580
    seg_N = revcomp(sequence, reversed).substr(Vend+1, Jstart-Vend-1); 
Mikaël Salson's avatar
Mikaël Salson committed
581

582
  code = germline->rep_5.label(best_V) +
Mikaël Salson's avatar
Mikaël Salson committed
583 584 585 586
    " "+ string_of_int(del_V) + 
    "/" + seg_N + 
    // chevauchement +
    "/" + string_of_int(del_J) +
587
    " " + germline->rep_3.label(best_J); 
Mikaël Salson's avatar
Mikaël Salson committed
588

Mikaël Salson's avatar
Mikaël Salson committed
589
    stringstream code_s;
590
   code_s<< germline->rep_5.label(best_V) <<
Mikaël Salson's avatar
Mikaël Salson committed
591 592 593 594
    " -" << string_of_int(del_V) << "/" 
    << seg_N.size()
    // chevauchement +
    << "/-" << string_of_int(del_J)
595
    <<" " << germline->rep_3.label(best_J);
Mikaël Salson's avatar
Mikaël Salson committed
596 597
    code_short=code_s.str();
    
598 599
  code_light = germline->rep_5.label(best_V) +
    "/ " + germline->rep_3.label(best_J); 
Mikaël Salson's avatar
Mikaël Salson committed
600 601

 
Mathieu Giraud's avatar
Mathieu Giraud committed
602
  info = string_of_int(Vend + FIRST_POS) + " " + string_of_int(Jstart + FIRST_POS) ;
Mikaël Salson's avatar
Mikaël Salson committed
603 604 605 606 607

  finishSegmentation();
}


608
void FineSegmenter::FineSegmentD(Germline *germline){
Mikaël Salson's avatar
Mikaël Salson committed
609 610 611 612
  
  if (segmented){
    
    int end = (int) string::npos ;
Mathieu Giraud's avatar
Mathieu Giraud committed
613
    int tag_D;
Mikaël Salson's avatar
Mikaël Salson committed
614 615 616 617
    int length = 0 ;
    int begin = 0;
    
    // Create a zone where to look for D, adding at most EXTEND_D_ZONE nucleotides at each side
Mathieu Giraud's avatar
Mathieu Giraud committed
618
    int l = Vend - EXTEND_D_ZONE;
Mikaël Salson's avatar
Mikaël Salson committed
619 620 621
    if (l<0) 
      l=0 ;

Mathieu Giraud's avatar
Mathieu Giraud committed
622
    int r = Jstart + EXTEND_D_ZONE;
Mikaël Salson's avatar
Mikaël Salson committed
623 624 625 626 627 628 629

    if (r > (int)getSequence().sequence.length()) 
      r = getSequence().sequence.length();
      
    string str = getSequence().sequence.substr(l, r-l);

    // Align
630
    end = align_against_collection(str, germline->rep_4, false, true, &tag_D, &del_D_right, &del_D_left, &begin,
Mikaël Salson's avatar
Mikaël Salson committed
631 632
				&length, &score_D, segment_cost);
    
Mathieu Giraud's avatar
Mathieu Giraud committed
633
    best_D = tag_D;
Mikaël Salson's avatar
Mikaël Salson committed
634
    
Mathieu Giraud's avatar
Mathieu Giraud committed
635 636
    Dstart = l + begin;
    Dend = l + end;
Mikaël Salson's avatar
Mikaël Salson committed
637 638 639 640 641 642
	
    string seq = getSequence().sequence;
    
    if (length>0) dSegmented=true;
    
    //overlap VD
Mathieu Giraud's avatar
Mathieu Giraud committed
643
    if(Dstart-Vend <=0){
Mikaël Salson's avatar
Mikaël Salson committed
644
      int b_r, b_l;
Mathieu Giraud's avatar
Mathieu Giraud committed
645 646 647
      int overlap=Vend-Dstart+1;
      string seq_left = seq.substr(0, Vend+1);
      string seq_right = seq.substr(Dstart, Dend-Dstart+1);
Mikaël Salson's avatar
Mikaël Salson committed
648 649

      best_align(overlap, seq_left, seq_right, 
650
		 germline->rep_5.sequence(best_V), germline->rep_4.sequence(best_D), &b_r,&b_l, segment_cost);
Mikaël Salson's avatar
Mikaël Salson committed
651 652

      // Trim V
Mathieu Giraud's avatar
Mathieu Giraud committed
653
      Vend -= b_l;
Mikaël Salson's avatar
Mikaël Salson committed
654 655 656
      del_V += b_l;

      // Trim D
Mathieu Giraud's avatar
Mathieu Giraud committed
657
      Dstart += b_r;
Mikaël Salson's avatar
Mikaël Salson committed
658
    }
Mathieu Giraud's avatar
Mathieu Giraud committed
659
    seg_N1 = seq.substr(Vend+1, Dstart-Vend-1) ; // From Vend+1 to Dstart-1
Mikaël Salson's avatar
Mikaël Salson committed
660 661
    
    //overlap DJ
Mathieu Giraud's avatar
Mathieu Giraud committed
662
    if(Jstart-Dend <=0){
Mikaël Salson's avatar
Mikaël Salson committed
663
      int b_r, b_l;
Mathieu Giraud's avatar
Mathieu Giraud committed
664 665 666
      int overlap=Dend-Jstart+1;
      string seq_right = seq.substr(Dstart, Dend-Dstart+1);
      string seq_left = seq.substr(Jstart, seq.length()-Jstart);
Mikaël Salson's avatar
Mikaël Salson committed
667 668

      best_align(overlap, seq_left, seq_right, 
669
		 germline->rep_4.sequence(best_D), germline->rep_3.sequence(best_J), &b_r,&b_l, segment_cost);
Mikaël Salson's avatar
Mikaël Salson committed
670 671

      // Trim D
Mathieu Giraud's avatar
Mathieu Giraud committed
672
      Dend -= b_l;
Mikaël Salson's avatar
Mikaël Salson committed
673 674

      // Trim J
Mathieu Giraud's avatar
Mathieu Giraud committed
675
      Jstart += b_r;
Mikaël Salson's avatar
Mikaël Salson committed
676 677 678
      del_J += b_r;

    }
Mathieu Giraud's avatar
Mathieu Giraud committed
679
    seg_N2 = seq.substr(Dend+1, Jstart-Dend-1) ; // From Dend+1 to right-1
680
    code = germline->rep_5.label(best_V) +
Mikaël Salson's avatar
Mikaël Salson committed
681 682 683 684
    " "+ string_of_int(del_V) + 
    "/" + seg_N1 + 
    
    "/" + string_of_int(del_D_left) +
685
    " " + germline->rep_4.label(best_D) +
Mikaël Salson's avatar
Mikaël Salson committed
686 687 688 689
    " " + string_of_int(del_D_right) +
    
    "/" + seg_N2 +
    "/" + string_of_int(del_J) +
690
    " " + germline->rep_3.label(best_J); 
Mikaël Salson's avatar
Mikaël Salson committed
691

Mikaël Salson's avatar
Mikaël Salson committed
692
    stringstream code_s;
693
    code_s << germline->rep_5.label(best_V) 
Mikaël Salson's avatar
Mikaël Salson committed
694 695 696 697
    << " -" << string_of_int(del_V) << "/" 
    << seg_N1.size()
    
    << "/-" << string_of_int(del_D_left) 
698
    << " " << germline->rep_4.label(best_D) 
Mikaël Salson's avatar
Mikaël Salson committed
699 700 701 702
    << " -" << string_of_int(del_D_right) << "/"
    
    << seg_N2.size()
    << "/-" << string_of_int(del_J) 
703
    << " " << germline->rep_3.label(best_J);
Mikaël Salson's avatar
Mikaël Salson committed
704 705 706
    code_short=code_s.str();
    
    
707 708 709
    code_light = germline->rep_5.label(best_V) +
    "/ " + germline->rep_4.label(best_D) +
    "/ " + germline->rep_3.label(best_J); 
Mikaël Salson's avatar
Mikaël Salson committed
710 711 712 713
    
    finishSegmentationD();
  }
}
Mikaël Salson's avatar
Mikaël Salson committed
714

715
JsonList FineSegmenter::toJsonList(Germline *germline){
Mathieu Giraud's avatar
Mathieu Giraud committed
716
  JsonList result;
Mikaël Salson's avatar
Mikaël Salson committed
717
  
718
  result.add("status", because);
Mathieu Giraud's avatar
Mathieu Giraud committed
719 720 721 722 723 724 725
  result.add("sequence", revcomp(sequence, reversed) );
  if (isSegmented()) {
    result.add("name", code_short);
    result.add("Jstart", Jstart);
    result.add("Nlength", (del_V+del_J+seg_N.size()) );
    result.add("Vend", Vend);

726

Mathieu Giraud's avatar
Mathieu Giraud committed
727 728 729 730 731
    JsonArray jsonV;
    JsonArray jsonJ;

    // TODO: what is going on if some list is smaller than JSON_REMEMBER_BEST ?
    
732
    for (int i=0; i<JSON_REMEMBER_BEST; i++) jsonV.add( germline->rep_5.label(score_V[i].second) ) ;
Mathieu Giraud's avatar
Mathieu Giraud committed
733 734 735 736 737 738 739 740
    result.add("V", jsonV);
    
    
    if (score_D.size()>0){
      result.add("Dstart", Dstart);
      result.add("Dend", Dend);      
      JsonArray jsonD;

741
      for (int i=0; i<JSON_REMEMBER_BEST; i++) jsonD.add( germline->rep_4.label(score_D[i].second) ) ;
Mathieu Giraud's avatar
Mathieu Giraud committed
742
      result.add("D", jsonD);
Mikaël Salson's avatar
Mikaël Salson committed
743
    }
Mathieu Giraud's avatar
Mathieu Giraud committed
744
    
745
    for (int i=0; i<JSON_REMEMBER_BEST; i++) jsonJ.add( germline->rep_3.label(score_J[i].second) ) ;
Mathieu Giraud's avatar
Mathieu Giraud committed
746
    result.add("J", jsonJ);
Mikaël Salson's avatar
Mikaël Salson committed
747
  }
Mathieu Giraud's avatar
Mathieu Giraud committed
748
  return result;
Mikaël Salson's avatar
Mikaël Salson committed
749 750 751
}