forked from lh3/samtools
-
Notifications
You must be signed in to change notification settings - Fork 0
/
bam_sort.c
571 lines (529 loc) · 18.2 KB
/
bam_sort.c
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
#include <stdlib.h>
#include <ctype.h>
#include <assert.h>
#include <errno.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include "bam.h"
#include "ksort.h"
static int g_is_by_qname = 0;
static int strnum_cmp(const char *_a, const char *_b)
{
const unsigned char *a = (const unsigned char*)_a, *b = (const unsigned char*)_b;
const unsigned char *pa = a, *pb = b;
while (*pa && *pb) {
if (isdigit(*pa) && isdigit(*pb)) {
while (*pa == '0') ++pa;
while (*pb == '0') ++pb;
while (isdigit(*pa) && isdigit(*pb) && *pa == *pb) ++pa, ++pb;
if (isdigit(*pa) && isdigit(*pb)) {
int i = 0;
while (isdigit(pa[i]) && isdigit(pb[i])) ++i;
return isdigit(pa[i])? 1 : isdigit(pb[i])? -1 : (int)*pa - (int)*pb;
} else if (isdigit(*pa)) return 1;
else if (isdigit(*pb)) return -1;
else if (pa - a != pb - b) return pa - a < pb - b? 1 : -1;
} else {
if (*pa != *pb) return (int)*pa - (int)*pb;
++pa; ++pb;
}
}
return *pa? 1 : *pb? -1 : 0;
}
#define HEAP_EMPTY 0xffffffffffffffffull
typedef struct {
int i;
uint64_t pos, idx;
bam1_t *b;
} heap1_t;
#define __pos_cmp(a, b) ((a).pos > (b).pos || ((a).pos == (b).pos && ((a).i > (b).i || ((a).i == (b).i && (a).idx > (b).idx))))
static inline int heap_lt(const heap1_t a, const heap1_t b)
{
if (g_is_by_qname) {
int t;
if (a.b == 0 || b.b == 0) return a.b == 0? 1 : 0;
t = strnum_cmp(bam1_qname(a.b), bam1_qname(b.b));
return (t > 0 || (t == 0 && (a.b->core.flag&0xc0) > (b.b->core.flag&0xc0)));
} else return __pos_cmp(a, b);
}
KSORT_INIT(heap, heap1_t, heap_lt)
static void swap_header_targets(bam_header_t *h1, bam_header_t *h2)
{
bam_header_t t;
t.n_targets = h1->n_targets, h1->n_targets = h2->n_targets, h2->n_targets = t.n_targets;
t.target_name = h1->target_name, h1->target_name = h2->target_name, h2->target_name = t.target_name;
t.target_len = h1->target_len, h1->target_len = h2->target_len, h2->target_len = t.target_len;
}
static void swap_header_text(bam_header_t *h1, bam_header_t *h2)
{
int tempi;
char *temps;
tempi = h1->l_text, h1->l_text = h2->l_text, h2->l_text = tempi;
temps = h1->text, h1->text = h2->text, h2->text = temps;
}
#define MERGE_RG 1
#define MERGE_UNCOMP 2
#define MERGE_LEVEL1 4
#define MERGE_FORCE 8
/*!
@abstract Merge multiple sorted BAM.
@param is_by_qname whether to sort by query name
@param out output BAM file name
@param headers name of SAM file from which to copy '@' header lines,
or NULL to copy them from the first file to be merged
@param n number of files to be merged
@param fn names of files to be merged
@discussion Padding information may NOT correctly maintained. This
function is NOT thread safe.
*/
int bam_merge_core2(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg, int n_threads, int level)
{
bamFile fpout, *fp;
heap1_t *heap;
bam_header_t *hout = 0;
bam_header_t *hheaders = NULL;
int i, j, *RG_len = 0;
uint64_t idx = 0;
char **RG = 0, mode[8];
bam_iter_t *iter = 0;
if (headers) {
tamFile fpheaders = sam_open(headers);
if (fpheaders == 0) {
const char *message = strerror(errno);
fprintf(stderr, "[bam_merge_core] cannot open '%s': %s\n", headers, message);
return -1;
}
hheaders = sam_header_read(fpheaders);
sam_close(fpheaders);
}
g_is_by_qname = by_qname;
fp = (bamFile*)calloc(n, sizeof(bamFile));
heap = (heap1_t*)calloc(n, sizeof(heap1_t));
iter = (bam_iter_t*)calloc(n, sizeof(bam_iter_t));
// prepare RG tag
if (flag & MERGE_RG) {
RG = (char**)calloc(n, sizeof(void*));
RG_len = (int*)calloc(n, sizeof(int));
for (i = 0; i != n; ++i) {
int l = strlen(fn[i]);
const char *s = fn[i];
if (l > 4 && strcmp(s + l - 4, ".bam") == 0) l -= 4;
for (j = l - 1; j >= 0; --j) if (s[j] == '/') break;
++j; l -= j;
RG[i] = calloc(l + 1, 1);
RG_len[i] = l;
strncpy(RG[i], s + j, l);
}
}
// read the first
for (i = 0; i != n; ++i) {
bam_header_t *hin;
fp[i] = bam_open(fn[i], "r");
if (fp[i] == 0) {
int j;
fprintf(stderr, "[bam_merge_core] fail to open file %s\n", fn[i]);
for (j = 0; j < i; ++j) bam_close(fp[j]);
free(fp); free(heap);
// FIXME: possible memory leak
return -1;
}
hin = bam_header_read(fp[i]);
if (i == 0) { // the first BAM
hout = hin;
} else { // validate multiple baf
int min_n_targets = hout->n_targets;
if (hin->n_targets < min_n_targets) min_n_targets = hin->n_targets;
for (j = 0; j < min_n_targets; ++j)
if (strcmp(hout->target_name[j], hin->target_name[j]) != 0) {
fprintf(stderr, "[bam_merge_core] different target sequence name: '%s' != '%s' in file '%s'\n",
hout->target_name[j], hin->target_name[j], fn[i]);
return -1;
}
// If this input file has additional target reference sequences,
// add them to the headers to be output
if (hin->n_targets > hout->n_targets) {
swap_header_targets(hout, hin);
// FIXME Possibly we should also create @SQ text headers
// for the newly added reference sequences
}
bam_header_destroy(hin);
}
}
if (hheaders) {
// If the text headers to be swapped in include any @SQ headers,
// check that they are consistent with the existing binary list
// of reference information.
if (hheaders->n_targets > 0) {
if (hout->n_targets != hheaders->n_targets) {
fprintf(stderr, "[bam_merge_core] number of @SQ headers in '%s' differs from number of target sequences\n", headers);
if (!reg) return -1;
}
for (j = 0; j < hout->n_targets; ++j)
if (strcmp(hout->target_name[j], hheaders->target_name[j]) != 0) {
fprintf(stderr, "[bam_merge_core] @SQ header '%s' in '%s' differs from target sequence\n", hheaders->target_name[j], headers);
if (!reg) return -1;
}
}
swap_header_text(hout, hheaders);
bam_header_destroy(hheaders);
}
if (reg) {
int tid, beg, end;
if (bam_parse_region(hout, reg, &tid, &beg, &end) < 0) {
fprintf(stderr, "[%s] Malformated region string or undefined reference name\n", __func__);
return -1;
}
for (i = 0; i < n; ++i) {
bam_index_t *idx;
idx = bam_index_load(fn[i]);
iter[i] = bam_iter_query(idx, tid, beg, end);
bam_index_destroy(idx);
}
}
for (i = 0; i < n; ++i) {
heap1_t *h = heap + i;
h->i = i;
h->b = (bam1_t*)calloc(1, sizeof(bam1_t));
if (bam_iter_read(fp[i], iter[i], h->b) >= 0) {
h->pos = ((uint64_t)h->b->core.tid<<32) | (uint32_t)((int32_t)h->b->core.pos+1)<<1 | bam1_strand(h->b);
h->idx = idx++;
}
else h->pos = HEAP_EMPTY;
}
if (flag & MERGE_UNCOMP) level = 0;
else if (flag & MERGE_LEVEL1) level = 1;
strcpy(mode, "w");
if (level >= 0) sprintf(mode + 1, "%d", level < 9? level : 9);
if ((fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w")) == 0) {
fprintf(stderr, "[%s] fail to create the output file.\n", __func__);
return -1;
}
bam_header_write(fpout, hout);
bam_header_destroy(hout);
if (!(flag & MERGE_UNCOMP)) bgzf_mt(fpout, n_threads, 256);
ks_heapmake(heap, n, heap);
while (heap->pos != HEAP_EMPTY) {
bam1_t *b = heap->b;
if (flag & MERGE_RG) {
uint8_t *rg = bam_aux_get(b, "RG");
if (rg) bam_aux_del(b, rg);
bam_aux_append(b, "RG", 'Z', RG_len[heap->i] + 1, (uint8_t*)RG[heap->i]);
}
bam_write1_core(fpout, &b->core, b->data_len, b->data);
if ((j = bam_iter_read(fp[heap->i], iter[heap->i], b)) >= 0) {
heap->pos = ((uint64_t)b->core.tid<<32) | (uint32_t)((int)b->core.pos+1)<<1 | bam1_strand(b);
heap->idx = idx++;
} else if (j == -1) {
heap->pos = HEAP_EMPTY;
free(heap->b->data); free(heap->b);
heap->b = 0;
} else fprintf(stderr, "[bam_merge_core] '%s' is truncated. Continue anyway.\n", fn[heap->i]);
ks_heapadjust(heap, 0, n, heap);
}
if (flag & MERGE_RG) {
for (i = 0; i != n; ++i) free(RG[i]);
free(RG); free(RG_len);
}
for (i = 0; i != n; ++i) {
bam_iter_destroy(iter[i]);
bam_close(fp[i]);
}
bam_close(fpout);
free(fp); free(heap); free(iter);
return 0;
}
int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg)
{
return bam_merge_core2(by_qname, out, headers, n, fn, flag, reg, 0, -1);
}
int bam_merge(int argc, char *argv[])
{
int c, is_by_qname = 0, flag = 0, ret = 0, n_threads = 0, level = -1;
char *fn_headers = NULL, *reg = 0;
while ((c = getopt(argc, argv, "h:nru1R:f@:l:")) >= 0) {
switch (c) {
case 'r': flag |= MERGE_RG; break;
case 'f': flag |= MERGE_FORCE; break;
case 'h': fn_headers = strdup(optarg); break;
case 'n': is_by_qname = 1; break;
case '1': flag |= MERGE_LEVEL1; break;
case 'u': flag |= MERGE_UNCOMP; break;
case 'R': reg = strdup(optarg); break;
case 'l': level = atoi(optarg); break;
case '@': n_threads = atoi(optarg); break;
}
}
if (optind + 2 >= argc) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: samtools merge [-nr] [-h inh.sam] <out.bam> <in1.bam> <in2.bam> [...]\n\n");
fprintf(stderr, "Options: -n sort by read names\n");
fprintf(stderr, " -r attach RG tag (inferred from file names)\n");
fprintf(stderr, " -u uncompressed BAM output\n");
fprintf(stderr, " -f overwrite the output BAM if exist\n");
fprintf(stderr, " -1 compress level 1\n");
fprintf(stderr, " -l INT compression level, from 0 to 9 [-1]\n");
fprintf(stderr, " -@ INT number of BAM compression threads [0]\n");
fprintf(stderr, " -R STR merge file in the specified region STR [all]\n");
fprintf(stderr, " -h FILE copy the header in FILE to <out.bam> [in1.bam]\n\n");
fprintf(stderr, "Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users\n");
fprintf(stderr, " must provide the correct header with -h, or uses Picard which properly maintains\n");
fprintf(stderr, " the header dictionary in merging.\n\n");
return 1;
}
if (!(flag & MERGE_FORCE) && strcmp(argv[optind], "-")) {
FILE *fp = fopen(argv[optind], "rb");
if (fp != NULL) {
fclose(fp);
fprintf(stderr, "[%s] File '%s' exists. Please apply '-f' to overwrite. Abort.\n", __func__, argv[optind]);
return 1;
}
}
if (bam_merge_core2(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg, n_threads, level) < 0) ret = 1;
free(reg);
free(fn_headers);
return ret;
}
/***************
* BAM sorting *
***************/
#include <pthread.h>
typedef bam1_t *bam1_p;
static int change_SO(bam_header_t *h, const char *so)
{
char *p, *q, *beg = 0, *end = 0, *newtext;
if (h->l_text > 3) {
if (strncmp(h->text, "@HD", 3) == 0) {
if ((p = strchr(h->text, '\n')) == 0) return -1;
*p = '\0';
if ((q = strstr(h->text, "\tSO:")) != 0) {
*p = '\n'; // change back
if (strncmp(q + 4, so, p - q - 4) != 0) {
beg = q;
for (q += 4; *q != '\n' && *q != '\t'; ++q);
end = q;
} else return 0; // no need to change
} else beg = end = p, *p = '\n';
}
}
if (beg == 0) { // no @HD
h->l_text += strlen(so) + 15;
newtext = malloc(h->l_text + 1);
sprintf(newtext, "@HD\tVN:1.3\tSO:%s\n", so);
strcat(newtext, h->text);
} else { // has @HD but different or no SO
h->l_text = (beg - h->text) + (4 + strlen(so)) + (h->text + h->l_text - end);
newtext = malloc(h->l_text + 1);
strncpy(newtext, h->text, beg - h->text);
sprintf(newtext + (beg - h->text), "\tSO:%s", so);
strcat(newtext, end);
}
free(h->text);
h->text = newtext;
return 0;
}
static inline int bam1_lt(const bam1_p a, const bam1_p b)
{
if (g_is_by_qname) {
int t = strnum_cmp(bam1_qname(a), bam1_qname(b));
return (t < 0 || (t == 0 && (a->core.flag&0xc0) < (b->core.flag&0xc0)));
} else return (((uint64_t)a->core.tid<<32|(a->core.pos+1)<<1|bam1_strand(a)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)<<1|bam1_strand(b)));
}
KSORT_INIT(sort, bam1_p, bam1_lt)
typedef struct {
size_t buf_len;
const char *prefix;
bam1_p *buf;
const bam_header_t *h;
int index;
} worker_t;
static void write_buffer(const char *fn, const char *mode, size_t l, bam1_p *buf, const bam_header_t *h, int n_threads)
{
size_t i;
bamFile fp;
fp = strcmp(fn, "-")? bam_open(fn, mode) : bam_dopen(fileno(stdout), mode);
if (fp == 0) return;
bam_header_write(fp, h);
if (n_threads > 1) bgzf_mt(fp, n_threads, 256);
for (i = 0; i < l; ++i)
bam_write1_core(fp, &buf[i]->core, buf[i]->data_len, buf[i]->data);
bam_close(fp);
}
static void *worker(void *data)
{
worker_t *w = (worker_t*)data;
char *name;
ks_mergesort(sort, w->buf_len, w->buf, 0);
name = (char*)calloc(strlen(w->prefix) + 20, 1);
sprintf(name, "%s.%.4d.bam", w->prefix, w->index);
write_buffer(name, "w1", w->buf_len, w->buf, w->h, 0);
free(name);
return 0;
}
static int sort_blocks(int n_files, size_t k, bam1_p *buf, const char *prefix, const bam_header_t *h, int n_threads)
{
int i;
size_t rest;
bam1_p *b;
pthread_t *tid;
pthread_attr_t attr;
worker_t *w;
if (n_threads < 1) n_threads = 1;
if (k < n_threads * 64) n_threads = 1; // use a single thread if we only sort a small batch of records
pthread_attr_init(&attr);
pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
w = calloc(n_threads, sizeof(worker_t));
tid = calloc(n_threads, sizeof(pthread_t));
b = buf; rest = k;
for (i = 0; i < n_threads; ++i) {
w[i].buf_len = rest / (n_threads - i);
w[i].buf = b;
w[i].prefix = prefix;
w[i].h = h;
w[i].index = n_files + i;
b += w[i].buf_len; rest -= w[i].buf_len;
pthread_create(&tid[i], &attr, worker, &w[i]);
}
for (i = 0; i < n_threads; ++i) pthread_join(tid[i], 0);
free(tid); free(w);
return n_files + n_threads;
}
/*!
@abstract Sort an unsorted BAM file based on the chromosome order
and the leftmost position of an alignment
@param is_by_qname whether to sort by query name
@param fn name of the file to be sorted
@param prefix prefix of the output and the temporary files; upon
sucessess, prefix.bam will be written.
@param max_mem approxiate maximum memory (very inaccurate)
@param full_path the given output path is the full path and not just the prefix
@discussion It may create multiple temporary subalignment files
and then merge them by calling bam_merge_core(). This function is
NOT thread safe.
*/
void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t _max_mem, int is_stdout, int n_threads, int level, int full_path)
{
int ret, i, n_files = 0;
size_t mem, max_k, k, max_mem;
bam_header_t *header;
bamFile fp;
bam1_t *b, **buf;
char *fnout = 0;
char const *suffix = ".bam";
if (full_path) suffix += 4;
if (n_threads < 2) n_threads = 1;
g_is_by_qname = is_by_qname;
max_k = k = 0; mem = 0;
max_mem = _max_mem * n_threads;
buf = 0;
fp = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
if (fp == 0) {
fprintf(stderr, "[bam_sort_core] fail to open file %s\n", fn);
return;
}
header = bam_header_read(fp);
if (is_by_qname) change_SO(header, "queryname");
else change_SO(header, "coordinate");
// write sub files
for (;;) {
if (k == max_k) {
size_t old_max = max_k;
max_k = max_k? max_k<<1 : 0x10000;
buf = realloc(buf, max_k * sizeof(void*));
memset(buf + old_max, 0, sizeof(void*) * (max_k - old_max));
}
if (buf[k] == 0) buf[k] = (bam1_t*)calloc(1, sizeof(bam1_t));
b = buf[k];
if ((ret = bam_read1(fp, b)) < 0) break;
if (b->data_len < b->m_data>>2) { // shrink
b->m_data = b->data_len;
kroundup32(b->m_data);
b->data = realloc(b->data, b->m_data);
}
mem += sizeof(bam1_t) + b->m_data + sizeof(void*) + sizeof(void*); // two sizeof(void*) for the data allocated to pointer arrays
++k;
if (mem >= max_mem) {
n_files = sort_blocks(n_files, k, buf, prefix, header, n_threads);
mem = k = 0;
}
}
if (ret != -1)
fprintf(stderr, "[bam_sort_core] truncated file. Continue anyway.\n");
// output file name
fnout = calloc(strlen(prefix) + 20, 1);
if (is_stdout) sprintf(fnout, "-");
else sprintf(fnout, "%s%s", prefix, suffix);
// write the final output
if (n_files == 0) { // a single block
char mode[8];
strcpy(mode, "w");
if (level >= 0) sprintf(mode + 1, "%d", level < 9? level : 9);
ks_mergesort(sort, k, buf, 0);
write_buffer(fnout, mode, k, buf, header, n_threads);
} else { // then merge
char **fns;
n_files = sort_blocks(n_files, k, buf, prefix, header, n_threads);
fprintf(stderr, "[bam_sort_core] merging from %d files...\n", n_files);
fns = (char**)calloc(n_files, sizeof(char*));
for (i = 0; i < n_files; ++i) {
fns[i] = (char*)calloc(strlen(prefix) + 20, 1);
sprintf(fns[i], "%s.%.4d%s", prefix, i, suffix);
}
bam_merge_core2(is_by_qname, fnout, 0, n_files, fns, 0, 0, n_threads, level);
for (i = 0; i < n_files; ++i) {
unlink(fns[i]);
free(fns[i]);
}
free(fns);
}
free(fnout);
// free
for (k = 0; k < max_k; ++k) {
if (!buf[k]) continue;
free(buf[k]->data);
free(buf[k]);
}
free(buf);
bam_header_destroy(header);
bam_close(fp);
}
void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem)
{
bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0, 0, -1, 0);
}
int bam_sort(int argc, char *argv[])
{
size_t max_mem = 768<<20; // 512MB
int c, is_by_qname = 0, is_stdout = 0, n_threads = 0, level = -1, full_path = 0;
while ((c = getopt(argc, argv, "fnom:@:l:")) >= 0) {
switch (c) {
case 'f': full_path = 1; break;
case 'o': is_stdout = 1; break;
case 'n': is_by_qname = 1; break;
case 'm': {
char *q;
max_mem = strtol(optarg, &q, 0);
if (*q == 'k' || *q == 'K') max_mem <<= 10;
else if (*q == 'm' || *q == 'M') max_mem <<= 20;
else if (*q == 'g' || *q == 'G') max_mem <<= 30;
break;
}
case '@': n_threads = atoi(optarg); break;
case 'l': level = atoi(optarg); break;
}
}
if (optind + 2 > argc) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: samtools sort [options] <in.bam> <out.prefix>\n\n");
fprintf(stderr, "Options: -n sort by read name\n");
fprintf(stderr, " -f use <out.prefix> as full file name instead of prefix\n");
fprintf(stderr, " -o final output to stdout\n");
fprintf(stderr, " -l INT compression level, from 0 to 9 [-1]\n");
fprintf(stderr, " -@ INT number of sorting and compression threads [1]\n");
fprintf(stderr, " -m INT max memory per thread; suffix K/M/G recognized [768M]\n");
fprintf(stderr, "\n");
return 1;
}
bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout, n_threads, level, full_path);
return 0;
}