forked from raymondr/cosmo
-
Notifications
You must be signed in to change notification settings - Fork 2
/
cosmo-color-pd.cpp
593 lines (470 loc) · 24.7 KB
/
cosmo-color-pd.cpp
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
#include <iostream>
#include <fstream>
#include <vector>
#include <string>
#include <libgen.h> // basename
#include "tclap/CmdLine.h"
#include <sdsl/bit_vectors.hpp>
#include <sdsl/wavelet_trees.hpp>
#include "io.hpp"
#include "debruijn_graph.hpp"
#include "algorithm.hpp"
#include "cosmo-color-pd.hpp"
using namespace std;
using namespace sdsl;
#include <sys/timeb.h>
bool trace = false;
int getMilliCount(){
timeb tb;
ftime(&tb);
int nCount = tb.millitm + (tb.time & 0xfffff) * 1000;
return nCount;
}
int getMilliSpan(int nTimeStart){
int nSpan = getMilliCount() - nTimeStart;
if(nSpan < 0)
nSpan += 0x100000 * 1000;
return nSpan;
}
string extension = ".dbg";
void parse_arguments(int argc, char **argv, parameters_t & params)
{
TCLAP::CmdLine cmd("Cosmo Copyright (c) Alex Bowe (alexbowe.com) 2014", ' ', VERSION);
TCLAP::UnlabeledValueArg<std::string> input_filename_arg("input",
".packed edge file (output from pack-edges).", true, "", "input_file", cmd);
TCLAP::UnlabeledValueArg<std::string> color_filename_arg("color",
".color file (output from pack-edges).", true, "", "color_file", cmd);
string output_short_form = "output_prefix";
TCLAP::ValueArg<std::string> output_prefix_arg("o", "output_prefix",
"Output prefix. Graph will be written to [" + output_short_form + "]" + extension + ". " +
"Default prefix: basename(input_file).", false, "", output_short_form, cmd);
string ref_color = "ref_color";
TCLAP::ValueArg<std::string> ref_color_arg("a", "ref_color",
"Ref color, ref_color [" + ref_color + "]", false, "", ref_color, cmd);
string sample_mask = "sample_mask";
TCLAP::ValueArg<std::string> sample_mask_arg("b", "sample_mask",
"Sample mask, sample_mask [" + sample_mask + "]", false, "", sample_mask, cmd);
string ref_fasta = "ref_fasta";
TCLAP::ValueArg<std::string> ref_fasta_arg("r", "ref_fasta",
"Reference FASTA filename, ref_fasta [" + ref_fasta + "]", false, "", ref_fasta, cmd);
cmd.parse( argc, argv );
params.input_filename = input_filename_arg.getValue();
params.color_filename = color_filename_arg.getValue();
params.output_prefix = output_prefix_arg.getValue();
params.ref_color = ref_color_arg.getValue();
params.sample_mask = sample_mask_arg.getValue();
params.ref_fasta = ref_fasta_arg.getValue();
}
static char base[] = {'?','A','C','G','T'};
void test_symmetry(debruijn_graph<> dbg) {
for (unsigned long x = 0; x<dbg.sigma+1;x++) {
ssize_t in = dbg.incoming(43, x);
if (in == -1)
continue;
for (unsigned long y = 0; y<dbg.sigma+1;y++) {
ssize_t out = dbg.outgoing(in, y);
if (out == -1)
continue;
cout << "Incoming " << in << ":" << out <<"\n";
}
}
}
void dump_nodes(debruijn_graph<> dbg, uint64_t * colors) {
for (size_t i = 0; i < dbg.num_nodes(); i++) {
cout << i << ":" << dbg.node_label(i) << colors[dbg._node_to_edge(i)] << "\n";
}
}
void dump_edges(debruijn_graph<> dbg, uint64_t * colors) {
for (size_t i = 0; i < dbg.num_edges(); i++) {
cout << i << "e:" << dbg.edge_label(i) << colors[i] << "\n";
}
}
ssize_t get_first_node(debruijn_graph<> dbg, rrr_vector<63> &colors, uint64_t ref_color, std::string& ref_fasta_content)
{
// find the first edge which is colored 'ref_color' and whose label we can find in the ref genome
// (since we generate revcomps and color them the same as given, the first edge's label may not
// be found in the ref genome; we'll just keep trying till we find one)
int num_colors = colors.size() / dbg.num_edges();
ssize_t zeroth_rank_edge = (unsigned long long)-1;
size_t pos = std::string::npos;
ssize_t node_num = 0;
std::string node_label;
std::string query = ref_fasta_content.substr(0, dbg.node_label(0).size()/*hack to get the edge kmer size*/);
for (; node_num < dbg.num_edges(); ++ node_num) {
if (colors[node_num * num_colors + ref_color]) {
zeroth_rank_edge = node_num;
node_label = dbg.node_label(zeroth_rank_edge);
if (node_label == query) {
//if ((pos = ref_fasta_content.find(edge_label)) == 0 /*!= std::string::npos*/){
std::cout << "Found fasta start at edge num " << node_num << std::endl;
return node_num;
break;
}
}
}
// if (pos != std::string::npos) {
// std::cout << "Found edge " << edge_label << " number " << edge_num << " in reference genome at position " << pos << "." << std::endl;
// std::cout << "ref_genome[" << pos - 1 << ":" << pos + edge_label.size() << " = "
// << ref_fasta_content.substr(pos - 1, 1 + edge_label.size()) << std::endl;
// }else{
// std::cerr << "ERROR: Can't find any ref color edges in the ref FASTA" << std::endl;
// exit(EXIT_FAILURE);
// }
// while (pos != 0) {
// now traverse the graph backward till we get back to the start of the ref genome
//while (pos != 0) {
}
unsigned dna_ord(char c)
{
switch(c) {
case 'A' : return 1;
case 'C': return 2;
case 'G': return 3;
case 'T': return 4;
default: std::cerr << "ERROR: Unknown base '" << c << "'." << std::endl;
exit(EXIT_FAILURE);
};
}
// this is meant to roughly mimic strcmp(), will return 0 if the paths starting at s_pos and node_k_pos match for the first L nodes
void advance(debruijn_graph<> dbg, const std::string& ref_fasta_content, const unsigned amount, ssize_t& node_k, ssize_t& node_k_pos)
{
unsigned node_label_size = dbg.k - 1;
for (unsigned i = 0; i < amount; ++i) {
ssize_t edge = dbg.outgoing_edge(node_k, dna_ord(ref_fasta_content[node_k_pos + node_label_size]));
if (edge == -1) {
std::cerr << "Reference fasta guides graph traversal through invalid path at position " << node_k_pos + node_label_size << "." << std::endl;
exit(EXIT_FAILURE);
}
node_k = dbg._edge_to_node(edge);
node_k_pos++;
}
}
int colored_outdegree(debruijn_graph<> dbg, ssize_t v, const uint64_t sample_mask, unsigned num_colors, rrr_vector<63> &colors)
{
unsigned out_count = 0;
// for each symbol of the alphabet
for (unsigned long x2 = 1; x2 < dbg.sigma + 1; x2++) {
// if there exists an outgoing edge for that symbol
ssize_t next_edge = dbg.outgoing_edge(v, x2);
if (next_edge != -1) {
// compute the colors of that edge
uint64_t color_mask = 0;
for (int c = 0; c < num_colors; c++)
color_mask |= colors[next_edge * num_colors + c] << c;
// and if any colors of that edge match the sample set of colors, increment the out degree counter
if (color_mask & sample_mask) {
out_count += 1;
}
}
}
return out_count;
}
int colored_indegree(debruijn_graph<> dbg, ssize_t v, const uint64_t sample_mask, unsigned num_colors, rrr_vector<63> &colors)
{
unsigned in_count = 0;
// for each symbol of the alphabet
for (unsigned long x2 = 1; x2 < dbg.sigma + 1; x2++) {
// if there exists an incoming edge for that symbol
ssize_t next_edge = dbg.incoming(v, x2);
if (next_edge != -1) {
// compute the colors of that edge
uint64_t color_mask = 0;
for (int c = 0; c < num_colors; c++)
color_mask |= colors[next_edge * num_colors + c] << c;
// and if any colors of that edge match the sample set of colors, increment the out degree counter
if (color_mask & sample_mask) {
in_count += 1;
}
}
}
return in_count;
}
//FIXME: add asserts to check the color for the reference genome; it's somewhat annoying user has to specify both the color and the reference genome; we should be able to derive one from the other for the overall flow and having the data replicated could lead to inconsistency errors.
/*FIXME: sample_mask is limited to 64 colors*/
// FIXME: how to handle multiple colors? Treat them all the same? Or do we have to bookkeep individual color results during one traversal. What to do about divergence in the latter case?
void get_supernode(debruijn_graph<> dbg, const ssize_t& node_i, const uint64_t sample_mask , std::vector<ssize_t>& s, unsigned num_colors, rrr_vector<63> &colors, int& node_i_pos_in_supernode)
{
node_i_pos_in_supernode = 0;
//FIXME: what happens if ref enters supernode at the side? do we need to backup to the beginning? supplement seems to imply no
if (colored_outdegree(dbg, node_i, sample_mask, num_colors, colors) == 1) {
for (unsigned long x = 1; x < dbg.sigma + 1; x++) { // iterate through the alphabet of outgoing edges from node i
// follow each strand or supernode
ssize_t edge = dbg.outgoing_edge(node_i, x);
if (edge == -1)
continue;
//branch[branch_num] += base[x];
// build color mask
uint64_t color_mask = 0;
for (int c = 0; c < num_colors; c++)
color_mask |= colors[edge * num_colors + c] << c;
if (color_mask & sample_mask) {
s.push_back(node_i);
// walk along edges until we encounter
ssize_t node_pos = dbg._edge_to_node(edge);
while (/*colored_indegree(dbg, node_pos, sample_mask, num_colors, colors) <= 1 /*FIXME: should be == 1*/ /*&&*/ colored_outdegree(dbg, node_pos, sample_mask, num_colors, colors) == 1) {
ssize_t next_edge = 0;
for (unsigned long x2 = 1; x2 < dbg.sigma + 1; x2++) { // iterate through the alphabet
next_edge = dbg.outgoing_edge(node_pos, x2);
if (next_edge != -1) {
uint64_t color_mask = 0;
for (int c = 0; c < num_colors; c++)
color_mask |= colors[next_edge * num_colors + c] << c;
if (color_mask & sample_mask) {
s.push_back(node_pos);
break;
}
//branch[branch_num] += base[x2];
}
}
node_pos = dbg._edge_to_node(next_edge);
//cout << node_pos << ":" << dbg.node_label(node_pos) << "\n";
}
if (trace) {
std::cout << " terminal supernode node label = " << dbg.node_label(node_pos) << std::endl;
std::cout << " terminal supernode node outdegree = " << colored_outdegree(dbg, node_pos, sample_mask, num_colors, colors) << std::endl;
std::cout << " terminal supernode node indegree = " << colored_indegree(dbg, node_pos, sample_mask, num_colors, colors) << std::endl;
}
}
}
}
}
// int get_divergent(debruijn_graph<> dbg, const std::string& ref_fasta_content, const std::vector<ssize_t>& s, ssize_t node_k, ssize_t node_k_pos)
// {
// for (unsigned i = 0;; ++i, advance(dbg, ref_fasta_content, 1, node_k, node_k_pos)) {
// if (node_k != s[i]) return i;
// }
// }
// int path_cmp(debruijn_graph<> dbg, const std::string& ref_fasta_content, const std::vector<ssize_t>& s, ssize_t s_pos, ssize_t node_k, ssize_t node_k_pos, const unsigned L)
// {
// for (unsigned int i = 0; i < L; ++i, advance(dbg, ref_fasta_content, 1, node_k, node_k_pos), ++s_pos) {
// if (s[s_pos] != node_k) return 1;
// }
// return 0;
// }
unsigned int match_length(debruijn_graph<> dbg, const std::string& ref_fasta_content, const std::vector<ssize_t>& s, ssize_t s_pos, ssize_t node_k, ssize_t node_k_pos, unsigned bound = -1)
{
unsigned int i = 0;
for (; s_pos < s.size() && node_k_pos < ref_fasta_content.size(); ++i, advance(dbg, ref_fasta_content, /* amount */ 1, node_k, node_k_pos), ++s_pos) {
if (s[s_pos] != node_k || i == bound) return i;
}
return i;
}
void dump_supernode(debruijn_graph<> dbg, const std::vector<ssize_t>& s, ssize_t lflanks, ssize_t lflanke, ssize_t rflanks)
{
assert(s.size());
std::cout << " Divergent supernode matches ref at (k-1)-mers [" << lflanks << ", " << lflanke << ") and [" << rflanks << ", " << s.size() << "). Label: " << dbg.node_label(s[0]);
for (unsigned i = 1; i < s.size(); ++i) {
std::string lab = dbg.node_label(s[i]);
std::cout << lab[lab.size()-1];
}
std::cout << std::endl;
}
// S is a path representing the supernode in the sample graph
// b is an index into S where sample and reference diverage
// L is the desired flank size
// i is the common node
// M is the maximum variant size
// n is the reference sequence
const unsigned L = 1; // number of (k-1)-mers to match in each flank
const unsigned M = 17000;
void find_divergent_paths(debruijn_graph<> dbg, rrr_vector<63> &colors, uint64_t ref_color, uint64_t sample_mask, std::string& ref_fasta_content)
{
int num_colors = colors.size() / dbg.num_edges();
// ssize_t first_node = 1875943; // get_first_node(dbg, colors, ref_color, ref_fasta_content);
ssize_t first_node = 2383686; // get_first_node(dbg, colors, ref_color, ref_fasta_content);
unsigned node_label_size = dbg.k - 1;
ssize_t node_i = first_node; // cdbg node labeled with a k-mer existing in the reference sequence
// ssize_t node_i_pos = 0; // starting position in the reference sequence for the above k-mer
ssize_t node_i_pos = 253396; // starting position in the reference sequence for the above k-mer
// for each node in ref_fasta, if it starts a sample supernode,
// scan through ref fasta looking for the other end of the supernode up to M nodes away
// /* - 2 in the following because we need min of 3 (k-1)-mers to have a bubble */
while(node_i_pos < ref_fasta_content.size() - node_label_size - 2 ) {
std::cout << "node_i_pos = " << node_i_pos << "." << std::endl;
std::vector<ssize_t> s; // supernode
int node_i_pos_in_supernode = -1;
trace = (node_i_pos == 253396); // turn on tracing for this node
get_supernode(dbg, node_i, sample_mask, s, num_colors, colors, node_i_pos_in_supernode);
if (s.size()) {
std::cout << " Got supernode of size " << s.size() << std::endl;
ssize_t overlap_len = match_length(dbg, ref_fasta_content, s, node_i_pos_in_supernode,
node_i, node_i_pos);
ssize_t b = node_i_pos_in_supernode + overlap_len;
if (node_i_pos == 253396) {
std::cout << " node_i label = " << dbg.node_label(node_i) << std::endl;
std::cout << " node_i = " << node_i << std::endl;
dump_supernode(dbg, s, node_i_pos_in_supernode, b, s.size() - L);
}
std::cout << " node_i_pos_in_supernode = " << node_i_pos_in_supernode
<< " overlap_len = " << overlap_len << std::endl;
// if the ref matches the supernode to the end, we can skip ahead
if (b == s.size()) {
std::cout << " Skipping remaining " << overlap_len
<< " nodes that match supernode." << std::endl;
advance(dbg, ref_fasta_content, overlap_len, node_i, node_i_pos);
continue;
}
if (overlap_len >= L ) {
std::cout << " searching for right flank match..." << std::endl;
ssize_t node_j = node_i;
ssize_t node_j_pos = node_i_pos;
advance(dbg, ref_fasta_content, overlap_len + 1, node_j, node_j_pos);
for (; node_j_pos <= node_i_pos + M;
advance(dbg, ref_fasta_content, /* amount */ 1, node_j, node_j_pos)) {
int right_overlap = match_length(dbg, ref_fasta_content, s, s.size() - L, node_j,
node_j_pos, L);
if (trace) std::cout << " overlap search depth: " << node_j_pos - node_i_pos << " found overlap: " << right_overlap << " node_j label: " << dbg.node_label(node_j)
<< " s[s.size() - L] label: " << dbg.node_label(s[s.size() - L]) << std::endl;
if (L == right_overlap) {
dump_supernode(dbg, s, node_i_pos_in_supernode, b, s.size() - L);
break;
}
}
}
}
advance(dbg, ref_fasta_content, 1, node_i, node_i_pos);
}
}
const char *const starts[] = {"GCCATACTGCGTCATGTCGCCCTGACGCGC","GCAGGTTCGAATCCTGCACGACCCACCAAT","GCTTAACCTCACAACCCGAAGATGTTTCTT","AAAACCCGCCGAAGCGGGTTTTTACGTAAA","AATCCTGCACGACCCACCAGTTTTAACATC","AGAGTTCCCCGCGCCAGCGGGGATAAACCG","GAATACGTGCGCAACAACCGTCTTCCGGAG"};
void find_bubbles(debruijn_graph<> dbg, rrr_vector<63> &colors, uint64_t ref_color, uint64_t sample_mask)
{
int t = getMilliCount();
int num_colors = colors.size() / dbg.num_edges();
//uint64_t combined_mask = ref_color | sample_mask;
bit_vector visited = bit_vector(dbg.num_nodes(), 0);
cout << "Starting to look for bubbles\n";
std::vector<std::string> branch(2);
bool found_miss = false;
for (size_t node_i = 0; node_i < dbg.num_nodes(); node_i++) {
ssize_t start_node = node_i; // place to store start of branch kmer
std::string start_label(dbg.node_label(start_node));
found_miss = false;
// for (int si = 0; si < 7; ++si) {
// if (!start_label.compare(starts[si])) {
// std::cerr << "Found missing start node " << starts[si] << " outdegree: " << dbg.outdegree(i) << std::endl;
// found_miss = true;
// }
// }
// cout << "Node " << i << ":" << dbg.node_label(i) << " color: " << color_mask << "\n";
if (!visited[node_i] && dbg.outdegree(node_i) == 2) { //FIXME: why do we only care about outdegree == 2?
// initialize bubble tracking variables
int branch_num = 0;
ssize_t end[2]; // place to store end of branch kmer
branch[0].clear();
branch[1].clear();
int branch_offset = 0;
uint64_t branch_color[2];
// start of a bubble handling
for (unsigned long x = 1; x < dbg.sigma + 1; x++) { // iterate through the alphabet of outgoing edges from node i
// follow each strand or supernode
ssize_t edge = dbg.outgoing_edge(node_i, x);
if (edge == -1)
continue;
branch[branch_num] += base[x];
// build color mask
uint64_t color_mask = 0;
for (int c = 0; c < num_colors; c++)
color_mask |= colors[edge * num_colors + c] << c;
branch_color[branch_num] = color_mask;
// walk along edges until we encounter
ssize_t node_pos = dbg._edge_to_node(edge);
while (dbg.indegree(node_pos) == 1 && dbg.outdegree(node_pos) == 1) {
visited[node_pos] = 1;
ssize_t next_edge = 0;
for (unsigned long x2 = 1; x2 < dbg.sigma + 1; x2++) { // iterate through the alphabet
next_edge = dbg.outgoing_edge(node_pos, x2);
if (next_edge != -1) {
branch[branch_num] += base[x2];
break;
}
}
node_pos = dbg._edge_to_node(next_edge);
//cout << node_pos << ":" << dbg.node_label(node_pos) << "\n";
}
if (found_miss) {
std::cerr << "dbg.indegree(node_pos) = " << dbg.indegree(node_pos) << " dbg.outdegree(node_pos) = " << dbg.outdegree(node_pos) << std::endl;
ssize_t next_edge = 0;
std::cerr << "outgoing bases: ";
for (unsigned long x2 = 1; x2 < dbg.sigma + 1; x2++) { // iterate through the alphabet
next_edge = dbg.outgoing_edge(node_pos, x2);
uint64_t color_mask = 0;
if (next_edge != -1) {
for (int c = 0; c < num_colors; c++)
color_mask |= colors[next_edge * num_colors + c] << c;
std::cerr << base[x2] << " (c " << color_mask << ") (p " << dbg._edge_to_node(next_edge) << ")" << std::endl;
;
}
}
std::cerr << std::endl;
}
// cout << "Stopped due to : " << dbg.indegree(node_pos) << ":" << dbg.outdegree(node_pos) << ":" << branch_offset << "\n";
end[branch_num++] = (dbg.indegree(node_pos) > 1) ? node_pos : 0;
branch_offset = 0;
}
// check if both branches ended on the same kmer and they pass the requested color masks
//cout << "Trying " << branch_color[0] << ":" << branch_color[1] << " " << end[0] << ":" << end[1] <<"\n";
//cout << ref_color << ":" << sample_mask << "\n";
//cout << "PutativeStart flank: " << dbg.node_label(start) << " c: " << branch_color[0] << ":" << branch_color[1] << "\n";
if (found_miss) {
std::cerr << "arm sizes: " << branch[0].size() << " " << branch[1].size() << std::endl;
std::cerr << branch[0] << std::endl << branch[1] << std::endl;
}
// check same end node
if ((end[0] && end[0] == end[1]) ) {
if (found_miss) std::cerr << "Missing bubble passed end check" << std::endl;
// check color:
if (true || ((ref_color & branch_color[0] && !(~ref_color & branch_color[0]) &&
sample_mask & branch_color[1] && !(~sample_mask & branch_color[1])) ||
(ref_color & branch_color[1] && !(~ref_color & branch_color[1]) &&
sample_mask & branch_color[0] && !(~sample_mask & branch_color[0])))) {
cout << "\nStart flank: " << dbg.node_label(start_node) << " c: " << branch_color[0] << ":" << branch_color[1] << "\n";
cout << "Branch: " << branch[0] << "\n";
cout << "Branch: " << branch[1] << "\n";
cout << "End flank: " << dbg.node_label(end[0]) << "\n";
if (found_miss) std::cerr << "Reported 'missing' bubble" << std::endl;
}
}
}
}
cerr << "Find bubbles time: " << getMilliSpan(t) << std::endl;
}
//FIXME : deal with uppercase/lowercase/unspecified NT in FASTA
int parse_fasta(const std::string& ref_fasta_fname, std::string& ref_fasta_content)
{
std::ifstream f(ref_fasta_fname);
std::string s;
if (!std::getline(f, s) || s[0] != '>') {
std::cerr << "ERROR: File " << ref_fasta_fname << " doesn't seem like a FASTA file." << std::endl;
exit(EXIT_FAILURE);
}
while(std::getline(f, s)) {
ref_fasta_content += s;
}
}
int main(int argc, char* argv[]) {
parameters_t p;
parse_arguments(argc, argv, p);
ifstream input(p.input_filename, ios::in|ios::binary|ios::ate);
// Can add this to save a couple seconds off traversal - not really worth it.
//vector<size_t> minus_positions;
debruijn_graph<> dbg = debruijn_graph<>::load_from_packed_edges(input, "$ACGT"/*, &minus_positions*/);
input.close();
rrr_vector<63> colors;
load_from_file(colors, p.color_filename);
cerr << "k : " << dbg.k << endl;
cerr << "num_nodes() : " << dbg.num_nodes() << endl;
cerr << "num_edges() : " << dbg.num_edges() << endl;
cerr << "colors : " << colors.size() / dbg.num_edges() << endl;
cerr << "Total size : " << size_in_mega_bytes(dbg) << " MB" << endl;
cerr << "Bits per edge : " << bits_per_element(dbg) << " Bits" << endl;
cerr << "Color size : " << size_in_mega_bytes(colors) << " MB" << endl;
//dump_nodes(dbg, colors);
//dump_edges(dbg, colors);
uint64_t mask1 = (p.ref_color.length() > 0) ? atoi(p.ref_color.c_str()) : -1;
uint64_t mask2 = (p.sample_mask.length() > 0) ? atoi(p.sample_mask.c_str()) : -1;
std::string ref_fasta_content;
std::cout << "Loading reference FASTA file " << p.ref_fasta << "...";
parse_fasta(p.ref_fasta, ref_fasta_content);
std::cout << " got " << ref_fasta_content.size() << " nucleotides." << std::endl;
find_divergent_paths(dbg, colors, mask1, mask2, ref_fasta_content);
}