Repository navigation
Expand file tree
/
Copy pathindex.c
More file actions
587 lines (544 loc) · 16.1 KB
/
Copy pathindex.c
File metadata and controls
587 lines (544 loc) · 16.1 KB
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
#include <stdlib.h>
#include <assert.h>
#if defined(WIN32) || defined(_WIN32)
#include <io.h> // for open(2)
#else
#include <unistd.h>
#endif
#include <fcntl.h>
#include <stdio.h>
#define __STDC_LIMIT_MACROS
#include "kthread.h"
#include "bseq.h"
#include "minimap.h"
#include "mmpriv.h"
#include "kvec.h"
#include "khash.h"
#define idx_hash(a) ((a)>>1)
#define idx_eq(a, b) ((a)>>1 == (b)>>1)
KHASH_INIT(idx, uint64_t, uint64_t, 1, idx_hash, idx_eq)
typedef khash_t(idx) idxhash_t;
KHASH_MAP_INIT_STR(str, uint32_t)
#define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x))
typedef struct mm_idx_bucket_s {
mm128_v a; // (minimizer, position) array
int32_t n; // size of the _p_ array
uint64_t *p; // position array for minimizers appearing >1 times
void *h; // hash table indexing _p_ and minimizers appearing once
} mm_idx_bucket_t;
mm_idx_t *mm_idx_init(int w, int k, int b, int flag)
{
mm_idx_t *mi;
if (k*2 < b) b = k * 2;
if (w < 1) w = 1;
mi = (mm_idx_t*)calloc(1, sizeof(mm_idx_t));
mi->w = w, mi->k = k, mi->b = b, mi->flag = flag;
mi->B = (mm_idx_bucket_t*)calloc(1<<b, sizeof(mm_idx_bucket_t));
if (!(mm_dbg_flag & 1)) mi->km = km_init();
return mi;
}
void mm_idx_destroy(mm_idx_t *mi)
{
uint32_t i;
if (mi == 0) return;
if (mi->h) kh_destroy(str, (khash_t(str)*)mi->h);
if (mi->B) {
for (i = 0; i < 1U<<mi->b; ++i) {
free(mi->B[i].p);
free(mi->B[i].a.a);
kh_destroy(idx, (idxhash_t*)mi->B[i].h);
}
}
if (!mi->km) {
for (i = 0; i < mi->n_seq; ++i)
free(mi->seq[i].name);
free(mi->seq);
} else km_destroy(mi->km);
free(mi->B); free(mi->S); free(mi);
}
const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n)
{
int mask = (1<<mi->b) - 1;
khint_t k;
mm_idx_bucket_t *b = &mi->B[minier&mask];
idxhash_t *h = (idxhash_t*)b->h;
*n = 0;
if (h == 0) return 0;
k = kh_get(idx, h, minier>>mi->b<<1);
if (k == kh_end(h)) return 0;
if (kh_key(h, k)&1) { // special casing when there is only one k-mer
*n = 1;
return &kh_val(h, k);
} else {
*n = (uint32_t)kh_val(h, k);
return &b->p[kh_val(h, k)>>32];
}
}
void mm_idx_stat(const mm_idx_t *mi)
{
int n = 0, n1 = 0;
uint32_t i;
uint64_t sum = 0, len = 0;
fprintf(stderr, "[M::%s] kmer size: %d; skip: %d; is_hpc: %d; #seq: %d\n", __func__, mi->k, mi->w, mi->flag&MM_I_HPC, mi->n_seq);
for (i = 0; i < mi->n_seq; ++i)
len += mi->seq[i].len;
for (i = 0; i < 1U<<mi->b; ++i)
if (mi->B[i].h) n += kh_size((idxhash_t*)mi->B[i].h);
for (i = 0; i < 1U<<mi->b; ++i) {
idxhash_t *h = (idxhash_t*)mi->B[i].h;
khint_t k;
if (h == 0) continue;
for (k = 0; k < kh_end(h); ++k)
if (kh_exist(h, k)) {
sum += kh_key(h, k)&1? 1 : (uint32_t)kh_val(h, k);
if (kh_key(h, k)&1) ++n1;
}
}
fprintf(stderr, "[M::%s::%.3f*%.2f] distinct minimizers: %d (%.2f%% are singletons); average occurrences: %.3lf; average spacing: %.3lf\n",
__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), n, 100.0*n1/n, (double)sum / n, (double)len / sum);
}
int mm_idx_index_name(mm_idx_t *mi)
{
khash_t(str) *h;
uint32_t i;
int has_dup = 0, absent;
if (mi->h) return 0;
h = kh_init(str);
for (i = 0; i < mi->n_seq; ++i) {
khint_t k;
k = kh_put(str, h, mi->seq[i].name, &absent);
if (absent) kh_val(h, k) = i;
else has_dup = 1;
}
mi->h = h;
if (has_dup && mm_verbose >= 2)
fprintf(stderr, "[WARNING] some database sequences have identical sequence names\n");
return has_dup;
}
int mm_idx_name2id(const mm_idx_t *mi, const char *name)
{
khash_t(str) *h = (khash_t(str)*)mi->h;
khint_t k;
if (h == 0) return -2;
k = kh_get(str, h, name);
return k == kh_end(h)? -1 : kh_val(h, k);
}
int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq)
{
uint64_t i, st1, en1;
if (rid >= mi->n_seq || st >= mi->seq[rid].len) return -1;
if (en > mi->seq[rid].len) en = mi->seq[rid].len;
st1 = mi->seq[rid].offset + st;
en1 = mi->seq[rid].offset + en;
for (i = st1; i < en1; ++i)
seq[i - st1] = mm_seq4_get(mi->S, i);
return en - st;
}
int32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f)
{
int i;
size_t n = 0;
uint32_t thres;
khint_t *a, k;
if (f <= 0.) return INT32_MAX;
for (i = 0; i < 1<<mi->b; ++i)
if (mi->B[i].h) n += kh_size((idxhash_t*)mi->B[i].h);
a = (uint32_t*)malloc(n * 4);
for (i = n = 0; i < 1<<mi->b; ++i) {
idxhash_t *h = (idxhash_t*)mi->B[i].h;
if (h == 0) continue;
for (k = 0; k < kh_end(h); ++k) {
if (!kh_exist(h, k)) continue;
a[n++] = kh_key(h, k)&1? 1 : (uint32_t)kh_val(h, k);
}
}
thres = ks_ksmall_uint32_t(n, a, (uint32_t)((1. - f) * n)) + 1;
free(a);
return thres;
}
/*********************************
* Sort and generate hash tables *
*********************************/
static void worker_post(void *g, long i, int tid)
{
int n, n_keys;
size_t j, start_a, start_p;
idxhash_t *h;
mm_idx_t *mi = (mm_idx_t*)g;
mm_idx_bucket_t *b = &mi->B[i];
if (b->a.n == 0) return;
// sort by minimizer
radix_sort_128x(b->a.a, b->a.a + b->a.n);
// count and preallocate
for (j = 1, n = 1, n_keys = 0, b->n = 0; j <= b->a.n; ++j) {
if (j == b->a.n || b->a.a[j].x>>8 != b->a.a[j-1].x>>8) {
++n_keys;
if (n > 1) b->n += n;
n = 1;
} else ++n;
}
h = kh_init(idx);
kh_resize(idx, h, n_keys);
b->p = (uint64_t*)calloc(b->n, 8);
// create the hash table
for (j = 1, n = 1, start_a = start_p = 0; j <= b->a.n; ++j) {
if (j == b->a.n || b->a.a[j].x>>8 != b->a.a[j-1].x>>8) {
khint_t itr;
int absent;
mm128_t *p = &b->a.a[j-1];
itr = kh_put(idx, h, p->x>>8>>mi->b<<1, &absent);
assert(absent && j == start_a + n);
if (n == 1) {
kh_key(h, itr) |= 1;
kh_val(h, itr) = p->y;
} else {
int k;
for (k = 0; k < n; ++k)
b->p[start_p + k] = b->a.a[start_a + k].y;
radix_sort_64(&b->p[start_p], &b->p[start_p + n]); // sort by position; needed as in-place radix_sort_128x() is not stable
kh_val(h, itr) = (uint64_t)start_p<<32 | n;
start_p += n;
}
start_a = j, n = 1;
} else ++n;
}
b->h = h;
assert(b->n == (int32_t)start_p);
// deallocate and clear b->a
kfree(0, b->a.a);
b->a.n = b->a.m = 0, b->a.a = 0;
}
static void mm_idx_post(mm_idx_t *mi, int n_threads)
{
kt_for(n_threads, worker_post, mi, 1<<mi->b);
}
/******************
* Generate index *
******************/
#include <string.h>
#include <zlib.h>
#include "bseq.h"
typedef struct {
int mini_batch_size;
uint64_t batch_size, sum_len;
mm_bseq_file_t *fp;
mm_idx_t *mi;
} pipeline_t;
typedef struct {
int n_seq;
mm_bseq1_t *seq;
mm128_v a;
} step_t;
static void mm_idx_add(mm_idx_t *mi, int n, const mm128_t *a)
{
int i, mask = (1<<mi->b) - 1;
for (i = 0; i < n; ++i) {
mm128_v *p = &mi->B[a[i].x>>8&mask].a;
kv_push(mm128_t, 0, *p, a[i]);
}
}
static void *worker_pipeline(void *shared, int step, void *in)
{
int i;
pipeline_t *p = (pipeline_t*)shared;
if (step == 0) { // step 0: read sequences
step_t *s;
if (p->sum_len > p->batch_size) return 0;
s = (step_t*)calloc(1, sizeof(step_t));
s->seq = mm_bseq_read(p->fp, p->mini_batch_size, 0, &s->n_seq); // read a mini-batch
if (s->seq) {
uint32_t old_m, m;
assert((uint64_t)p->mi->n_seq + s->n_seq <= UINT32_MAX); // to prevent integer overflow
// make room for p->mi->seq
old_m = p->mi->n_seq, m = p->mi->n_seq + s->n_seq;
kroundup32(m); kroundup32(old_m);
if (old_m != m)
p->mi->seq = (mm_idx_seq_t*)krealloc(p->mi->km, p->mi->seq, m * sizeof(mm_idx_seq_t));
// make room for p->mi->S
if (!(p->mi->flag & MM_I_NO_SEQ)) {
uint64_t sum_len, old_max_len, max_len;
for (i = 0, sum_len = 0; i < s->n_seq; ++i) sum_len += s->seq[i].l_seq;
old_max_len = (p->sum_len + 7) / 8;
max_len = (p->sum_len + sum_len + 7) / 8;
kroundup64(old_max_len); kroundup64(max_len);
if (old_max_len != max_len) {
p->mi->S = (uint32_t*)realloc(p->mi->S, max_len * 4);
memset(&p->mi->S[old_max_len], 0, 4 * (max_len - old_max_len));
}
}
// populate p->mi->seq
for (i = 0; i < s->n_seq; ++i) {
mm_idx_seq_t *seq = &p->mi->seq[p->mi->n_seq];
uint32_t j;
if (!(p->mi->flag & MM_I_NO_NAME)) {
seq->name = (char*)kmalloc(p->mi->km, strlen(s->seq[i].name) + 1);
strcpy(seq->name, s->seq[i].name);
} else seq->name = 0;
seq->len = s->seq[i].l_seq;
seq->offset = p->sum_len;
// copy the sequence
if (!(p->mi->flag & MM_I_NO_SEQ)) {
for (j = 0; j < seq->len; ++j) { // TODO: this is not the fastest way, but let's first see if speed matters here
uint64_t o = p->sum_len + j;
int c = seq_nt4_table[(uint8_t)s->seq[i].seq[j]];
mm_seq4_set(p->mi->S, o, c);
}
}
// update p->sum_len and p->mi->n_seq
p->sum_len += seq->len;
s->seq[i].rid = p->mi->n_seq++;
}
return s;
} else free(s);
} else if (step == 1) { // step 1: compute sketch
step_t *s = (step_t*)in;
for (i = 0; i < s->n_seq; ++i) {
mm_bseq1_t *t = &s->seq[i];
if (t->l_seq > 0)
mm_sketch(0, t->seq, t->l_seq, p->mi->w, p->mi->k, t->rid, p->mi->flag&MM_I_HPC, &s->a);
else if (mm_verbose >= 2)
fprintf(stderr, "[WARNING] the length database sequence '%s' is 0\n", t->name);
free(t->seq); free(t->name);
}
free(s->seq); s->seq = 0;
return s;
} else if (step == 2) { // dispatch sketch to buckets
step_t *s = (step_t*)in;
mm_idx_add(p->mi, s->a.n, s->a.a);
kfree(0, s->a.a); free(s);
}
return 0;
}
mm_idx_t *mm_idx_gen(mm_bseq_file_t *fp, int w, int k, int b, int flag, int mini_batch_size, int n_threads, uint64_t batch_size)
{
pipeline_t pl;
if (fp == 0 || mm_bseq_eof(fp)) return 0;
memset(&pl, 0, sizeof(pipeline_t));
pl.mini_batch_size = (uint64_t)mini_batch_size < batch_size? mini_batch_size : batch_size;
pl.batch_size = batch_size;
pl.fp = fp;
pl.mi = mm_idx_init(w, k, b, flag);
kt_pipeline(n_threads < 3? n_threads : 3, worker_pipeline, &pl, 3);
if (mm_verbose >= 3)
fprintf(stderr, "[M::%s::%.3f*%.2f] collected minimizers\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0));
mm_idx_post(pl.mi, n_threads);
if (mm_verbose >= 3)
fprintf(stderr, "[M::%s::%.3f*%.2f] sorted minimizers\n", __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0));
return pl.mi;
}
mm_idx_t *mm_idx_build(const char *fn, int w, int k, int flag, int n_threads) // a simpler interface; deprecated
{
mm_bseq_file_t *fp;
mm_idx_t *mi;
fp = mm_bseq_open(fn);
if (fp == 0) return 0;
mi = mm_idx_gen(fp, w, k, 14, flag, 1<<18, n_threads, UINT64_MAX);
mm_bseq_close(fp);
return mi;
}
mm_idx_t *mm_idx_str(int w, int k, int is_hpc, int bucket_bits, int n, const char **seq, const char **name)
{
uint64_t sum_len = 0;
mm128_v a = {0,0,0};
mm_idx_t *mi;
khash_t(str) *h;
int i, flag = 0;
if (n <= 0) return 0;
for (i = 0; i < n; ++i) // get the total length
sum_len += strlen(seq[i]);
if (is_hpc) flag |= MM_I_HPC;
if (name == 0) flag |= MM_I_NO_NAME;
if (bucket_bits < 0) bucket_bits = 14;
mi = mm_idx_init(w, k, bucket_bits, flag);
mi->n_seq = n;
mi->seq = (mm_idx_seq_t*)kcalloc(mi->km, n, sizeof(mm_idx_seq_t)); // ->seq is allocated from km
mi->S = (uint32_t*)calloc((sum_len + 7) / 8, 4);
mi->h = h = kh_init(str);
for (i = 0, sum_len = 0; i < n; ++i) {
const char *s = seq[i];
mm_idx_seq_t *p = &mi->seq[i];
uint32_t j;
if (name && name[i]) {
int absent;
p->name = (char*)kmalloc(mi->km, strlen(name[i]) + 1);
strcpy(p->name, name[i]);
kh_put(str, h, p->name, &absent);
assert(absent);
}
p->offset = sum_len;
p->len = strlen(s);
for (j = 0; j < p->len; ++j) {
int c = seq_nt4_table[(uint8_t)s[j]];
uint64_t o = sum_len + j;
mm_seq4_set(mi->S, o, c);
}
sum_len += p->len;
if (p->len > 0) {
a.n = 0;
mm_sketch(0, s, p->len, w, k, i, is_hpc, &a);
mm_idx_add(mi, a.n, a.a);
}
}
free(a.a);
mm_idx_post(mi, 1);
return mi;
}
/*************
* index I/O *
*************/
void mm_idx_dump(FILE *fp, const mm_idx_t *mi)
{
uint64_t sum_len = 0;
uint32_t x[5], i;
x[0] = mi->w, x[1] = mi->k, x[2] = mi->b, x[3] = mi->n_seq, x[4] = mi->flag;
fwrite(MM_IDX_MAGIC, 1, 4, fp);
fwrite(x, 4, 5, fp);
for (i = 0; i < mi->n_seq; ++i) {
if (mi->seq[i].name) {
uint8_t l = strlen(mi->seq[i].name);
fwrite(&l, 1, 1, fp);
fwrite(mi->seq[i].name, 1, l, fp);
} else {
uint8_t l = 0;
fwrite(&l, 1, 1, fp);
}
fwrite(&mi->seq[i].len, 4, 1, fp);
sum_len += mi->seq[i].len;
}
for (i = 0; i < 1<<mi->b; ++i) {
mm_idx_bucket_t *b = &mi->B[i];
khint_t k;
idxhash_t *h = (idxhash_t*)b->h;
uint32_t size = h? h->size : 0;
fwrite(&b->n, 4, 1, fp);
fwrite(b->p, 8, b->n, fp);
fwrite(&size, 4, 1, fp);
if (size == 0) continue;
for (k = 0; k < kh_end(h); ++k) {
uint64_t x[2];
if (!kh_exist(h, k)) continue;
x[0] = kh_key(h, k), x[1] = kh_val(h, k);
fwrite(x, 8, 2, fp);
}
}
if (!(mi->flag & MM_I_NO_SEQ))
fwrite(mi->S, 4, (sum_len + 7) / 8, fp);
fflush(fp);
}
mm_idx_t *mm_idx_load(FILE *fp)
{
char magic[4];
uint32_t x[5], i;
uint64_t sum_len = 0;
mm_idx_t *mi;
if (fread(magic, 1, 4, fp) != 4) return 0;
if (strncmp(magic, MM_IDX_MAGIC, 4) != 0) return 0;
if (fread(x, 4, 5, fp) != 5) return 0;
mi = mm_idx_init(x[0], x[1], x[2], x[4]);
mi->n_seq = x[3];
mi->seq = (mm_idx_seq_t*)kcalloc(mi->km, mi->n_seq, sizeof(mm_idx_seq_t));
for (i = 0; i < mi->n_seq; ++i) {
uint8_t l;
mm_idx_seq_t *s = &mi->seq[i];
fread(&l, 1, 1, fp);
if (l) {
s->name = (char*)kmalloc(mi->km, l + 1);
fread(s->name, 1, l, fp);
s->name[l] = 0;
}
fread(&s->len, 4, 1, fp);
s->offset = sum_len;
sum_len += s->len;
}
for (i = 0; i < 1<<mi->b; ++i) {
mm_idx_bucket_t *b = &mi->B[i];
uint32_t j, size;
khint_t k;
idxhash_t *h;
fread(&b->n, 4, 1, fp);
b->p = (uint64_t*)malloc(b->n * 8);
fread(b->p, 8, b->n, fp);
fread(&size, 4, 1, fp);
if (size == 0) continue;
b->h = h = kh_init(idx);
kh_resize(idx, h, size);
for (j = 0; j < size; ++j) {
uint64_t x[2];
int absent;
fread(x, 8, 2, fp);
k = kh_put(idx, h, x[0], &absent);
assert(absent);
kh_val(h, k) = x[1];
}
}
if (!(mi->flag & MM_I_NO_SEQ)) {
mi->S = (uint32_t*)malloc((sum_len + 7) / 8 * 4);
fread(mi->S, 4, (sum_len + 7) / 8, fp);
}
return mi;
}
int64_t mm_idx_is_idx(const char *fn)
{
int fd, is_idx = 0;
int64_t ret, off_end;
char magic[4];
if (strcmp(fn, "-") == 0) return 0; // read from pipe; not an index
fd = open(fn, O_RDONLY);
if (fd < 0) return -1; // error
#ifdef WIN32
if ((off_end = _lseeki64(fd, 0, SEEK_END)) >= 4) {
_lseeki64(fd, 0, SEEK_SET);
#else
if ((off_end = lseek(fd, 0, SEEK_END)) >= 4) {
lseek(fd, 0, SEEK_SET);
#endif // WIN32
ret = read(fd, magic, 4);
if (ret == 4 && strncmp(magic, MM_IDX_MAGIC, 4) == 0)
is_idx = 1;
}
close(fd);
return is_idx? off_end : 0;
}
mm_idx_reader_t *mm_idx_reader_open(const char *fn, const mm_idxopt_t *opt, const char *fn_out)
{
int64_t is_idx;
mm_idx_reader_t *r;
is_idx = mm_idx_is_idx(fn);
if (is_idx < 0) return 0; // failed to open the index
r = (mm_idx_reader_t*)calloc(1, sizeof(mm_idx_reader_t));
r->is_idx = is_idx;
if (opt) r->opt = *opt;
else mm_idxopt_init(&r->opt);
if (r->is_idx) {
r->fp.idx = fopen(fn, "rb");
r->idx_size = is_idx;
} else r->fp.seq = mm_bseq_open(fn);
if (fn_out) r->fp_out = fopen(fn_out, "wb");
return r;
}
void mm_idx_reader_close(mm_idx_reader_t *r)
{
if (r->is_idx) fclose(r->fp.idx);
else mm_bseq_close(r->fp.seq);
if (r->fp_out) fclose(r->fp_out);
free(r);
}
mm_idx_t *mm_idx_reader_read(mm_idx_reader_t *r, int n_threads)
{
mm_idx_t *mi;
if (r->is_idx) {
mi = mm_idx_load(r->fp.idx);
if (mi && mm_verbose >= 2 && (mi->k != r->opt.k || mi->w != r->opt.w || (mi->flag&MM_I_HPC) != (r->opt.flag&MM_I_HPC)))
fprintf(stderr, "[WARNING]\033[1;31m Indexing parameters (-k, -w or -H) overridden by parameters used in the prebuilt index.\033[0m\n");
} else
mi = mm_idx_gen(r->fp.seq, r->opt.w, r->opt.k, r->opt.bucket_bits, r->opt.flag, r->opt.mini_batch_size, n_threads, r->opt.batch_size);
if (mi) {
if (r->fp_out) mm_idx_dump(r->fp_out, mi);
mi->index = r->n_parts++;
}
return mi;
}
int mm_idx_reader_eof(const mm_idx_reader_t *r) // TODO: in extremely rare cases, mm_bseq_eof() might not work
{
return r->is_idx? (feof(r->fp.idx) || ftell(r->fp.idx) == r->idx_size) : mm_bseq_eof(r->fp.seq);
}