Mise à jour terminée. Pour connaître les apports de la version 13.8.4 par rapport à notre ancienne version vous pouvez lire les "Release Notes" suivantes :
https://about.gitlab.com/releases/2021/02/11/security-release-gitlab-13-8-4-released/
https://about.gitlab.com/releases/2021/02/05/gitlab-13-8-3-released/

segment.h 5.51 KB
Newer Older
Mikaël Salson's avatar
Mikaël Salson committed
1 2 3 4 5 6 7 8
#ifndef SEGMENT_H
#define SEGMENT_H

#include <string>
#include <iostream>
#include "fasta.h"
#include "dynprog.h"
#include "tools.h"
9
#include "germline.h"
Mikaël Salson's avatar
Mikaël Salson committed
10 11
#include "kmerstore.h"
#include "kmeraffect.h"
Mathieu Giraud's avatar
Mathieu Giraud committed
12 13
#include "affectanalyser.h"
#include "json.h"
Mikaël Salson's avatar
Mikaël Salson committed
14 15

#define EXTEND_D_ZONE 5
Mikaël Salson's avatar
Mikaël Salson committed
16 17 18
#define RATIO_STRAND 5          /* The ratio between the affectations in one
                                   strand and the other, to safely attribute a
                                   segment to a given strand */
Mikaël Salson's avatar
Mikaël Salson committed
19

20
#define DETECT_THRESHOLD 5      /* If the number of both V and J affectations
21 22 23 24
                                   is above this threshold, then the sequence
                                   will be labeled as 'detected', and, if it
                                   not segmented, the remaining germlines will
                                   not be tested */
25

Mathieu Giraud's avatar
Mathieu Giraud committed
26 27
#define JSON_REMEMBER_BEST  4   /* The number of V/D/J predictions to keep  */

Mikaël Salson's avatar
Mikaël Salson committed
28 29 30 31
using namespace std;

enum SEGMENTED { DONT_KNOW, SEG_PLUS, SEG_MINUS, UNSEG_TOO_SHORT, UNSEG_STRAND_NOT_CONSISTENT, 
		 UNSEG_TOO_FEW_ZERO,  UNSEG_TOO_FEW_V, UNSEG_TOO_FEW_J, 
32
		 UNSEG_BAD_DELTA_MIN, UNSEG_BAD_DELTA_MAX, UNSEG_AMBIGUOUS,
Mikaël Salson's avatar
Mikaël Salson committed
33 34 35 36
		 TOTAL_SEG_AND_WINDOW, 
		 TOTAL_SEG_BUT_TOO_SHORT_FOR_THE_WINDOW,
		 STATS_SIZE } ;
const char* const segmented_mesg[] = { "?", "SEG_+", "SEG_-", "UNSEG too short", "UNSEG strand",  
37
				       "UNSEG too few (0)", "UNSEG too few V", "UNSEG too few J",
38
				       "UNSEG < delta_min", "UNSEG > delta_max", "UNSEG ambiguous",
Mikaël Salson's avatar
Mikaël Salson committed
39
                                       "= SEG, with window",
40
                                       "= SEG, no window",
Mikaël Salson's avatar
Mikaël Salson committed
41
                                      } ;
Mikaël Salson's avatar
Mikaël Salson committed
42 43 44 45 46

class Segmenter {
protected:
  string label;
  string sequence;
Mathieu Giraud's avatar
Mathieu Giraud committed
47 48
  int Vend, Jstart;
  int Dstart, Dend;
Marc Duez's avatar
Marc Duez committed
49
  int CDR3start, CDR3end;
Mikaël Salson's avatar
Mikaël Salson committed
50 51 52 53 54 55 56
  bool reversed, segmented, dSegmented;

  string removeChevauchement();
  bool finishSegmentation();
  bool finishSegmentationD();

 public:
57
  Germline *segmented_germline;
Mikaël Salson's avatar
Mikaël Salson committed
58
  string code;
Mikaël Salson's avatar
Mikaël Salson committed
59
  string code_short;
Mikaël Salson's avatar
Mikaël Salson committed
60
  string code_light;
61 62
  string info;        // .vdj.fa header, fixed fields
  string info_extra;  // .vdj.fa header, other information, at the end of the header
Mikaël Salson's avatar
Mikaël Salson committed
63 64
  int best_V, best_J ;
  int del_V, del_D_left, del_D_right, del_J ;
65
  string seg_V, seg_N, seg_J, system;
66

Mikaël Salson's avatar
Mikaël Salson committed
67 68 69 70
  int best_D;
  string seg_N1, seg_D, seg_N2;
  Cost segment_cost;

Mathieu Giraud's avatar
Mathieu Giraud committed
71
  virtual ~Segmenter();
Mikaël Salson's avatar
Mikaël Salson committed
72

Mathieu Giraud's avatar
Mathieu Giraud committed
73
  /* Queries */
Mikaël Salson's avatar
Mikaël Salson committed
74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136



  Sequence getSequence() const ;

  /**
   * @param l: length around the junction
   * @return the string centered on the junction (ie. at position
   *         (getLeft() + getRight())/2).
   *         The string has length l unless the original string 
   *         is not long enough.
   *         The junction is revcomp-ed if the original string comes from reverse
   *         strand.
   */
  string getJunction(int l) const;

  /**
   * @return the left position (on forward strand) of the segmentation.
   */
  int getLeft() const;
  
  /**
   * @return the right position (on forward strand) of the segmentation
   */
  int getRight() const;
  
  /**
   * @return the left position (on forward strand) of the D segmentation.
   */
  int getLeftD() const;
  
  /**
   * @return the right position (on forward strand) of the D segmentation
   */
  int getRightD() const;

  /**
   * @return true iff the string comes from reverse strand
   */
  bool isReverse() const;

  /**
   * @return true iff the sequence has been successfully segmented
   */
  bool isSegmented() const;
  
  /**
   * @return true if a D gene was found in the N region
   */
  bool isDSegmented() const;


  friend ostream &operator<<(ostream &out, const Segmenter &s);
};



ostream &operator<<(ostream &out, const Segmenter &s);



class KmerSegmenter : public Segmenter
{
Mathieu Giraud's avatar
Mathieu Giraud committed
137
 private:
138
  int detected;
Mathieu Giraud's avatar
Mathieu Giraud committed
139
  int because;                  
140
  KmerAffectAnalyser *kaa;
Mikaël Salson's avatar
Mikaël Salson committed
141 142 143 144
 protected:
  string affects;

 public:
145
  bool isDetected() const;
146
  int score;
147 148

  KmerSegmenter();
Mikaël Salson's avatar
Mikaël Salson committed
149 150 151
  /**
   * Build a segmenter based on KmerSegmentation
   * @param seq: An object read from a FASTA/FASTQ file
152
   * @param germline: the germline
Mikaël Salson's avatar
Mikaël Salson committed
153
   */
154
  KmerSegmenter(Sequence seq, Germline *germline);
Mathieu Giraud's avatar
Mathieu Giraud committed
155

156 157
  KmerSegmenter(const KmerSegmenter &seg);

Mathieu Giraud's avatar
Mathieu Giraud committed
158 159 160 161 162
  ~KmerSegmenter();

  /**
   * @return the KmerAffectAnalyser of the current sequence.
   */
163
  KmerAffectAnalyser *getKmerAffectAnalyser() const;
Mathieu Giraud's avatar
Mathieu Giraud committed
164 165 166 167 168 169 170 171 172 173

  /**
   * @return the status of the segmentation. Tells if the Sequence has been segmented
   *         of if it has not, what the reason is.
   * @assert getSegmentationStatus() == SEG_PLUS || getSegmentationStatus() == SEG_MINUS
   *         <==> isSegmented()
   */
  int getSegmentationStatus() const;

 private:
174
  void computeSegmentation(int strand, KmerAffect left, KmerAffect right);
Mikaël Salson's avatar
Mikaël Salson committed
175 176
};

177 178 179 180 181 182 183 184

class KmerMultiSegmenter
{
 public:
  /**
   * @param seq: An object read from a FASTA/FASTQ file
   * @param multigermline: the multigermline
   */
185
  KmerMultiSegmenter(Sequence seq, MultiGermline *multigermline, ostream *out_unsegmented);
186 187
  ~KmerMultiSegmenter();

188
  KmerSegmenter *the_kseg;
189 190 191
};


Mikaël Salson's avatar
Mikaël Salson committed
192 193 194
class FineSegmenter : public Segmenter
{
 public:
195
   int because;
Mikaël Salson's avatar
Mikaël Salson committed
196 197 198 199
   vector<pair<int, int> > score_V;
   vector<pair<int, int> > score_D;
   vector<pair<int, int> > score_J;
   
Mikaël Salson's avatar
Mikaël Salson committed
200 201 202
   /**
   * Build a fineSegmenter based on KmerSegmentation
   * @param seq: An object read from a FASTA/FASTQ file
203
   * @param germline: germline used
Mikaël Salson's avatar
Mikaël Salson committed
204
   */
205
  FineSegmenter(Sequence seq, Germline *germline, Cost segment_cost);
Mikaël Salson's avatar
Mikaël Salson committed
206 207 208
  
  /**
  * extend segmentation from VJ to VDJ
209
  * @param germline: germline used
Mikaël Salson's avatar
Mikaël Salson committed
210
  */
211
  void FineSegmentD(Germline *germline);
Marc Duez's avatar
Marc Duez committed
212
  void findCDR3();
Mathieu Giraud's avatar
Mathieu Giraud committed
213

214
  JsonList toJsonList(Germline *germline);
Mikaël Salson's avatar
Mikaël Salson committed
215
  
Mikaël Salson's avatar
Mikaël Salson committed
216 217 218 219 220
};



#endif