kmerstore.h 15.2 KB
Newer Older
Mikaël Salson's avatar
Mikaël Salson committed
1 2 3 4 5 6 7 8
#ifndef KMERSTORE_H
#define KMERSTORE_H

#include <map>
#include <string>
#include <list>
#include <stdexcept>
#include <stdint.h>
9
#include <math.h>
Mikaël Salson's avatar
Mikaël Salson committed
10 11 12 13 14 15 16 17 18 19
#include "fasta.h"
#include "tools.h"

using namespace std;

class Kmer {
public:
  unsigned int count;

  Kmer();
20 21 22 23

  /**
   * This constructor is used via a IKmerStore<Kmer> index (hence the argument list)       
   */
24
  Kmer(const string &label, int strand=1);
25

Mikaël Salson's avatar
Mikaël Salson committed
26
  Kmer &operator+=(const Kmer &);
27 28 29 30 31

  /**
   * When indexing revcomp, should the value be the same or not?
   * In other words, does the information stored by the class is strand-dependent?
   */
Mikaël Salson's avatar
Mikaël Salson committed
32
  static bool hasRevcompSymetry();
33 34 35 36 37

  /**
   * @return true if the element is the same as when initialised with default constructor.
   */
  bool isNull();
Mikaël Salson's avatar
Mikaël Salson committed
38 39 40 41 42 43 44 45 46 47 48 49 50
} ;
ostream &operator<<(ostream &os, const Kmer &kmer);


/* K-mer indexing */

template <class T> class IKmerStore
{
protected:
  bool revcomp_indexed;
  int k; // weight of the seed
  int s; // span of the seed (s >= k)
  string seed ;
51
  size_t nb_kmers_inserted;
52
  size_t max_size_indexing;
Mikaël Salson's avatar
Mikaël Salson committed
53 54 55 56 57

public:

  virtual ~IKmerStore();

58 59
  static int last_id;
  int id; // id of this index
60
  int refs; // number of germlines using this index
61

62
  list< pair <T, Fasta> > labels;
63

64 65
  IKmerStore();

Mikaël Salson's avatar
Mikaël Salson committed
66 67 68
  /**
   * @param input: A single FASTA file
   * @param label: label that must be associated to the given files
69
   * @param seed: the seed to use for indexing. By default it will be the seed of the index
70
   * @post All the sequences in the FASTA files have been indexed, and the label is stored in the list of labels
Mikaël Salson's avatar
Mikaël Salson committed
71
   */
72
  void insert(Fasta& input, const string& label="", int keep_only = 0, string seed = "");
Mikaël Salson's avatar
Mikaël Salson committed
73 74 75 76

  /**
   * @param input: A list of FASTA files
   * @param label: label that must be associated to the given files
77
   * @param seed: the seed to use for indexing. By default it will be the seed of the index
78
   * @post All the sequences in the FASTA files have been indexed, and the label is stored in the list of labels
Mikaël Salson's avatar
Mikaël Salson committed
79
   */
80
  void insert(list<Fasta>& input, const string& label="", int keep_only = 0, string seed = "");
Mikaël Salson's avatar
Mikaël Salson committed
81 82 83 84
  
  /**
   * @param input: A sequence to be cut in k-mers
   * @param label: label that must be associated to the given files
85 86 87 88
   * @param keep_only: if > 0 will keep at most the last keep_only nucleotides
   *                   of the sequence. if < 0 will keep at most the first
   *                   keep_only nucleotides of the sequence. if == 0,
   *                   will keep all the sequence.
89
   * @param seed: the seed to use for indexing. By default it will be the seed of the index
Mikaël Salson's avatar
Mikaël Salson committed
90 91
   * @post All the k-mers in the sequence have been indexed.
   */
92 93 94 95 96 97 98 99 100 101 102
  virtual void insert(const seqtype &sequence,
                      const string &label,
                      bool ignore_extended_nucleotides=true, int keep_only = 0,
                      string seed="");

  /**
   * Perform extra steps to finish the building of the index. After using
   * that function, we are not supposed to insert any other sequence.
   * No query function should be called before calling that function.
   */
  void finish_building();
Mikaël Salson's avatar
Mikaël Salson committed
103 104 105 106 107

  /**
   * @param word: a k-mer
   * @return the value for the kmer as stored in the structure (don't do revcomp)
   */ 
108
  virtual T& get(seqtype &word) = 0;
Mikaël Salson's avatar
Mikaël Salson committed
109

110 111 112
  /**
   * @return the percentage of kmers that are set in the index
   */
113
  float getIndexLoad(T kmer) const;
114 115
  float getIndexLoad() const;

116 117 118 119 120 121
  /**
   * @return the given integer (size of a read),
   *         but limit this size to max_size_indexing if it was defined
   */
  int atMostMaxSizeIndexing(int n) const;

122 123 124
  /**
   * @return probability that the number of kmers is 'at_least' or more in a sequence of length 'length'
   */
125
  double getProbabilityAtLeastOrAbove(T kmer, int at_least, int length) const;
126

Mikaël Salson's avatar
Mikaël Salson committed
127 128 129 130 131 132 133 134 135 136
  /**
   * @return the value of k
   */
  int getK() const;

  /**
   * @return the value of s
   */
  int getS() const;

137 138 139 140 141
  /**
   * @return the seed used
   */
  string getSeed() const;

142 143 144 145
  /**
   * @param kmer: a kmer
   * @return one label associated with the kmer
   */
146
  Fasta getLabel(T kmer) const;
147

Mikaël Salson's avatar
Mikaël Salson committed
148 149 150 151
  /**
   * @param seq: a sequence
   * @param no_revcomp: force not to revcomp the sequence, even if
   *                    the index was built with revcomp.
152 153
   * @return a vector of length seq.length() - smallestAnalysableLength() + 1
   * containing for each position the corresponding value in the index.
Mikaël Salson's avatar
Mikaël Salson committed
154
   */
155
  virtual vector<T> getResults(const seqtype &seq, bool no_revcomp=false, string seed="") = 0;
Mikaël Salson's avatar
Mikaël Salson committed
156

157 158 159 160 161 162 163
  /**
   * @return the smallest analysable sequence length by the index. For an
   * index just storing k-mers it will obviously be getK(). But for more
   * sophisticated data structures it could be 1 for instance.
   */
  size_t smallestAnalysableLength() const;

Mikaël Salson's avatar
Mikaël Salson committed
164 165 166 167 168 169 170 171 172 173 174
  /**
   * @return true iff the revcomp is indexed
   */
  bool isRevcomp() const;

  /**
   * @param string: a k-mer
   * @return the value in the index associated to the given k-mer.
   *         isRevcomp() ==> the revcomp of the k-mer may be considered
   * @pre word.length() == this->k
   */
175
  virtual T& operator[](seqtype& word) = 0;
Mikaël Salson's avatar
Mikaël Salson committed
176 177
};

178 179 180 181 182
template<class T>
IKmerStore<T>::IKmerStore() {
  id = ++last_id;
}

183
template<class T> int IKmerStore<T>::last_id = 0;
Mikaël Salson's avatar
Mikaël Salson committed
184 185 186 187 188

template <class T> 
class MapKmerStore : public IKmerStore<T>
{
public:	
189
  map<seqtype, T> store;
Mikaël Salson's avatar
Mikaël Salson committed
190 191 192 193 194 195 196

  /**
   * @param bool: if true, will also index revcomp
   * @param seed: the seed
   */
  MapKmerStore(string seed, bool=false);
  MapKmerStore(int k, bool=false);
197

198
  vector<T> getResults(const seqtype &seq, bool no_revcomp=false, string seed="");
199 200
  T& get(seqtype &word);
  T& operator[](seqtype & word);
201 202 203

 private:
  void init();
Mikaël Salson's avatar
Mikaël Salson committed
204 205 206 207 208 209 210
};

template <class T> 
class ArrayKmerStore : public IKmerStore<T>
{
  T* store;
	
211
  int index(const seqtype& word) const;
212 213 214 215 216 217 218 219

  /**
   * Allocates memory for store
   * @throws bad_alloc: when there is not enough memory or when the
   *                    the total number of kmers cannot be stored in an 
   *                    unsigned int
   */
  void init();
Mikaël Salson's avatar
Mikaël Salson committed
220 221 222 223 224 225 226 227
public:
  /**
   * @param bool: if true, will also index revcomp
   * @param seed: the seed
   */
  ArrayKmerStore(string seed, bool=false);
  ArrayKmerStore(int k, bool=false);
  ~ArrayKmerStore();
228

229
  vector<T> getResults(const seqtype &seq, bool no_revcomp=false, const string seed="");
230 231
  T& get(seqtype &word);
  T& operator[](seqtype & word);
232
  T& operator[](int word);
Mikaël Salson's avatar
Mikaël Salson committed
233 234 235 236 237 238 239 240 241 242
};


// IKmerStore

template<class T>
IKmerStore<T>::~IKmerStore(){}

template<class T> 
void IKmerStore<T>::insert(list<Fasta>& input,
243
                           const string &label,
244 245
                           int keep_only,
                           string seed){
Mikaël Salson's avatar
Mikaël Salson committed
246
  for(list<Fasta>::iterator it = input.begin() ; it != input.end() ; it++){
247
    insert(*it, label, keep_only, seed);
Mikaël Salson's avatar
Mikaël Salson committed
248 249 250 251 252
  }
}

template<class T> 
void IKmerStore<T>::insert(Fasta& input,
253
                           const string &label,
254 255
                           int keep_only,
                           string seed){
Mikaël Salson's avatar
Mikaël Salson committed
256
  for (int r = 0; r < input.size(); r++) {
257
    insert(input.sequence(r), label, true, keep_only, seed);
Mikaël Salson's avatar
Mikaël Salson committed
258
  }
259

260
  labels.push_back(make_pair(T(label, 1), input)) ;
261 262

  if (revcomp_indexed  && ! T::hasRevcompSymetry()) {
263
    labels.push_back(make_pair(T(label, -1), input)) ;
264
  }
Mikaël Salson's avatar
Mikaël Salson committed
265 266 267
}

template<class T> 
268
void IKmerStore<T>::insert(const seqtype &sequence,
269
                           const string &label,
270
                           bool ignore_extended_nucleotides,
271 272
                           int keep_only,
                           string seed){
273 274 275 276 277 278 279
  size_t start_indexing = 0;
  size_t end_indexing = sequence.length();
  if (keep_only > 0 && sequence.length() > (size_t)keep_only) {
    start_indexing = sequence.length() - keep_only;
  } else if (keep_only < 0 && sequence.length() > (size_t) -keep_only) {
    end_indexing = -keep_only;
  }
280

281 282 283 284
  if (seed.empty())
    seed = this->seed;

  size_t seed_span = seed.length();
285 286 287 288 289
  size_t size_indexing = end_indexing - start_indexing;
  if (size_indexing > max_size_indexing) {
    max_size_indexing = size_indexing;
  }

290 291
  for(size_t i = start_indexing ; i + seed_span < end_indexing + 1 ; i++) {
    seqtype substr = sequence.substr(i, seed_span);
292
    seqtype kmer = spaced(substr, seed);
293

294
    if (ignore_extended_nucleotides && has_extended_nucleotides(kmer))
295 296
      continue;

Mikaël Salson's avatar
Mikaël Salson committed
297 298
    int strand = 1;
    if (revcomp_indexed && T::hasRevcompSymetry()) {
299
      seqtype rc_kmer = revcomp(kmer);
Mikaël Salson's avatar
Mikaël Salson committed
300 301 302 303 304
      if (rc_kmer.compare(kmer) < 0) {
        strand = -1;
        kmer = rc_kmer;
      }
    }
305 306 307 308 309
    T &this_kmer = this->get(kmer);
    if (this_kmer.isNull()) {
      nb_kmers_inserted++;
    }
    this_kmer += T(label, strand);
Mikaël Salson's avatar
Mikaël Salson committed
310
    if (revcomp_indexed && ! T::hasRevcompSymetry()) {
311
      seqtype rc_kmer = spaced(revcomp(substr), seed);
312 313 314 315
      T &this_rc_kmer = this->get(rc_kmer);
      if (this_rc_kmer.isNull())
        nb_kmers_inserted++;
      this_rc_kmer += T(label, -1);
Mikaël Salson's avatar
Mikaël Salson committed
316 317 318
    }
  }
}
319

320 321 322
template<class T>
void IKmerStore<T>::finish_building() {}

323 324
template<class T>
float IKmerStore<T>::getIndexLoad(const T kmer) const {
325
  return kmer.isUnknown() ? 1 - getIndexLoad() : getIndexLoad();
326
}
327 328
template<class T>
float IKmerStore<T>::getIndexLoad() const {
329
  return nb_kmers_inserted / pow(4.0, k);
330
}
Mikaël Salson's avatar
Mikaël Salson committed
331

332 333 334 335 336 337 338
template<class T>
int IKmerStore<T>::atMostMaxSizeIndexing(int n) const {
  if (!max_size_indexing || n < max_size_indexing)
    return n ;

  return max_size_indexing ;
}
339 340

template<class T>
341
double IKmerStore<T>::getProbabilityAtLeastOrAbove(const T kmer, int at_least, int length) const {
342 343 344

  // n: number of kmers in the sequence
  int n = length - getS() + 1;
345
  float index_load = getIndexLoad(kmer) ;
346 347 348 349 350 351 352 353 354 355 356 357 358 359 360

  double proba = 0;
  double probability_having_system = pow(index_load, at_least);
  double probability_not_having_system = pow(1 - index_load, n - at_least);
  for (int i=at_least; i<=n; i++) {
    proba += nChoosek(n, i) * probability_having_system * probability_not_having_system;
    probability_having_system *= index_load;
    probability_not_having_system /= (1 - index_load);
  }

  return proba;
}



Mikaël Salson's avatar
Mikaël Salson committed
361 362 363 364 365 366 367 368 369 370
template<class T>
int IKmerStore<T>::getK() const {
  return k;
}

template<class T>
int IKmerStore<T>::getS() const {
  return s;
}

371 372 373 374 375
template<class T>
string IKmerStore<T>::getSeed() const {
  return seed;
}

376
template<class T>
377 378
Fasta IKmerStore<T>::getLabel(T kmer) const {
  for (typename list< pair<T, Fasta> >::const_iterator it = labels.begin(); it != labels.end(); ++it)
379 380
    if (it->first == kmer)
      return it->second ;
381
  return FASTA_AMBIGUOUS ;
382
}
383 384

// .getResults()
Mikaël Salson's avatar
Mikaël Salson committed
385
template<class T>
386
vector<T> MapKmerStore<T>::getResults(const seqtype &seq, bool no_revcomp, string seed) {
387

Mikaël Salson's avatar
Mikaël Salson committed
388
  string local_seed = seed;
389
  if (! seed.size())
Mikaël Salson's avatar
Mikaël Salson committed
390 391
    local_seed = IKmerStore<T>::seed;
  int s = local_seed.size();
392

Mikaël Salson's avatar
Mikaël Salson committed
393 394 395 396 397
  if ((int)seq.length() < s - 1) {
    return vector<T>(0);
  }
  vector<T> result(seq.length() - s + 1);
  for (size_t i=0; i + s < seq.length() + 1; i++) {
Mikaël Salson's avatar
Mikaël Salson committed
398
    seqtype kmer = spaced(seq.substr(i, s), local_seed);
399
    //    seqtype kmer = seq.substr(i, s);
Mikaël Salson's avatar
Mikaël Salson committed
400
    // cout << kmer << endl << kmer0 << endl << endl ;
401
    if (IKmerStore<T>::revcomp_indexed && no_revcomp) {
Mikaël Salson's avatar
Mikaël Salson committed
402 403 404 405 406 407 408 409
      result[i] = get(kmer);
    } else {
      result[i] = (*this)[kmer];
    }
  }
  return result;
}

410
template<class T>
411
vector<T> ArrayKmerStore<T>::getResults(const seqtype &seq, bool no_revcomp, string seed) {
Mikaël Salson's avatar
Mikaël Salson committed
412 413

  string local_seed = seed;
414
  if (! seed.size())
Mikaël Salson's avatar
Mikaël Salson committed
415 416
    local_seed = IKmerStore<T>::seed;
  int s = local_seed.size();
417 418 419 420 421 422 423 424 425 426 427 428

  int N = (int)seq.length();

  if (N < s - 1) {
    return vector<T>(0);
  }
  vector<T> result(N - s + 1);

  /* Read once the sequence, convert it to int* */
  int* intseq = new int[N];
  for (int i=0; i<N; i++)
    {
429
      intseq[i] = nuc_to_int(seq[i]);
430 431 432 433
    }

  /* Compute results */
  for (size_t i=0; (int) i+s < N+1; i++) {
Mikaël Salson's avatar
Mikaël Salson committed
434
    int kmer = spaced_int(intseq + i, local_seed);
435 436 437 438
    if (IKmerStore<T>::revcomp_indexed && no_revcomp) {
      result[i] = store[kmer]; // getfromint(kmer); // store[kmer];
      // cout << i << "/" << N << "  " << kmer << result[i] << endl ;
    } else {
439
      result[i] = (*this)[kmer]; // Deals with revcomp
440 441 442 443 444 445 446
    }
  }

  delete[] intseq ;
  return result;
}

Mikaël Salson's avatar
Mikaël Salson committed
447 448 449 450 451 452

template<class T>
bool IKmerStore<T>::isRevcomp() const {
  return revcomp_indexed;
}

453 454 455 456 457
template<class T>
size_t IKmerStore<T>::smallestAnalysableLength() const {
  return getK();
}

Mikaël Salson's avatar
Mikaël Salson committed
458 459 460
// MapKmerStore

template <class T>
461
MapKmerStore<T>::MapKmerStore(string seed, bool revcomp):IKmerStore<T>(){
Mikaël Salson's avatar
Mikaël Salson committed
462 463 464 465 466
  this->seed = seed;   
  int k = seed_weight(seed);
  this->k = k;
  this->s = seed.size();
  this->revcomp_indexed = revcomp;
467
  init();
Mikaël Salson's avatar
Mikaël Salson committed
468 469 470
}

template <class T>
471
MapKmerStore<T>::MapKmerStore(int k, bool revcomp):IKmerStore<T>(){
Mikaël Salson's avatar
Mikaël Salson committed
472 473 474 475
  this->seed = seed_contiguous(k);
  this->k = k;
  this->s = k;
  this->revcomp_indexed = revcomp;
476 477 478 479 480 481
  init();
}

template <class T>
void MapKmerStore<T>::init() {
  this->nb_kmers_inserted = 0;
482
  this->max_size_indexing = 0;
Mikaël Salson's avatar
Mikaël Salson committed
483 484 485
}

template <class T> 
486
T& MapKmerStore<T>::get(seqtype& word){
Mikaël Salson's avatar
Mikaël Salson committed
487 488 489 490
  return store[word];
}

template <class T> 
491
T& MapKmerStore<T>::operator[](seqtype& word){
Mikaël Salson's avatar
Mikaël Salson committed
492
  if (this->isRevcomp() && T::hasRevcompSymetry()) {
493
    seqtype rc_kmer = revcomp(word);
Mikaël Salson's avatar
Mikaël Salson committed
494 495 496 497 498 499 500 501 502
    if (rc_kmer.compare(word) < 0)
      word = rc_kmer;
  }
  return store[word];
}

// ArrayKmerStore

template <class T> 
503
ArrayKmerStore<T>::ArrayKmerStore(int k, bool revcomp):IKmerStore<T>() {
Mikaël Salson's avatar
Mikaël Salson committed
504 505 506 507
  this->seed = seed_contiguous(k);
  this->k = k;
  this->s = k;
  this->revcomp_indexed = revcomp;
508
  init();
Mikaël Salson's avatar
Mikaël Salson committed
509 510 511 512
}


template <class T> 
513
ArrayKmerStore<T>::ArrayKmerStore(string seed, bool revcomp):IKmerStore<T>(){
Mikaël Salson's avatar
Mikaël Salson committed
514 515 516 517 518
  this->seed = seed; 
  int k = seed_weight(seed);
  this->k = k;
  this->s = seed.size();
  this->revcomp_indexed = revcomp;
519 520 521 522 523
  init();
}

template <class T>
void ArrayKmerStore<T>::init() {
524
  this->nb_kmers_inserted = 0;
525
  this->max_size_indexing = 0;
526
  if ((size_t)(this->k << 1) >= sizeof(int) * 8)
Mikaël Salson's avatar
Mikaël Salson committed
527
    throw std::bad_alloc();
528
  store = new T[(unsigned int)1 << (this->k << 1)];
Mikaël Salson's avatar
Mikaël Salson committed
529 530 531 532 533 534 535 536 537 538 539 540 541 542
  if (! store)
    throw std::bad_alloc();
}

template <class T> 
ArrayKmerStore<T>::~ArrayKmerStore(){
  delete [] store;
}

/**	Returns index of word in an array of size 4^k
	Considering B(A) = 0, B(C) = 1, B(T) = 2, B(G) = 3
	index_word = \sum_{i=0}^{k-1}B(word[i])*4^(k-i-1)
**/
template <class T> 
543
int ArrayKmerStore<T>::index(const seqtype& word) const{
Mikaël Salson's avatar
Mikaël Salson committed
544
  return dna_to_int(word, this->k);
Mikaël Salson's avatar
Mikaël Salson committed
545 546 547
}

template <class T> 
548
T& ArrayKmerStore<T>::get(seqtype& word){
Mikaël Salson's avatar
Mikaël Salson committed
549 550 551 552
  return store[index(word)];
}

template <class T> 
553
T& ArrayKmerStore<T>::operator[](seqtype& word){
554 555 556 557 558
  return (*this)[index(word)];
}

template <class T> 
T& ArrayKmerStore<T>::operator[](int word){
Mikaël Salson's avatar
Mikaël Salson committed
559
  if (this->isRevcomp() && T::hasRevcompSymetry()) {
560 561
    int rc_kmer = revcomp_int(word, IKmerStore<T>::k);
    if (rc_kmer < word)
Mikaël Salson's avatar
Mikaël Salson committed
562 563
      word = rc_kmer;
  }
564
  return store[word];
Mikaël Salson's avatar
Mikaël Salson committed
565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585
}


/**
 * KmerStoreFactory is a factory that allows to create an index that best fits
 * your needs!
 */
class KmerStoreFactory {
 public:
  template<class T>
    static IKmerStore<T> *createIndex(string seed, bool revcomp=false);
  template<class T>
    static IKmerStore<T> *createIndex(int k, bool revcomp=false);
};

template<class T>
IKmerStore<T> *KmerStoreFactory::createIndex(string seed, bool revcomp) {
  IKmerStore<T> *index;
  try{
    index = new ArrayKmerStore<T>(seed, revcomp);
  }catch(exception e){
586
    cout << "  (using a MapKmer to fit into memory)" << endl;
Mikaël Salson's avatar
Mikaël Salson committed
587 588
    index = new MapKmerStore<T>(seed, revcomp);
  }
589

Mikaël Salson's avatar
Mikaël Salson committed
590 591 592 593 594 595 596 597 598
  return index;
}

template<class T>
IKmerStore<T> *KmerStoreFactory::createIndex(int k, bool revcomp) {
  return createIndex<T>(seed_contiguous(k), revcomp);
}

#endif