-
Notifications
You must be signed in to change notification settings - Fork 2
/
graph.h
657 lines (560 loc) · 19 KB
/
graph.h
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
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
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
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
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
#ifndef GRAPH_H__
#define GRAPH_H__
#include <string>
#include <boost/serialization/vector.hpp>
#include "unordered_map.hpp"
#include "unordered_set.hpp"
#include "logdouble.hpp"
#include <algorithm>
#include <random>
#include <cassert>
using namespace std;
extern const double kSmooth;
extern const char kContigSeparator;
extern default_random_engine generator;
typedef string Seq;
template <class T>
inline void hash_combine(std::size_t & seed, const T & v) {
std::hash<T> hasher;
seed ^= hasher(v) + 0x9e3779b9 + (seed << 6) + (seed >> 2);
}
namespace std {
template<typename S, typename T> struct hash<pair<S, T>> {
inline size_t operator()(const pair<S, T> & v) const {
size_t seed = 0;
::hash_combine(seed, v.first);
::hash_combine(seed, v.second);
return seed;
}
};
template<typename T> struct hash<vector<T>> {
inline size_t operator()(const vector<T>& v) const {
size_t seed = 0;
for (int i = 0; i < v.size(); i++) {
::hash_combine(seed, v[i]);
}
return seed;
}
};
}
inline int ConvertNodeId(int x) {
if (x > 0)
return 2*(x-1);
else
return 2*(-x-1)+1;
}
inline int InvertNode(int x) {
return x ^ 1;
}
inline char ReverseBase(char a) {
if (a == 'A') return 'T';
if (a == 'C') return 'G';
if (a == 'G') return 'C';
if (a == 'T') return 'A';
return a;
}
inline Seq ReverseSeq(const Seq& x) {
Seq ret;
for (int i = x.length()-1; i >= 0; i--) {
ret += ReverseBase(x[i]);
}
return ret;
}
class Node {
public:
int id;
Seq s;
vector<Node*> next;
vector<double> next_prob;
double next_sum;
/* Node* inv;
Seq GetNodeSeq(int kmer) const {
if (inv->s.length() >= kmer-1) {
Seq ss = inv->s.substr(inv->s.length() - kmer + 1);
Seq retval = ReverseSeq(inv->s.substr(inv->s.length()-kmer+1)) + s;
return retval;
} else {
Seq pred = ReverseSeq(inv->s);
Node* cur = next[0];
while (pred.length() < kmer-1) {
pred += ReverseSeq(cur->inv->s);
cur = cur->next[0];
}
pred = pred.substr(0, kmer-1);
return pred + s;
}
}*/
int GetNodeLen(int kmer) const {
return s.length() + kmer - 1;
}
void CalcProbSums() {
next_sum = accumulate(next_prob.begin(), next_prob.end(), 0);
}
Node* SampleNext() const {
if (next_prob.size() == 0) return NULL;
uniform_real_distribution<double> dist(0.0, next_sum);
double samp = dist(generator);
double ss = 0;
for (int i = 0; i < next_prob.size(); i++) {
ss += next_prob[i];
if (ss > samp || i == next_prob.size() - 1) {
return next[i];
}
}
}
pair<Node*,double> SampleNextWithProb() const {
if (next_prob.size() == 0) return make_pair((Node*)NULL, 0);
uniform_real_distribution<double> dist(0.0, next_sum);
double samp = dist(generator);
double ss = 0;
for (int i = 0; i < next_prob.size(); i++) {
ss += next_prob[i];
if (ss > samp || i == next_prob.size() - 1) {
double prob = next_prob[i] / next_sum;
return make_pair(next[i], prob);
}
}
}
// Precond - next.size() >= 2
pair<Node*, double> SampleNextWithProbAndBan(int ban) const {
double next_sum_ban = 0;
for (int i = 0; i < next.size(); i++) {
if (next[i]->id == ban) continue;
next_sum_ban += next_prob[i];
}
uniform_real_distribution<double> dist(0.0, next_sum_ban);
double samp = dist(generator);
double ss = 0;
for (int i = 0; i < next_prob.size(); i++) {
if (next[i]->id == ban) continue;
ss += next_prob[i];
if (ss > samp || i == next_prob.size() - 1) {
double prob = next_prob[i] / next_sum_ban;
return make_pair(next[i], prob);
}
}
}
double GetNextProb(int next_id) const {
for (int i = 0; i < next.size(); i++) {
if (next[i]->id == next_id) {
return next_prob[i] / next_sum;
}
}
assert(false);
return 0;
}
double GetNextProbBan(int next_id, int ban) const {
double next_sum_ban = 0;
for (int i = 0; i < next.size(); i++) {
if (next[i]->id == ban) continue;
next_sum_ban += next_prob[i];
}
for (int i = 0; i < next.size(); i++) {
if (next[i]->id == ban) continue;
if (next[i]->id == next_id) {
return next_prob[i] / next_sum_ban;
}
}
assert(false);
return 0;
}
void InitProbs() {
next_prob.clear();
for (auto &x: next) {
next_prob.push_back(kSmooth);
}
}
// TODO: refactor!!!!
void AddJump(int jump) {
for (int i = 0; i < next.size(); i++) {
if (next[i]->id == jump) {
next_prob[i]++;
return;
}
}
assert(false);
}
bool HasNext(int next_id) {
for (int i = 0; i < next.size(); i++) {
if (next[i]->id == next_id) {
return true;
}
}
return false;
}
};
struct Aligment {
int position;
int edit_dist;
int read_id;
int orientation;
template<class Archive>
void serialize(Archive & ar, const unsigned int version) {
ar & position;
ar & edit_dist;
ar & read_id;
ar & orientation;
}
Aligment() {}
Aligment(int pos, int ed, int read_id, int orientation) :
position(pos), edit_dist(ed), read_id(read_id), orientation(orientation) {}
bool operator<(const Aligment& b) const {
if (position == b.position) return read_id < b.read_id;
return position < b.position;
}
};
class Graph {
public:
vector<Node*> nodes;
Node* operator[](int i) {
return nodes[i];
}
// vector<unordered_set<int> > reach_sets_;
// from->to->path between
vector<unordered_map<int, vector<int> > > reach_big_;
vector<unordered_map<int, vector<int> > > reach_limit_;
vector<vector<vector<int>>> reach_self_;
vector<int> normalize_map;
void CalcNormalizeMap() {
unordered_map<string, int> small_strs;
printf("norm map start %d\n", nodes.size());
normalize_map.resize(nodes.size());
for (int i = 0; i < nodes.size(); i++) {
normalize_map[i] = i;
}
for (int i = 0; i < nodes.size(); i++) {
if (nodes[i]->s.length() > 3) {
continue;
}
if (small_strs.count(nodes[i]->s)) {
normalize_map[i] = small_strs[nodes[i]->s];
} else {
small_strs[nodes[i]->s] = i;
}
}
}
void NormalizePath(vector<int>& path) const {
for (int i = 0; i < path.size(); i++) {
if (path[i] >= 0)
path[i] = normalize_map[path[i]];
}
}
void CalcReachability();
void CalcReachabilityBig(int threshold);
void CalcReachabilityLimit(int max_dist);
void CalcProbSums() {
for (auto &x: nodes) {
x->CalcProbSums();
}
}
void RecalculateProbsByPath(const vector<int>& path) {
for (auto &x: nodes) {
x->InitProbs();
}
for (int i = 1; i < path.size(); i++) {
nodes[path[i-1]]->AddJump(path[i]);
nodes[InvertNode(path[i])]->AddJump(InvertNode(path[i-1]));
}
CalcProbSums();
}
void OutputPath(const vector<int>& path, int kmer);
void OutputPath(const vector<int>& path, int kmer, string filename);
void OutputPathA(const vector<int>& path, int kmer, string filename, int cid);
void OutputPathC(const vector<int>& path, int kmer, string filename, int cid);
void OutputPathAT(const vector<int>& path, int kmer, string filename, int cid, int threshold);
private:
};
bool LoadGraph(const string& filename, Graph& gr);
class ReadIndexTrivial {
public:
ReadIndexTrivial() {
trans['A'] = 1;
trans['T'] = 2;
trans['C'] = 3;
trans['G'] = 0;
}
void AddRead(const string& seq, int read_id);
void GetReadCands(const string& seq, unordered_set<int>& read_cands);
void GetReadCandsWithPoses(const string& seq, unordered_map<int, vector<int>>& read_cands);
void PrintSizeInfo();
unordered_map<unsigned long long, vector<int> > read_index_;
char trans[256];
};
class ReadIndexMinHash {
public:
ReadIndexMinHash() {
trans['A'] = 1;
trans['T'] = 2;
trans['C'] = 3;
trans['G'] = 0;
}
void AddRead(const string& seq, int read_id);
void GetMinHashWithPoses(const string& seq, vector<pair<unsigned long long, int>>& mhs);
void GetReadCands(const string& seq, unordered_set<int>& read_cands);
void GetReadCandsWithPoses(const string& seq, unordered_map<int, vector<int>>& read_cands);
void PrintSizeInfo();
unsigned long long Hash(unsigned long long x);
unsigned long long GetMinHashForSeq(const string& seq);
unordered_map<unsigned long long, vector<int> > read_index_;
char trans[256];
int read_len;
};
class ReadSet {
public:
// TODO: Calculate readlens from reads_file not from aligments
ReadSet(const string& name, const string& filename, double match_prob, double mismatch_prob) :
save_changes_(0),
reads_num_(0), name_(name), filename_(filename), match_prob_(match_prob),
mismatch_prob_(mismatch_prob), load_success_(false), external_aligner_(false),
advice_index_build_(false) {}
void PreprocessReads();
void PrepareReadIndex();
// positions: read_id -> (position -> edit_dist, orientation)
vector<vector<pair<int, pair<int, int> > > >& GetPositionsSlow(
const Graph& gr, const vector<int>& path, int& total_len);
// positions: read_id -> (position, (edit_dist, orientation))
vector<vector<pair<int, pair<int, int> > > >& GetPositions(
const Graph& gr, const vector<int>& path, int& total_len);
vector<vector<pair<int, pair<int, int> > > >& AddPositions(
const Graph& gr, const vector<int>& path, int& total_len, int st);
vector<vector<pair<int, pair<int, int> > > >& GetPositions();
void GetPositionsOnlyPath(
const Graph& gr, const vector<int>& path, int st, unordered_map<int, vector<Aligment>>& current_aligments);
void PrecomputeAlignmentForPaths(const vector<vector<int>>& paths, const Graph& gr);
unordered_map<int, vector<int>>& GetAdviceIndex() { return advice_index_; }
unordered_map<int, vector<int>>& GetAdviceIndex1() { return advice_index1_; }
void BuildAdviceIndex(const Graph& gr, int threshold);
void ClearPositions();
int GetNumberOfReads() const {
return reads_num_;
}
int GetReadLen(int read_id) const {
return read_lens_[read_id];
}
int save_changes_;
void LoadAligments();
void SaveAligments(bool force=false);
const string& GetName() const { return name_; }
double match_prob_;
double mismatch_prob_;
vector<double> match_probs_;
vector<double> mismatch_probs_;
private:
const vector<Aligment>& GetAligmentForSubpath(
const Graph& gr, const vector<int>& subpath);
bool GetAligmentForSubpath(
const Graph& gr, const vector<int>& subpath, vector<Aligment>& align);
void PrecomputeAligmentForSubpaths(
const Graph& gr, const vector<vector<int> >& subpaths);
void AlignSubpathInternal(
const Graph& gr, const vector<int>& path);
void AlignSubpathsInternal(
const Graph& gr, const vector<vector<int> >& subpaths);
int GetReadId(const string& read_name) {
if (read_map_.count(read_name) == 0) {
assert(load_success_ == false);
int id = reads_num_;
read_map_[read_name] = id;
read_map_inv_[id] = read_name;
reads_num_++;
read_lens_.resize(reads_num_);
}
return read_map_[read_name];
}
void CalcMaxReadLen();
void GetSubpathsFromPath(const vector<int>& path, const Graph& gr, unordered_set<vector<int>>& subpaths_precomp);
int reads_num_;
unordered_map<vector<int>, vector<Aligment> > aligment_cache_;
unordered_map<string, int> read_map_;
unordered_map<int, string> read_map_inv_;
unordered_map<int, string> read_seqs_;
vector<int> read_lens_;
int max_read_len_;
string name_;
string filename_;
bool load_success_;
vector<vector<pair<int, pair<int, int> > > > positions_;
ReadIndexMinHash read_index_;
//ReadIndexTrivial read_index_;
bool external_aligner_;
bool advice_index_build_;
unordered_map<int, vector<int>> advice_index_, advice_index1_;
};
class PacbioReadSet {
public:
PacbioReadSet(const string& name, const string& filename, double match_prob, double mismatch_prob) :
save_changes_(0),
reads_num_(0), name_(name), filename_(filename), match_prob_(match_prob),
mismatch_prob_(mismatch_prob), min_match_prob_(1-2*(1-match_prob)), load_success_(false) {}
int GetNumberOfReads() const {
return reads_num_;
}
int GetReadLen(int read_id) const {
return read_lens_[read_id];
}
void PreprocessReads();
void ComputeAnchors(const Graph& gr);
// read_id -> (position -> logprob)
vector<vector<pair<int, logdouble> > >& GetReadProbabilitiesSlow(
const Graph& gr, const vector<int>& path, int& total_len,
bool save_to_cache=true);
vector<vector<pair<int, logdouble> > >& GetReadProbabilitiesAnchor(
const Graph& gr, const vector<int>& path, int& total_len,
int anchor);
vector<vector<pair<pair<int, int>, logdouble> > >& GetReadProbabilities(
const Graph& gr, const vector<int>& path, int& total_len);
vector<vector<pair<int, logdouble> > >& GetExactReadProbabilities(
const Graph& gr, const vector<int>& path, int ps, int& total_len,
int& total_len2);
logdouble GetMinReadProb(int read_id) const {
return (mismatch_prob_ ^ (read_lens_[read_id]*0.25)) *
(match_prob_ ^ (read_lens_[read_id]*0.75));
}
string GetReadName(int read_id) const {
auto it = read_map_inv_.find(read_id);
return it->second;
}
void LoadAligments();
void SaveAligments();
void NormalizeCache(const Graph& gr);
int GetMaxReadLen() const {
return max_read_len_;
}
int GetGap(const Graph& gr, int first, int second, int read_id);
private:
int save_changes_;
struct PacbioAligmentData {
string name;
int flags;
int len;
int posstart;
int posend;
int sstart;
int send;
int slen;
int tstart;
int tend;
int edit_dist;
vector<pair<int, char> > cigar;
PacbioAligmentData() {}
};
struct PacbioAligment {
int position;
int position_end;
int read_id;
logdouble prob;
template<class Archive>
void serialize(Archive & ar, const unsigned int version) {
ar & position;
ar & position_end;
ar & prob.logval;
ar & read_id;
}
PacbioAligment() {}
PacbioAligment(int pos, int pos_end, int read_id, logdouble prob) :
position(pos), position_end(pos_end), read_id(read_id), prob(prob) {}
bool operator<(const PacbioAligment& b) const {
return position < b.position;
}
};
void FilterReads(string out_filename, const unordered_set<int>& filter);
int GetReadId(const string& read_name) {
if (read_map_.count(read_name) == 0) {
assert(load_success_ == false);
int id = reads_num_;
read_map_[read_name] = id;
read_map_inv_[id] = read_name;
reads_num_++;
read_lens_.resize(reads_num_);
read_seq_.resize(reads_num_);
}
return read_map_[read_name];
}
logdouble MatchProbability(const char c1, const char c2) const {
if (c1 == kContigSeparator || c2 == kContigSeparator)
return 0;
if (c1 != c2) {
return mismatch_prob_;
} else {
return match_prob_;
}
}
void CalcMaxReadLen();
PacbioAligmentData ParseAligment(const string& buf, int total_len, bool do_reverse=true) const;
vector<pair<int, char> > ParseCigar(const string& cigar) const;
logdouble AligmentProbability(
const std::string &s1, const std::string &s2,
const PacbioAligmentData& align_data, int band=2) const;
int reads_num_;
string name_;
string filename_;
logdouble match_prob_;
logdouble mismatch_prob_;
double min_match_prob_;
bool load_success_;
vector<int> read_lens_;
int max_read_len_;
unordered_map<string, int> read_map_;
unordered_map<int, string> read_map_inv_;
vector<vector<pair<int, logdouble> > > positions_;
vector<vector<pair<pair<int, int>, logdouble> > > positions2_;
vector<string> read_seq_;
unordered_map<vector<int>, vector<PacbioAligment> > aligment_cache_;
public:
unordered_map<int, unordered_set<int> > anchors_cache_;
unordered_map<int, unordered_set<int> > anchors_begin_;
unordered_map<int, unordered_set<int> > anchors_end_;
unordered_map<int, unordered_set<int> > anchors_reverse_;
};
double CalcScoreForPath(const Graph& gr, const vector<int>& path, int kmer,
ReadSet& read_set, bool use_caching = true);
double CalcScoreForPath(const Graph& gr, const vector<int>& path, int kmer,
ReadSet& read_set1, ReadSet& read_set2,
double insert_mean, double insert_std,
bool use_caching = true);
double CalcScoreForPaths(const Graph& gr, const vector<vector<int>>& paths,
ReadSet& read_set1, ReadSet& read_set2,
double insert_mean, double insert_std,
int& zero_reads, int& total_len,
bool use_caching = true,
double no_cov_penalty=0.0, double exp_cov_move=0.75,
bool use_all_to_cov=false,
double min_prob_per_base=-0.7, double min_prob_start=-10);
struct ScoringState {
vector<vector<int>> old_paths;
int bad_bases;
vector<double> probs;
ScoringState() : bad_bases(0) {
}
};
double CalcScoreForPathsNew(const Graph& gr, const vector<vector<int>>& paths,
ReadSet& read_set1, ReadSet& read_set2,
double insert_mean, double insert_std,
int& zero_reads, int& total_len,
ScoringState& scoring_state,
bool use_caching = true,
double no_cov_penalty=0.0, double exp_cov_move=0.75,
bool use_all_to_cov=false,
double min_prob_per_base=-0.7, double min_prob_start=-10);
double CalcScoreForPaths(const Graph& gr, const vector<vector<int>>& paths,
ReadSet& read_set1,
int& zero_reads, int& total_len,
bool use_caching = true,
double no_cov_penalty=0.0, double exp_cov_move=0.75,
double min_prob_per_base=-0.7, double min_prob_start=-10);
double CalcScoreForPacbio(const Graph& gr, vector<int> path,
PacbioReadSet& read_set, int& zero_reads,
int& total_len, bool use_caching = true);
double CalcExactScoreForPacbio(const Graph& gr, vector<int> path,
PacbioReadSet& read_set, int& zero_reads,
int& total_len, int ps, bool use_caching = true);
double CalcScoreForPacbio2(const Graph& gr, vector<int> path, int kmer,
PacbioReadSet& read_set, int& zero_reads,
int& total_len,
bool use_caching = true);
double CalcScoreForPacbio(const Graph& gr, vector<vector<int> > paths,
PacbioReadSet& read_set, int& zero_reads,
int& total_len, bool use_caching = true,
double no_cov_penalty=0.0, double exp_cov_move=0.75,
double min_prob_per_base=-0.7, double min_prob_start=-10);
#endif