/
bt2_io.h
1030 lines (970 loc) · 34.3 KB
/
bt2_io.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
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
/*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 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.
*
* Bowtie 2 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 Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef EBWT_IO_H_
#define EBWT_IO_H_
#include <string>
#include <stdexcept>
#include <iostream>
#include <fstream>
#include <stdlib.h>
#include "bt2_idx.h"
using namespace std;
///////////////////////////////////////////////////////////////////////
//
// Functions for reading and writing Ebwts
//
///////////////////////////////////////////////////////////////////////
/**
* Read an Ebwt from file with given filename.
*/
template <typename index_t>
void Ebwt<index_t>::readIntoMemory(
int color,
int needEntireRev,
bool loadSASamp,
bool loadFtab,
bool loadRstarts,
bool justHeader,
EbwtParams<index_t> *params,
bool mmSweep,
bool loadNames,
bool startVerbose)
{
bool switchEndian; // dummy; caller doesn't care
#ifdef BOWTIE_MM
char *mmFile[] = { NULL, NULL };
#endif
if(_in1Str.length() > 0) {
if(_verbose || startVerbose) {
cerr << " About to open input files: ";
logTime(cerr);
}
// Initialize our primary and secondary input-stream fields
if(_in1 != NULL) fclose(_in1);
if(_verbose || startVerbose) cerr << "Opening \"" << _in1Str.c_str() << "\"" << endl;
if((_in1 = fopen(_in1Str.c_str(), "rb")) == NULL) {
cerr << "Could not open index file " << _in1Str.c_str() << endl;
}
if(loadSASamp) {
if(_in2 != NULL) fclose(_in2);
if(_verbose || startVerbose) cerr << "Opening \"" << _in2Str.c_str() << "\"" << endl;
if((_in2 = fopen(_in2Str.c_str(), "rb")) == NULL) {
cerr << "Could not open index file " << _in2Str.c_str() << endl;
}
}
if(_verbose || startVerbose) {
cerr << " Finished opening input files: ";
logTime(cerr);
}
#ifdef BOWTIE_MM
if(_useMm /*&& !justHeader*/) {
const char *names[] = {_in1Str.c_str(), _in2Str.c_str()};
int fds[] = { fileno(_in1), fileno(_in2) };
for(int i = 0; i < (loadSASamp ? 2 : 1); i++) {
if(_verbose || startVerbose) {
cerr << " Memory-mapping input file " << (i+1) << ": ";
logTime(cerr);
}
struct stat sbuf;
if (stat(names[i], &sbuf) == -1) {
perror("stat");
cerr << "Error: Could not stat index file " << names[i] << " prior to memory-mapping" << endl;
throw 1;
}
mmFile[i] = (char*)mmap((void *)0, (size_t)sbuf.st_size,
PROT_READ, MAP_SHARED, fds[(size_t)i], 0);
if(mmFile[i] == (void *)(-1)) {
perror("mmap");
cerr << "Error: Could not memory-map the index file " << names[i] << endl;
throw 1;
}
if(mmSweep) {
int sum = 0;
for(off_t j = 0; j < sbuf.st_size; j += 1024) {
sum += (int) mmFile[i][j];
}
if(startVerbose) {
cerr << " Swept the memory-mapped ebwt index file 1; checksum: " << sum << ": ";
logTime(cerr);
}
}
}
mmFile1_ = mmFile[0];
mmFile2_ = loadSASamp ? mmFile[1] : NULL;
}
#endif
}
#ifdef BOWTIE_MM
else if(_useMm && !justHeader) {
mmFile[0] = mmFile1_;
mmFile[1] = mmFile2_;
}
if(_useMm && !justHeader) {
assert(mmFile[0] == mmFile1_);
assert(mmFile[1] == mmFile2_);
}
#endif
if(_verbose || startVerbose) {
cerr << " Reading header: ";
logTime(cerr);
}
// Read endianness hints from both streams
size_t bytesRead = 0;
switchEndian = false;
uint32_t one = readU32(_in1, switchEndian); // 1st word of primary stream
bytesRead += 4;
if(loadSASamp) {
#ifndef NDEBUG
assert_eq(one, readU32(_in2, switchEndian)); // should match!
#else
readU32(_in2, switchEndian);
#endif
}
if(one != 1) {
assert_eq((1u<<24), one);
assert_eq(1, endianSwapU32(one));
switchEndian = true;
}
// Can't switch endianness and use memory-mapped files; in order to
// support this, someone has to modify the file to switch
// endiannesses appropriately, and we can't do this inside Bowtie
// or we might be setting up a race condition with other processes.
if(switchEndian && _useMm) {
cerr << "Error: Can't use memory-mapped files when the index is the opposite endianness" << endl;
throw 1;
}
// Reads header entries one by one from primary stream
index_t len = readIndex<index_t>(_in1, switchEndian);
bytesRead += sizeof(index_t);
int32_t lineRate = readI32(_in1, switchEndian);
bytesRead += 4;
/*int32_t linesPerSide =*/ readI32(_in1, switchEndian);
bytesRead += 4;
int32_t offRate = readI32(_in1, switchEndian);
bytesRead += 4;
// TODO: add isaRate to the actual file format (right now, the
// user has to tell us whether there's an ISA sample and what the
// sampling rate is.
int32_t ftabChars = readI32(_in1, switchEndian);
bytesRead += 4;
// chunkRate was deprecated in an earlier version of Bowtie; now
// we use it to hold flags.
int32_t flags = readI32(_in1, switchEndian);
bool entireRev = false;
if(flags < 0 && (((-flags) & EBWT_COLOR) != 0)) {
if(color != -1 && !color) {
cerr << "Error: -C was not specified when running Centrifuge, but index is in colorspace. If" << endl
<< "your reads are in colorspace, please use the -C option. If your reads are not" << endl
<< "in colorspace, please use a normal index (one built without specifying -C to" << endl
<< "centrifuge-build)." << endl;
throw 1;
}
color = 1;
} else if(flags < 0) {
if(color != -1 && color) {
cerr << "Error: -C was specified when running Centrifuge, but index is not in colorspace. If" << endl
<< "your reads are in colorspace, please use a colorspace index (one built using" << endl
<< "centrifuge-build -C). If your reads are not in colorspace, don't specify -C when" << endl
<< "running centrifuge." << endl;
throw 1;
}
color = 0;
}
if(flags < 0 && (((-flags) & EBWT_ENTIRE_REV) == 0)) {
if(needEntireRev != -1 && needEntireRev != 0) {
cerr << "Error: This index is compatible with 0.* versions of Bowtie, but not with 2.*" << endl
<< "versions. Please build or download a version of the index that is compitble" << endl
<< "with Bowtie 2.* (i.e. built with centrifuge-build 2.* or later)" << endl;
throw 1;
}
} else entireRev = true;
bytesRead += 4;
// Create a new EbwtParams from the entries read from primary stream
EbwtParams<index_t> *eh;
bool deleteEh = false;
if(params != NULL) {
params->init(len, lineRate, offRate, ftabChars, color, entireRev);
if(_verbose || startVerbose) params->print(cerr);
eh = params;
} else {
eh = new EbwtParams<index_t>(len, lineRate, offRate, ftabChars, color, entireRev);
deleteEh = true;
}
// Set up overridden suffix-array-sample parameters
index_t offsLen = eh->_offsLen;
// uint64_t offsSz = eh->_offsSz;
index_t offRateDiff = 0;
index_t offsLenSampled = offsLen;
if(_overrideOffRate > offRate) {
offRateDiff = _overrideOffRate - offRate;
}
if(offRateDiff > 0) {
offsLenSampled >>= offRateDiff;
if((offsLen & ~((index_t)OFF_MASK << offRateDiff)) != 0) {
offsLenSampled++;
}
}
// Can't override the offrate or isarate and use memory-mapped
// files; ultimately, all processes need to copy the sparser sample
// into their own memory spaces.
if(_useMm && (offRateDiff)) {
cerr << "Error: Can't use memory-mapped files when the offrate is overridden" << endl;
throw 1;
}
// Read nPat from primary stream
this->_nPat = readIndex<index_t>(_in1, switchEndian);
bytesRead += sizeof(index_t);
_plen.reset();
// Read plen from primary stream
if(_useMm) {
#ifdef BOWTIE_MM
_plen.init((index_t*)(mmFile[0] + bytesRead), _nPat, false);
bytesRead += _nPat*sizeof(index_t);
fseek(_in1, _nPat*sizeof(index_t), SEEK_CUR);
#endif
} else {
try {
if(_verbose || startVerbose) {
cerr << "Reading plen (" << this->_nPat << "): ";
logTime(cerr);
}
_plen.init(new index_t[_nPat], _nPat, true);
if(switchEndian) {
for(index_t i = 0; i < this->_nPat; i++) {
plen()[i] = readIndex<index_t>(_in1, switchEndian);
}
} else {
size_t r = MM_READ(_in1, (void*)(plen()), _nPat*sizeof(index_t));
if(r != (size_t)(_nPat*sizeof(index_t))) {
cerr << "Error reading _plen[] array: " << r << ", " << _nPat*sizeof(index_t) << endl;
throw 1;
}
}
} catch(bad_alloc& e) {
cerr << "Out of memory allocating plen[] in Ebwt::read()"
<< " at " << __FILE__ << ":" << __LINE__ << endl;
throw e;
}
}
this->_offw = this->_nPat > std::numeric_limits<uint16_t>::max();
bool shmemLeader;
size_t OFFSET_SIZE;
// TODO: I'm not consistent on what "header" means. Here I'm using
// "header" to mean everything that would exist in memory if we
// started to build the Ebwt but stopped short of the build*() step
// (i.e. everything up to and including join()).
if(justHeader) goto done;
this->_nFrag = readIndex<index_t>(_in1, switchEndian);
bytesRead += sizeof(index_t);
if(_verbose || startVerbose) {
cerr << "Reading rstarts (" << this->_nFrag*3 << "): ";
logTime(cerr);
}
assert_geq(this->_nFrag, this->_nPat);
_rstarts.reset();
if(loadRstarts) {
if(_useMm) {
#ifdef BOWTIE_MM
_rstarts.init((index_t*)(mmFile[0] + bytesRead), _nFrag*3, false);
bytesRead += this->_nFrag*sizeof(index_t)*3;
fseek(_in1, this->_nFrag*sizeof(index_t)*3, SEEK_CUR);
#endif
} else {
_rstarts.init(new index_t[_nFrag*3], _nFrag*3, true);
if(switchEndian) {
for(size_t i = 0; i < (size_t)(this->_nFrag*3); i += 3) {
// fragment starting position in joined reference
// string, text id, and fragment offset within text
this->rstarts()[i] = readIndex<index_t>(_in1, switchEndian);
this->rstarts()[i+1] = readIndex<index_t>(_in1, switchEndian);
this->rstarts()[i+2] = readIndex<index_t>(_in1, switchEndian);
}
} else {
size_t r = MM_READ(_in1, (void *)rstarts(), this->_nFrag*sizeof(index_t)*3);
if(r != (size_t)(this->_nFrag*sizeof(index_t)*3)) {
cerr << "Error reading _rstarts[] array: " << r << ", " << (this->_nFrag*sizeof(index_t)*3) << endl;
throw 1;
}
}
}
} else {
// Skip em
assert(rstarts() == NULL);
bytesRead += this->_nFrag*sizeof(index_t)*3;
fseek(_in1, this->_nFrag*sizeof(index_t)*3, SEEK_CUR);
}
_ebwt.reset();
if(_useMm) {
#ifdef BOWTIE_MM
_ebwt.init((uint8_t*)(mmFile[0] + bytesRead), eh->_ebwtTotLen, false);
bytesRead += eh->_ebwtTotLen;
fseek(_in1, eh->_ebwtTotLen, SEEK_CUR);
#endif
} else {
// Allocate ebwt (big allocation)
if(_verbose || startVerbose) {
cerr << "Reading ebwt (" << eh->_ebwtTotLen << "): ";
logTime(cerr);
}
bool shmemLeader = true;
if(useShmem_) {
uint8_t *tmp = NULL;
shmemLeader = ALLOC_SHARED_U8(
(_in1Str + "[ebwt]"), eh->_ebwtTotLen, &tmp,
"ebwt[]", (_verbose || startVerbose));
assert(tmp != NULL);
_ebwt.init(tmp, eh->_ebwtTotLen, false);
if(_verbose || startVerbose) {
cerr << " shared-mem " << (shmemLeader ? "leader" : "follower") << endl;
}
} else {
try {
_ebwt.init(new uint8_t[eh->_ebwtTotLen], eh->_ebwtTotLen, true);
} catch(bad_alloc& e) {
cerr << "Out of memory allocating the ebwt[] array for the Bowtie index. Please try" << endl
<< "again on a computer with more memory." << endl;
throw 1;
}
}
if(shmemLeader) {
// Read ebwt from primary stream
uint64_t bytesLeft = eh->_ebwtTotLen;
char *pebwt = (char*)this->ebwt();
while (bytesLeft>0){
size_t r = MM_READ(this->_in1, (void *)pebwt, bytesLeft);
if(MM_IS_IO_ERR(this->_in1, r, bytesLeft)) {
cerr << "Error reading _ebwt[] array: " << r << ", "
<< bytesLeft << endl;
throw 1;
}
pebwt += r;
bytesLeft -= r;
}
if(switchEndian) {
uint8_t *side = this->ebwt();
for(size_t i = 0; i < eh->_numSides; i++) {
index_t *cums = reinterpret_cast<index_t*>(side + eh->_sideSz - sizeof(index_t)*2);
cums[0] = endianSwapIndex(cums[0]);
cums[1] = endianSwapIndex(cums[1]);
side += this->_eh._sideSz;
}
}
#ifdef BOWTIE_SHARED_MEM
if(useShmem_) NOTIFY_SHARED(ebwt(), eh->_ebwtTotLen);
#endif
} else {
// Seek past the data and wait until master is finished
fseek(_in1, eh->_ebwtTotLen, SEEK_CUR);
#ifdef BOWTIE_SHARED_MEM
if(useShmem_) WAIT_SHARED(ebwt(), eh->_ebwtTotLen);
#endif
}
}
// Read zOff from primary stream
_zOff = readIndex<index_t>(_in1, switchEndian);
bytesRead += sizeof(index_t);
assert_lt(_zOff, len);
try {
// Read fchr from primary stream
if(_verbose || startVerbose) cerr << "Reading fchr (5)" << endl;
_fchr.reset();
if(_useMm) {
#ifdef BOWTIE_MM
_fchr.init((index_t*)(mmFile[0] + bytesRead), 5, false);
bytesRead += 5*sizeof(index_t);
fseek(_in1, 5*sizeof(index_t), SEEK_CUR);
#endif
} else {
_fchr.init(new index_t[5], 5, true);
for(int i = 0; i < 5; i++) {
this->fchr()[i] = readIndex<index_t>(_in1, switchEndian);
assert_leq(this->fchr()[i], len);
assert(i <= 0 || this->fchr()[i] >= this->fchr()[i-1]);
}
}
assert_gt(this->fchr()[4], this->fchr()[0]);
// Read ftab from primary stream
if(_verbose || startVerbose) {
if(loadFtab) {
cerr << "Reading ftab (" << eh->_ftabLen << "): ";
logTime(cerr);
} else {
cerr << "Skipping ftab (" << eh->_ftabLen << "): ";
}
}
_ftab.reset();
if(loadFtab) {
if(_useMm) {
#ifdef BOWTIE_MM
_ftab.init((index_t*)(mmFile[0] + bytesRead), eh->_ftabLen, false);
bytesRead += eh->_ftabLen*sizeof(index_t);
fseek(_in1, eh->_ftabLen*sizeof(index_t), SEEK_CUR);
#endif
} else {
_ftab.init(new index_t[eh->_ftabLen], eh->_ftabLen, true);
if(switchEndian) {
for(size_t i = 0; i < eh->_ftabLen; i++)
this->ftab()[i] = readIndex<index_t>(_in1, switchEndian);
} else {
size_t r = MM_READ(_in1, (void *)ftab(), eh->_ftabLen*sizeof(index_t));
if(r != (size_t)(eh->_ftabLen*sizeof(index_t))) {
cerr << "Error reading _ftab[] array: " << r << ", " << (eh->_ftabLen*sizeof(index_t)) << endl;
throw 1;
}
}
}
// Read etab from primary stream
if(_verbose || startVerbose) {
if(loadFtab) {
cerr << "Reading eftab (" << eh->_eftabLen << "): ";
logTime(cerr);
} else {
cerr << "Skipping eftab (" << eh->_eftabLen << "): ";
}
}
_eftab.reset();
if(_useMm) {
#ifdef BOWTIE_MM
_eftab.init((index_t*)(mmFile[0] + bytesRead), eh->_eftabLen, false);
bytesRead += eh->_eftabLen*sizeof(index_t);
fseek(_in1, eh->_eftabLen*sizeof(index_t), SEEK_CUR);
#endif
} else {
_eftab.init(new index_t[eh->_eftabLen], eh->_eftabLen, true);
if(switchEndian) {
for(size_t i = 0; i < eh->_eftabLen; i++)
this->eftab()[i] = readIndex<index_t>(_in1, switchEndian);
} else {
size_t r = MM_READ(_in1, (void *)this->eftab(), eh->_eftabLen*sizeof(index_t));
if(r != (size_t)(eh->_eftabLen*sizeof(index_t))) {
cerr << "Error reading _eftab[] array: " << r << ", " << (eh->_eftabLen*sizeof(index_t)) << endl;
throw 1;
}
}
}
for(index_t i = 0; i < eh->_eftabLen; i++) {
if(i > 0 && this->eftab()[i] > 0) {
assert_geq(this->eftab()[i], this->eftab()[i-1]);
} else if(i > 0 && this->eftab()[i-1] == 0) {
assert_eq(0, this->eftab()[i]);
}
}
} else {
assert(ftab() == NULL);
assert(eftab() == NULL);
// Skip ftab
bytesRead += eh->_ftabLen*sizeof(index_t);
fseek(_in1, eh->_ftabLen*sizeof(index_t), SEEK_CUR);
// Skip eftab
bytesRead += eh->_eftabLen*sizeof(index_t);
fseek(_in1, eh->_eftabLen*sizeof(index_t), SEEK_CUR);
}
} catch(bad_alloc& e) {
cerr << "Out of memory allocating fchr[], ftab[] or eftab[] arrays for the Bowtie index." << endl
<< "Please try again on a computer with more memory." << endl;
throw 1;
}
// Read reference sequence names from primary index file (or not,
// if --refidx is specified)
if(loadNames) {
while(true) {
char c = '\0';
if(MM_READ(_in1, (void *)(&c), (size_t)1) != (size_t)1) break;
bytesRead++;
if(c == '\0') break;
else if(c == '\n') {
this->_refnames.push_back("");
} else {
if(this->_refnames.size() == 0) {
this->_refnames.push_back("");
}
this->_refnames.back().push_back(c);
}
}
if(this->_refnames.back().empty()) {
this->_refnames.pop_back();
}
}
OFFSET_SIZE = (this->_offw ? 4 : 2);
_offs.reset();
_offsw.reset();
if(loadSASamp) {
bytesRead = 4; // reset for secondary index file (already read 1-sentinel)
shmemLeader = true;
if(_verbose || startVerbose) {
cerr << "Reading offs (" << offsLenSampled << " " << std::setw(2) << sizeof(index_t)*8 << "-bit words): ";
logTime(cerr);
}
if(!_useMm) {
if(!useShmem_) {
// Allocate offs_
try {
if(this->_offw) {
_offsw.init(new uint32_t[offsLenSampled], offsLenSampled, true);
} else {
_offs.init(new uint16_t[offsLenSampled], offsLenSampled, true);
}
} catch(bad_alloc& e) {
cerr << "Out of memory allocating the offs[] array for the Bowtie index." << endl
<< "Please try again on a computer with more memory." << endl;
throw 1;
}
} else {
if(this->_offw) {
uint32_t *tmp = NULL;
shmemLeader = ALLOC_SHARED_U32(
(_in2Str + "[offs]"), offsLenSampled*OFFSET_SIZE, &tmp,
"offs", (_verbose || startVerbose));
_offsw.init((uint32_t*)tmp, offsLenSampled, false);
} else {
uint16_t *tmp = NULL;
shmemLeader = ALLOC_SHARED_U32(
(_in2Str + "[offs]"), offsLenSampled*OFFSET_SIZE, &tmp,
"offs", (_verbose || startVerbose));
_offs.init((uint16_t*)tmp, offsLenSampled, false);
}
}
}
if(_overrideOffRate < 32) {
if(shmemLeader) {
// Allocate offs (big allocation)
if(switchEndian || offRateDiff > 0) {
assert(!_useMm);
const index_t blockMaxSz = (index_t)(2 * 1024 * 1024); // 2 MB block size
const index_t blockMaxSzU = (blockMaxSz / OFFSET_SIZE); // # U32s per block
char *buf;
try {
buf = new char[blockMaxSz];
} catch(std::bad_alloc& e) {
cerr << "Error: Out of memory allocating part of _offs array: '" << e.what() << "'" << endl;
throw e;
}
for(index_t i = 0; i < offsLen; i += blockMaxSzU) {
index_t block = min<index_t>((index_t)blockMaxSzU, (index_t)(offsLen - i));
size_t r = MM_READ(_in2, (void *)buf, block * OFFSET_SIZE);
if(r != (size_t)(block * OFFSET_SIZE)) {
cerr << "Error reading block of _offs[] array: " << r << ", " << (block * OFFSET_SIZE) << endl;
throw 1;
}
index_t idx = i >> 1;
for(index_t j = 0; j < block; j += OFFSET_SIZE) {
assert_lt(idx, offsLenSampled);
if(this->_offw) {
this->offsw()[idx] = ((uint32_t*)buf)[j];
if(switchEndian) {
this->offsw()[idx] = endianSwapIndex((uint32_t)this->offs()[idx]);
}
} else {
this->offs()[idx] = ((uint16_t*)buf)[j];
if(switchEndian) {
this->offs()[idx] = endianSwapIndex((uint16_t)this->offs()[idx]);
}
}
idx++;
}
}
delete[] buf;
} else {
if(_useMm) {
#ifdef BOWTIE_MM
if(this->_offw) {
_offsw.init((uint32_t*)(mmFile[1] + bytesRead), offsLen, false);
} else {
_offs.init((uint16_t*)(mmFile[1] + bytesRead), offsLen, false);
}
bytesRead += (offsLen * OFFSET_SIZE);
fseek(_in2, (offsLen * OFFSET_SIZE), SEEK_CUR);
#endif
} else {
// Workaround for small-index mode where MM_READ may
// not be able to handle read amounts greater than 2^32
// bytes.
uint64_t bytesLeft = (offsLen * OFFSET_SIZE);
char *offs = NULL;
if(this->_offw) {
offs = (char *)this->offsw();
} else {
offs = (char *)this->offs();
}
while(bytesLeft > 0) {
size_t r = MM_READ(_in2, (void*)offs, bytesLeft);
if(MM_IS_IO_ERR(_in2, r, bytesLeft)) {
cerr << "Error reading block of _offs[] array: "
<< r << ", " << bytesLeft << gLastIOErrMsg << endl;
throw 1;
}
offs += r;
bytesLeft -= r;
}
}
}
#ifdef BOWTIE_SHARED_MEM
if(useShmem_) {
if(this->_offw) {
NOTIFY_SHARED(offsw(), offsLenSampled*OFFSET_SIZE);
} else {
NOTIFY_SHARED(offs(), offsLenSampled*OFFSET_SIZE);
}
}
#endif
} else {
// Not the shmem leader
fseek(_in2, offsLenSampled*OFFSET_SIZE, SEEK_CUR);
#ifdef BOWTIE_SHARED_MEM
if(this->_offw) {
NOTIFY_SHARED(offsw(), offsLenSampled*OFFSET_SIZE);
} else {
NOTIFY_SHARED(offs(), offsLenSampled*OFFSET_SIZE);
}
#endif
}
}
}
this->postReadInit(*eh); // Initialize fields of Ebwt not read from file
if(_verbose || startVerbose) print(cerr, *eh);
// The fact that _ebwt and friends actually point to something
// (other than NULL) now signals to other member functions that the
// Ebwt is loaded into memory.
done: // Exit hatch for both justHeader and !justHeader
// Be kind
if(deleteEh) delete eh;
#ifdef BOWTIE_MM
if(_in1 != NULL) fseek(_in1, 0, SEEK_SET);
if(_in2 != NULL) fseek(_in2, 0, SEEK_SET);
#else
if(_in1 != NULL) rewind(_in1);
if(_in2 != NULL) rewind(_in2);
#endif
}
/**
* Read reference names from an input stream 'in' for an Ebwt primary
* file and store them in 'refnames'.
*/
template <typename index_t>
void readEbwtRefnames(istream& in, EList<string>& refnames) {
// _in1 must already be open with the get cursor at the
// beginning and no error flags set.
assert(in.good());
assert_eq((streamoff)in.tellg(), ios::beg);
// Read endianness hints from both streams
bool switchEndian = false;
uint32_t one = readU32(in, switchEndian); // 1st word of primary stream
if(one != 1) {
assert_eq((1u<<24), one);
switchEndian = true;
}
// Reads header entries one by one from primary stream
index_t len = readIndex<index_t>(in, switchEndian);
int32_t lineRate = readI32(in, switchEndian);
/*int32_t linesPerSide =*/ readI32(in, switchEndian);
int32_t offRate = readI32(in, switchEndian);
int32_t ftabChars = readI32(in, switchEndian);
// BTL: chunkRate is now deprecated
int32_t flags = readI32(in, switchEndian);
bool color = false;
bool entireReverse = false;
if(flags < 0) {
color = (((-flags) & EBWT_COLOR) != 0);
entireReverse = (((-flags) & EBWT_ENTIRE_REV) != 0);
}
// Create a new EbwtParams from the entries read from primary stream
EbwtParams<index_t> eh(len, lineRate, offRate, ftabChars, color, entireReverse);
index_t nPat = readIndex<index_t>(in, switchEndian); // nPat
in.seekg(nPat*sizeof(index_t), ios_base::cur); // skip plen
// Skip rstarts
index_t nFrag = readIndex<index_t>(in, switchEndian);
in.seekg(nFrag*sizeof(index_t)*3, ios_base::cur);
// Skip ebwt
in.seekg(eh._ebwtTotLen, ios_base::cur);
// Skip zOff from primary stream
readIndex<index_t>(in, switchEndian);
// Skip fchr
in.seekg(5 * sizeof(index_t), ios_base::cur);
// Skip ftab
in.seekg(eh._ftabLen*sizeof(index_t), ios_base::cur);
// Skip eftab
in.seekg(eh._eftabLen*sizeof(index_t), ios_base::cur);
// Read reference sequence names from primary index file
while(true) {
char c = '\0';
in.read(&c, 1);
if(in.eof()) break;
if(c == '\0') break;
else if(c == '\n') {
refnames.push_back("");
} else {
if(refnames.size() == 0) {
refnames.push_back("");
}
refnames.back().push_back(c);
}
}
if(refnames.back().empty()) {
refnames.pop_back();
}
// Be kind
in.clear(); in.seekg(0, ios::beg);
assert(in.good());
}
/**
* Read reference names from the index with basename 'in' and store
* them in 'refnames'.
*/
template <typename index_t>
void readEbwtRefnames(const string& instr, EList<string>& refnames) {
ifstream in;
// Initialize our primary and secondary input-stream fields
in.open((instr + ".1." + gEbwt_ext).c_str(), ios_base::in | ios::binary);
if(!in.is_open()) {
throw EbwtFileOpenException("Cannot open file " + instr);
}
assert(in.is_open());
assert(in.good());
assert_eq((streamoff)in.tellg(), ios::beg);
readEbwtRefnames<index_t>(in, refnames);
}
/**
* Read just enough of the Ebwt's header to get its flags
*/
template <typename index_t>
int32_t Ebwt<index_t>::readFlags(const string& instr) {
ifstream in;
// Initialize our primary and secondary input-stream fields
in.open((instr + ".1." + gEbwt_ext).c_str(), ios_base::in | ios::binary);
if(!in.is_open()) {
throw EbwtFileOpenException("Cannot open file " + instr);
}
assert(in.is_open());
assert(in.good());
bool switchEndian = false;
uint32_t one = readU32(in, switchEndian); // 1st word of primary stream
if(one != 1) {
assert_eq((1u<<24), one);
assert_eq(1, endianSwapU32(one));
switchEndian = true;
}
readIndex<index_t>(in, switchEndian);
readI32(in, switchEndian);
readI32(in, switchEndian);
readI32(in, switchEndian);
readI32(in, switchEndian);
int32_t flags = readI32(in, switchEndian);
return flags;
}
/**
* Read just enough of the Ebwt's header to determine whether it's
* colorspace.
*/
bool
readEbwtColor(const string& instr) {
int32_t flags = Ebwt<>::readFlags(instr);
if(flags < 0 && (((-flags) & EBWT_COLOR) != 0)) {
return true;
} else {
return false;
}
}
/**
* Read just enough of the Ebwt's header to determine whether it's
* entirely reversed.
*/
bool
readEntireReverse(const string& instr) {
int32_t flags = Ebwt<>::readFlags(instr);
if(flags < 0 && (((-flags) & EBWT_ENTIRE_REV) != 0)) {
return true;
} else {
return false;
}
}
/**
* Write an extended Burrows-Wheeler transform to a pair of output
* streams.
*
* @param out1 output stream to primary file
* @param out2 output stream to secondary file
* @param be write in big endian?
*/
template <typename index_t>
void Ebwt<index_t>::writeFromMemory(bool justHeader,
ostream& out1,
ostream& out2) const
{
const EbwtParams<index_t>& eh = this->_eh;
assert(eh.repOk());
uint32_t be = this->toBe();
assert(out1.good());
assert(out2.good());
// When building an Ebwt, these header parameters are known
// "up-front", i.e., they can be written to disk immediately,
// before we join() or buildToDisk()
writeI32(out1, 1, be); // endian hint for priamry stream
writeI32(out2, 1, be); // endian hint for secondary stream
writeIndex<index_t>(out1, eh._len, be); // length of string (and bwt and suffix array)
writeI32(out1, eh._lineRate, be); // 2^lineRate = size in bytes of 1 line
writeI32(out1, 2, be); // not used
writeI32(out1, eh._offRate, be); // every 2^offRate chars is "marked"
writeI32(out1, eh._ftabChars, be); // number of 2-bit chars used to address ftab
int32_t flags = 1;
if(eh._color) flags |= EBWT_COLOR;
if(eh._entireReverse) flags |= EBWT_ENTIRE_REV;
writeI32(out1, -flags, be); // BTL: chunkRate is now deprecated
if(!justHeader) {
assert(rstarts() != NULL);
assert(offs() != NULL);
assert(ftab() != NULL);
assert(eftab() != NULL);
assert(isInMemory());
// These Ebwt parameters are known after the inputs strings have
// been joined() but before they have been built(). These can
// written to the disk next and then discarded from memory.
writeIndex<index_t>(out1, this->_nPat, be);
for(index_t i = 0; i < this->_nPat; i++)
writeIndex<index_t>(out1, this->plen()[i], be);
assert_geq(this->_nFrag, this->_nPat);
writeIndex<index_t>(out1, this->_nFrag, be);
for(size_t i = 0; i < this->_nFrag*3; i++)
writeIndex<index_t>(out1, this->rstarts()[i], be);
// These Ebwt parameters are discovered only as the Ebwt is being
// built (in buildToDisk()). Of these, only 'offs' and 'ebwt' are
// terribly large. 'ebwt' is written to the primary file and then
// discarded from memory as it is built; 'offs' is similarly
// written to the secondary file and discarded.
out1.write((const char *)this->ebwt(), eh._ebwtTotLen);
writeIndex<index_t>(out1, this->zOff(), be);
index_t offsLen = eh._offsLen;
for(index_t i = 0; i < offsLen; i++)
writeIndex<index_t>(out2, this->offs()[i], be);
// 'fchr', 'ftab' and 'eftab' are not fully determined until the
// loop is finished, so they are written to the primary file after
// all of 'ebwt' has already been written and only then discarded
// from memory.
for(int i = 0; i < 5; i++)
writeIndex<index_t>(out1, this->fchr()[i], be);
for(index_t i = 0; i < eh._ftabLen; i++)
writeIndex<index_t>(out1, this->ftab()[i], be);
for(index_t i = 0; i < eh._eftabLen; i++)
writeIndex<index_t>(out1, this->eftab()[i], be);
}
}
/**
* Given a pair of strings representing output filenames, and assuming
* this Ebwt object is currently in memory, write out this Ebwt to the
* specified files.
*
* If sanity-checking is enabled, then once the streams have been
* fully written and closed, we reopen them and read them into a
* (hopefully) exact copy of this Ebwt. We then assert that the
* current Ebwt and the copy match in all of their fields.
*/
template <typename index_t>
void Ebwt<index_t>::writeFromMemory(bool justHeader,
const string& out1,
const string& out2) const
{
ASSERT_ONLY(const EbwtParams<index_t>& eh = this->_eh);
assert(isInMemory());
assert(eh.repOk());
ofstream fout1(out1.c_str(), ios::binary);
ofstream fout2(out2.c_str(), ios::binary);
writeFromMemory(justHeader, fout1, fout2);
fout1.close();
fout2.close();
// Read the file back in and assert that all components match
if(_sanity) {
#if 0
if(_verbose)
cout << "Re-reading \"" << out1 << "\"/\"" << out2 << "\" for sanity check" << endl;
Ebwt copy(out1, out2, _verbose, _sanity);
assert(!isInMemory());
copy.loadIntoMemory(eh._color ? 1 : 0, true, false, false);
assert(isInMemory());
assert_eq(eh._lineRate, copy.eh()._lineRate);
assert_eq(eh._offRate, copy.eh()._offRate);
assert_eq(eh._ftabChars, copy.eh()._ftabChars);
assert_eq(eh._len, copy.eh()._len);
assert_eq(_zOff, copy.zOff());
assert_eq(_zEbwtBpOff, copy.zEbwtBpOff());
assert_eq(_zEbwtByteOff, copy.zEbwtByteOff());
assert_eq(_nPat, copy.nPat());
for(index_t i = 0; i < _nPat; i++)
assert_eq(this->_plen[i], copy.plen()[i]);
assert_eq(this->_nFrag, copy.nFrag());
for(size_t i = 0; i < this->nFrag*3; i++) {
assert_eq(this->_rstarts[i], copy.rstarts()[i]);
}
for(index_t i = 0; i < 5; i++)
assert_eq(this->_fchr[i], copy.fchr()[i]);
for(size_t i = 0; i < eh._ftabLen; i++)
assert_eq(this->ftab()[i], copy.ftab()[i]);
for(size_t i = 0; i < eh._eftabLen; i++)
assert_eq(this->eftab()[i], copy.eftab()[i]);
for(index_t i = 0; i < eh._offsLen; i++)
assert_eq(this->_offs[i], copy.offs()[i]);
for(index_t i = 0; i < eh._ebwtTotLen; i++)
assert_eq(this->ebwt()[i], copy.ebwt()[i]);
copy.sanityCheckAll();
if(_verbose)
cout << "Read-in check passed for \"" << out1 << "\"/\"" << out2 << "\"" << endl;
#endif
}
}
/**
* Write the rstarts array given the szs array for the reference.
*/
template <typename index_t>
void Ebwt<index_t>::szsToDisk(const EList<RefRecord>& szs, ostream& os, int reverse) {
#ifdef CENTRIFUGE
if(rstarts() == NULL) {
_rstarts.init(new index_t[this->_nFrag*3], this->_nFrag*3, true);
}
#endif
size_t seq = 0;
index_t off = 0;
index_t totlen = 0;
index_t rstarts_idx = 0;
for(size_t i = 0; i < szs.size(); i++) {