MAJ terminée. Nous sommes passés en version 14.6.2 . Pour consulter les "releases notes" associées c'est ici :

https://about.gitlab.com/releases/2022/01/11/security-release-gitlab-14-6-2-released/
https://about.gitlab.com/releases/2022/01/04/gitlab-14-6-1-released/

segment.cpp 19.3 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
178
179
  // Iterate over the germlines
  for (list<Germline*>::const_iterator it = multigermline->germlines.begin(); it != multigermline->germlines.end(); ++it)
    {
      Germline *germline = *it ;

180
  int s = (size_t)germline->index->getS() ;
Mikaël Salson's avatar
Mikaël Salson committed
181
  int length = sequence.length() ;
Mikaël Salson's avatar
Mikaël Salson committed
182

183
  if (length < s) 
Mikaël Salson's avatar
Mikaël Salson committed
184
    {
Mathieu Giraud's avatar
Mathieu Giraud committed
185
186
      because = UNSEG_TOO_SHORT;
      kaa = NULL;
187
      continue ;
Mikaël Salson's avatar
Mikaël Salson committed
188
189
    }
 
190
  kaa = new KmerAffectAnalyser(*(germline->index), sequence);
Mikaël Salson's avatar
Mikaël Salson committed
191
192
  
  // Check strand consistency among the affectations.
Mikaël Salson's avatar
Mikaël Salson committed
193
194
195
196
197
198
199
200
201
  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
202
203
204
    }
  }

Mikaël Salson's avatar
Mikaël Salson committed
205
206
207
208
209
210
211
212
213
214
215
216
217
  // 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;
  }

218
  computeSegmentation(strand, germline);
Mathieu Giraud's avatar
Mathieu Giraud committed
219
220
221
222

  if (segmented)
    {
      // Yes, it is segmented
223
      segmented_germline = germline;
224
      germline->stats.insert(length);
Mathieu Giraud's avatar
Mathieu Giraud committed
225
226
227
228
229

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

      info = string_of_int(Vend + FIRST_POS) + " " + string_of_int(Jstart + FIRST_POS)  ;
230
231
      // 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
232
      finishSegmentation();
233
      system = germline->code;
234
      return ;
Mathieu Giraud's avatar
Mathieu Giraud committed
235
    } 
236
237
238
239
240

  // If a read is AMBIGUOUS, do not test other germlines
  if (because == UNSEG_AMBIGUOUS)
    return ;

241
  } // end for (Germlines)
Mathieu Giraud's avatar
Mathieu Giraud committed
242
}
Mikaël Salson's avatar
Mikaël Salson committed
243

Mathieu Giraud's avatar
Mathieu Giraud committed
244
245
246
247
248
KmerSegmenter::~KmerSegmenter() {
  if (kaa)
    delete kaa;
}

249
void KmerSegmenter::computeSegmentation(int strand, Germline* germline) {
250
251
252
  // 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
253
  segmented = true ;
Mathieu Giraud's avatar
Mathieu Giraud committed
254
  because = 0 ; // Cause of unsegmentation
Mikaël Salson's avatar
Mikaël Salson committed
255
256
257
258

  // Zero information
  if (strand == 0)
    {
Mikaël Salson's avatar
Mikaël Salson committed
259
      because = UNSEG_TOO_FEW_ZERO ;
Mathieu Giraud's avatar
Mathieu Giraud committed
260
261
    } 
  else if (strand == 2) // Ambiguous
Mikaël Salson's avatar
Mikaël Salson committed
262
    {
Mikaël Salson's avatar
Mikaël Salson committed
263
      because = UNSEG_STRAND_NOT_CONSISTENT ;
Mathieu Giraud's avatar
Mathieu Giraud committed
264
    } 
265
  else
Mikaël Salson's avatar
Mikaël Salson committed
266
    {
267
268
      affect_infos max;
      if (strand == 1)
269
270
        max = kaa->getMaximum(KmerAffect(germline->affect_5, 1), 
			      KmerAffect(germline->affect_3, 1));
271
      else
272
273
        max = kaa->getMaximum(KmerAffect(germline->affect_3, -1), 
			      KmerAffect(germline->affect_5, -1));
274
275

      if (! max.max_found) {
276
277
        if ((strand == 1 && max.nb_before_left == 0)
            || (strand == -1 && max.nb_after_right == 0)) 
278
          because = UNSEG_TOO_FEW_V ;
279
280
        else if ((strand == 1 && max.nb_after_right == 0)
                 || (strand == -1 && max.nb_before_left == 0))
Mikaël Salson's avatar
Mikaël Salson committed
281
	{
Mikaël Salson's avatar
Mikaël Salson committed
282
	  because = UNSEG_TOO_FEW_J ;
283
	} else 
284
          because = UNSEG_AMBIGUOUS; 
285
286
287
288
289
290
291

        // The sequence is not segmented.
        // We labeled it AMBIGUOUS if there were both enough affect_5 and enough affect_3
        if ((max.nb_before_left + max.nb_after_left >= AMBIGUOUS_THRESHOLD)
            && (max.nb_before_right + max.nb_after_right >= AMBIGUOUS_THRESHOLD))
          because = UNSEG_AMBIGUOUS; 

292
293
294
295
296
297
298
299
300
      } 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
301
302
    } 
  
Mathieu Giraud's avatar
Mathieu Giraud committed
303
  if (! because)
Mikaël Salson's avatar
Mikaël Salson committed
304
    {
Mathieu Giraud's avatar
Mathieu Giraud committed
305
      // Now we check the delta between Vend and right
Mikaël Salson's avatar
Mikaël Salson committed
306
   
307
      if (Jstart - Vend < germline->delta_min)
Mikaël Salson's avatar
Mikaël Salson committed
308
309
310
	{
	  because = UNSEG_BAD_DELTA_MIN ;
	}
Mikaël Salson's avatar
Mikaël Salson committed
311

312
      if (Jstart - Vend > germline->delta_max)
Mikaël Salson's avatar
Mikaël Salson committed
313
314
315
	{
	  because = UNSEG_BAD_DELTA_MAX ;
	}
Mathieu Giraud's avatar
Mathieu Giraud committed
316
317
318
319
    } 
  if (because)
    segmented = false;
}
Mikaël Salson's avatar
Mikaël Salson committed
320

321
KmerAffectAnalyser *KmerSegmenter::getKmerAffectAnalyser() const {
Mathieu Giraud's avatar
Mathieu Giraud committed
322
323
  return kaa;
}
Mikaël Salson's avatar
Mikaël Salson committed
324

Mathieu Giraud's avatar
Mathieu Giraud committed
325
326
int KmerSegmenter::getSegmentationStatus() const {
  return because;
Mikaël Salson's avatar
Mikaël Salson committed
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
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
}

// 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
384
385
386
387
388
bool comp_pair (pair<int,int> i,pair<int,int> j)
{
  return ( i.first > j.first);
}

Mathieu Giraud's avatar
Mathieu Giraud committed
389
int align_against_collection(string &read, Fasta &rep, bool reverse_both, bool local, int *tag, 
Mikaël Salson's avatar
Mikaël Salson committed
390
			     int *del, int *del2, int *begin, int *length, vector<pair<int, int> > *score
Mikaël Salson's avatar
Mikaël Salson committed
391
392
393
394
395
396
397
398
399
400
			    , 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
401
  vector<pair<int, int> > score_r;
Mikaël Salson's avatar
Mikaël Salson committed
402
403
404
405
406
407
408
409
410
411
412

  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
413
      
Mikaël Salson's avatar
Mikaël Salson committed
414
415
416
417
418
419
420
421
422
423
424
425
426
427
      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
428
429
	
	score_r.push_back(make_pair(score, r));
Mathieu Giraud's avatar
Mathieu Giraud committed
430
431
432
433
434
435

	// #define DEBUG_SEGMENT      

#ifdef DEBUG_SEGMENT	
	cout << rep.label(r) << " " << score << " " << dp.best_i << endl ;
#endif
Mikaël Salson's avatar
Mikaël Salson committed
436
437

    }
Mikaël Salson's avatar
Mikaël Salson committed
438
    sort(score_r.begin(),score_r.end(),comp_pair);
Mikaël Salson's avatar
Mikaël Salson committed
439
440
441
442

  *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
443
  *tag = best_r ; 
Mikaël Salson's avatar
Mikaël Salson committed
444
445
  
  *length -= *del ;
Mikaël Salson's avatar
Mikaël Salson committed
446
447
  
  *score=score_r;
Mathieu Giraud's avatar
Mathieu Giraud committed
448
449
450
451
452
453

#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
454
455
456
457
458
459
460
461
462
  
  return best_best_i ;
}

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

463
FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c)
Mikaël Salson's avatar
Mikaël Salson committed
464
465
{

466
  info_extra = "" ;
Mikaël Salson's avatar
Mikaël Salson committed
467
468
  label = seq.label ;
  sequence = seq.sequence ;
Mathieu Giraud's avatar
Mathieu Giraud committed
469
  Dend=0;
Mikaël Salson's avatar
Mikaël Salson committed
470
471
472
473
474
475
476
  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
477
  int tag_plus_V, tag_plus_J;
Mikaël Salson's avatar
Mikaël Salson committed
478
479
480
481
  int plus_length = 0 ;
  int del_plus_V, del_plus_J ;
  int del2=0;
  int beg=0;
Mikaël Salson's avatar
Mikaël Salson committed
482
483
484
485
  
  vector<pair<int, int> > score_plus_V;
  vector<pair<int, int> > score_plus_J;
  
486
  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
487
488
					   &plus_length, &score_plus_V
					   , segment_cost);
489
  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
490
491
					    &plus_length, &score_plus_J
					    , segment_cost);
Mikaël Salson's avatar
Mikaël Salson committed
492
493
  plus_length += plus_right - plus_left ;

Mikaël Salson's avatar
Mikaël Salson committed
494
495
  plus_score=score_plus_V[0].first + score_plus_J[0].first ;
  
Mikaël Salson's avatar
Mikaël Salson committed
496
497
498
  // Strand -
  string rc = revcomp(sequence) ;
  int minus_score = 0 ;
Mathieu Giraud's avatar
Mathieu Giraud committed
499
  int tag_minus_V, tag_minus_J;
Mikaël Salson's avatar
Mikaël Salson committed
500
501
  int minus_length = 0 ;
  int del_minus_V, del_minus_J ;
Mikaël Salson's avatar
Mikaël Salson committed
502
503
504
505
  
  vector<pair<int, int> > score_minus_V;
  vector<pair<int, int> > score_minus_J;
  
506
  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
507
508
					    &minus_length, &score_minus_V
					    ,  segment_cost);
509
  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
510
511
					     &minus_length, &score_minus_J
					     , segment_cost);
Mikaël Salson's avatar
Mikaël Salson committed
512
513
  minus_length += minus_right - minus_left ;

Mikaël Salson's avatar
Mikaël Salson committed
514
515
  minus_score=score_minus_V[0].first + score_minus_J[0].first ;
  
Mikaël Salson's avatar
Mikaël Salson committed
516
517
518
519
  reversed = (minus_score > plus_score) ;

  if (!reversed)
    {
Mathieu Giraud's avatar
Mathieu Giraud committed
520
521
522
523
      Vend = plus_left ;
      Jstart = plus_right ;
      best_V = tag_plus_V ;
      best_J = tag_plus_J ;
Mikaël Salson's avatar
Mikaël Salson committed
524
525
      del_V = del_plus_V ;
      del_J = del_plus_J ;
Mikaël Salson's avatar
Mikaël Salson committed
526
527
      score_V=score_plus_V;
      score_J=score_plus_J;
Mikaël Salson's avatar
Mikaël Salson committed
528
529
530
    }
  else
    {
Mathieu Giraud's avatar
Mathieu Giraud committed
531
532
533
534
      Vend = minus_left ;
      Jstart = minus_right ;
      best_V = tag_minus_V ;
      best_J = tag_minus_J ;
Mikaël Salson's avatar
Mikaël Salson committed
535
536
      del_V = del_minus_V ;
      del_J = del_minus_J ;
Mikaël Salson's avatar
Mikaël Salson committed
537
538
      score_V=score_minus_V;
      score_J=score_minus_J;
Mikaël Salson's avatar
Mikaël Salson committed
539
540
    }

Mathieu Giraud's avatar
Mathieu Giraud committed
541
  segmented = (Vend != (int) string::npos) && (Jstart != (int) string::npos) && 
542
    (Jstart - Vend >= germline->delta_min) && (Jstart - Vend <= germline->delta_max);
Mikaël Salson's avatar
Mikaël Salson committed
543
544
545
546
547
    
  dSegmented=false;

  if (!segmented)
    {
548
      because = DONT_KNOW;
Mathieu Giraud's avatar
Mathieu Giraud committed
549
      info = " @" + string_of_int (Vend + FIRST_POS) + "  @" + string_of_int(Jstart + FIRST_POS) ;
550
      
551
      if (Jstart - Vend < germline->delta_min)
552
553
554
555
        {
          because = UNSEG_BAD_DELTA_MIN  ;
        }

556
      if (Jstart - Vend > germline->delta_max)
557
558
559
560
561
562
563
564
565
566
567
568
569
570
        {
          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
571
572
573
      return ;
    }
    
574
575
    because = reversed ? SEG_MINUS : SEG_PLUS ;
    
Mikaël Salson's avatar
Mikaël Salson committed
576
    //overlap VJ
Mathieu Giraud's avatar
Mathieu Giraud committed
577
    if(Jstart-Vend <=0){
Mikaël Salson's avatar
Mikaël Salson committed
578
      int b_r, b_l;
Mathieu Giraud's avatar
Mathieu Giraud committed
579
      int overlap=Vend-Jstart+1;
Mikaël Salson's avatar
Mikaël Salson committed
580
      
Mathieu Giraud's avatar
Mathieu Giraud committed
581
582
      string seq_left = sequence.substr(0, Vend+1);
      string seq_right = sequence.substr(Jstart);
Mikaël Salson's avatar
Mikaël Salson committed
583
584

      best_align(overlap, seq_left, seq_right, 
585
		 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
586
      // Trim V
Mathieu Giraud's avatar
Mathieu Giraud committed
587
      Vend -= b_l;
Mikaël Salson's avatar
Mikaël Salson committed
588
589
590
      del_V += b_l;

      // Trim J
Mathieu Giraud's avatar
Mathieu Giraud committed
591
      Jstart += b_r;
Mikaël Salson's avatar
Mikaël Salson committed
592
      del_J += b_r;
593
      if (Jstart>=(int) sequence.length())
Mathieu Giraud's avatar
Mathieu Giraud committed
594
	  Jstart=sequence.length()-1;
Mikaël Salson's avatar
Mikaël Salson committed
595
596
597
    }

    // string chevauchement = removeChevauchement();
Mikaël Salson's avatar
Mikaël Salson committed
598
599

    /// used only below, then recomputed in finishSegmentation() ;
Mathieu Giraud's avatar
Mathieu Giraud committed
600
    seg_N = revcomp(sequence, reversed).substr(Vend+1, Jstart-Vend-1); 
Mikaël Salson's avatar
Mikaël Salson committed
601

602
  code = germline->rep_5.label(best_V) +
Mikaël Salson's avatar
Mikaël Salson committed
603
604
605
606
    " "+ string_of_int(del_V) + 
    "/" + seg_N + 
    // chevauchement +
    "/" + string_of_int(del_J) +
607
    " " + germline->rep_3.label(best_J); 
Mikaël Salson's avatar
Mikaël Salson committed
608

Mikaël Salson's avatar
Mikaël Salson committed
609
    stringstream code_s;
610
   code_s<< germline->rep_5.label(best_V) <<
Mikaël Salson's avatar
Mikaël Salson committed
611
612
613
614
    " -" << string_of_int(del_V) << "/" 
    << seg_N.size()
    // chevauchement +
    << "/-" << string_of_int(del_J)
615
    <<" " << germline->rep_3.label(best_J);
Mikaël Salson's avatar
Mikaël Salson committed
616
617
    code_short=code_s.str();
    
618
619
  code_light = germline->rep_5.label(best_V) +
    "/ " + germline->rep_3.label(best_J); 
Mikaël Salson's avatar
Mikaël Salson committed
620
621

 
Mathieu Giraud's avatar
Mathieu Giraud committed
622
  info = string_of_int(Vend + FIRST_POS) + " " + string_of_int(Jstart + FIRST_POS) ;
Mikaël Salson's avatar
Mikaël Salson committed
623
624
625
626
627

  finishSegmentation();
}


628
void FineSegmenter::FineSegmentD(Germline *germline){
Mikaël Salson's avatar
Mikaël Salson committed
629
630
631
632
  
  if (segmented){
    
    int end = (int) string::npos ;
Mathieu Giraud's avatar
Mathieu Giraud committed
633
    int tag_D;
Mikaël Salson's avatar
Mikaël Salson committed
634
635
636
637
    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
638
    int l = Vend - EXTEND_D_ZONE;
Mikaël Salson's avatar
Mikaël Salson committed
639
640
641
    if (l<0) 
      l=0 ;

Mathieu Giraud's avatar
Mathieu Giraud committed
642
    int r = Jstart + EXTEND_D_ZONE;
Mikaël Salson's avatar
Mikaël Salson committed
643
644
645
646
647
648
649

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

    // Align
650
    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
651
652
				&length, &score_D, segment_cost);
    
Mathieu Giraud's avatar
Mathieu Giraud committed
653
    best_D = tag_D;
Mikaël Salson's avatar
Mikaël Salson committed
654
    
Mathieu Giraud's avatar
Mathieu Giraud committed
655
656
    Dstart = l + begin;
    Dend = l + end;
Mikaël Salson's avatar
Mikaël Salson committed
657
658
659
660
661
662
	
    string seq = getSequence().sequence;
    
    if (length>0) dSegmented=true;
    
    //overlap VD
Mathieu Giraud's avatar
Mathieu Giraud committed
663
    if(Dstart-Vend <=0){
Mikaël Salson's avatar
Mikaël Salson committed
664
      int b_r, b_l;
Mathieu Giraud's avatar
Mathieu Giraud committed
665
666
667
      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
668
669

      best_align(overlap, seq_left, seq_right, 
670
		 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
671
672

      // Trim V
Mathieu Giraud's avatar
Mathieu Giraud committed
673
      Vend -= b_l;
Mikaël Salson's avatar
Mikaël Salson committed
674
675
676
      del_V += b_l;

      // Trim D
Mathieu Giraud's avatar
Mathieu Giraud committed
677
      Dstart += b_r;
Mikaël Salson's avatar
Mikaël Salson committed
678
    }
Mathieu Giraud's avatar
Mathieu Giraud committed
679
    seg_N1 = seq.substr(Vend+1, Dstart-Vend-1) ; // From Vend+1 to Dstart-1
Mikaël Salson's avatar
Mikaël Salson committed
680
681
    
    //overlap DJ
Mathieu Giraud's avatar
Mathieu Giraud committed
682
    if(Jstart-Dend <=0){
Mikaël Salson's avatar
Mikaël Salson committed
683
      int b_r, b_l;
Mathieu Giraud's avatar
Mathieu Giraud committed
684
685
686
      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
687
688

      best_align(overlap, seq_left, seq_right, 
689
		 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
690
691

      // Trim D
Mathieu Giraud's avatar
Mathieu Giraud committed
692
      Dend -= b_l;
Mikaël Salson's avatar
Mikaël Salson committed
693
694

      // Trim J
Mathieu Giraud's avatar
Mathieu Giraud committed
695
      Jstart += b_r;
Mikaël Salson's avatar
Mikaël Salson committed
696
697
698
      del_J += b_r;

    }
Mathieu Giraud's avatar
Mathieu Giraud committed
699
    seg_N2 = seq.substr(Dend+1, Jstart-Dend-1) ; // From Dend+1 to right-1
700
    code = germline->rep_5.label(best_V) +
Mikaël Salson's avatar
Mikaël Salson committed
701
702
703
704
    " "+ string_of_int(del_V) + 
    "/" + seg_N1 + 
    
    "/" + string_of_int(del_D_left) +
705
    " " + germline->rep_4.label(best_D) +
Mikaël Salson's avatar
Mikaël Salson committed
706
707
708
709
    " " + string_of_int(del_D_right) +
    
    "/" + seg_N2 +
    "/" + string_of_int(del_J) +
710
    " " + germline->rep_3.label(best_J); 
Mikaël Salson's avatar
Mikaël Salson committed
711

Mikaël Salson's avatar
Mikaël Salson committed
712
    stringstream code_s;
713
    code_s << germline->rep_5.label(best_V) 
Mikaël Salson's avatar
Mikaël Salson committed
714
715
716
717
    << " -" << string_of_int(del_V) << "/" 
    << seg_N1.size()
    
    << "/-" << string_of_int(del_D_left) 
718
    << " " << germline->rep_4.label(best_D) 
Mikaël Salson's avatar
Mikaël Salson committed
719
720
721
722
    << " -" << string_of_int(del_D_right) << "/"
    
    << seg_N2.size()
    << "/-" << string_of_int(del_J) 
723
    << " " << germline->rep_3.label(best_J);
Mikaël Salson's avatar
Mikaël Salson committed
724
725
726
    code_short=code_s.str();
    
    
727
728
729
    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
730
731
732
733
    
    finishSegmentationD();
  }
}
Mikaël Salson's avatar
Mikaël Salson committed
734

735
JsonList FineSegmenter::toJsonList(Germline *germline){
Mathieu Giraud's avatar
Mathieu Giraud committed
736
  JsonList result;
Mikaël Salson's avatar
Mikaël Salson committed
737
  
Mathieu Giraud's avatar
Mathieu Giraud committed
738
739
740
741
  result.add("sequence", revcomp(sequence, reversed) );
  if (isSegmented()) {
    result.add("name", code_short);
    
742
    JsonList seg;
Marc Duez's avatar
Marc Duez committed
743
    seg.add("5", germline->rep_5.label(best_V));
744
745
    seg.add("5start", 0);
    seg.add("5end", Vend);
Mathieu Giraud's avatar
Mathieu Giraud committed
746
747
    
    if (score_D.size()>0){
Marc Duez's avatar
Marc Duez committed
748
      seg.add("4", germline->rep_4.label(best_D));
Marc Duez's avatar
Marc Duez committed
749
750
      seg.add("4start", Dstart);
      seg.add("4end", Dend);      
Mikaël Salson's avatar
Mikaël Salson committed
751
    }
Mathieu Giraud's avatar
Mathieu Giraud committed
752
    
Marc Duez's avatar
Marc Duez committed
753
    seg.add("3", germline->rep_3.label(best_J));
754
755
756
    seg.add("3start", Jstart);
    
    result.add("seg", seg);
Mikaël Salson's avatar
Mikaël Salson committed
757
  }
Mathieu Giraud's avatar
Mathieu Giraud committed
758
  return result;
Mikaël Salson's avatar
Mikaël Salson committed
759
760
761
}