0
|
1 #include <stdlib.h>
|
|
2 #include <ctype.h>
|
|
3 #include <assert.h>
|
|
4 #include <errno.h>
|
|
5 #include <stdio.h>
|
|
6 #include <string.h>
|
|
7 #include <unistd.h>
|
|
8 #include "bam.h"
|
|
9 #include "ksort.h"
|
|
10
|
|
11 static int g_is_by_qname = 0;
|
|
12
|
|
13 static int strnum_cmp(const char *_a, const char *_b)
|
|
14 {
|
|
15 const unsigned char *a = (const unsigned char*)_a, *b = (const unsigned char*)_b;
|
|
16 const unsigned char *pa = a, *pb = b;
|
|
17 while (*pa && *pb) {
|
|
18 if (isdigit(*pa) && isdigit(*pb)) {
|
|
19 while (*pa == '0') ++pa;
|
|
20 while (*pb == '0') ++pb;
|
|
21 while (isdigit(*pa) && isdigit(*pb) && *pa == *pb) ++pa, ++pb;
|
|
22 if (isdigit(*pa) && isdigit(*pb)) {
|
|
23 int i = 0;
|
|
24 while (isdigit(pa[i]) && isdigit(pb[i])) ++i;
|
|
25 return isdigit(pa[i])? 1 : isdigit(pb[i])? -1 : (int)*pa - (int)*pb;
|
|
26 } else if (isdigit(*pa)) return 1;
|
|
27 else if (isdigit(*pb)) return -1;
|
|
28 else if (pa - a != pb - b) return pa - a < pb - b? 1 : -1;
|
|
29 } else {
|
|
30 if (*pa != *pb) return (int)*pa - (int)*pb;
|
|
31 ++pa; ++pb;
|
|
32 }
|
|
33 }
|
|
34 return *pa? 1 : *pb? -1 : 0;
|
|
35 }
|
|
36
|
|
37 #define HEAP_EMPTY 0xffffffffffffffffull
|
|
38
|
|
39 typedef struct {
|
|
40 int i;
|
|
41 uint64_t pos, idx;
|
|
42 bam1_t *b;
|
|
43 } heap1_t;
|
|
44
|
|
45 #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))))
|
|
46
|
|
47 static inline int heap_lt(const heap1_t a, const heap1_t b)
|
|
48 {
|
|
49 if (g_is_by_qname) {
|
|
50 int t;
|
|
51 if (a.b == 0 || b.b == 0) return a.b == 0? 1 : 0;
|
|
52 t = strnum_cmp(bam1_qname(a.b), bam1_qname(b.b));
|
|
53 return (t > 0 || (t == 0 && (a.b->core.flag&0xc0) > (b.b->core.flag&0xc0)));
|
|
54 } else return __pos_cmp(a, b);
|
|
55 }
|
|
56
|
|
57 KSORT_INIT(heap, heap1_t, heap_lt)
|
|
58
|
|
59 static void swap_header_targets(bam_header_t *h1, bam_header_t *h2)
|
|
60 {
|
|
61 bam_header_t t;
|
|
62 t.n_targets = h1->n_targets, h1->n_targets = h2->n_targets, h2->n_targets = t.n_targets;
|
|
63 t.target_name = h1->target_name, h1->target_name = h2->target_name, h2->target_name = t.target_name;
|
|
64 t.target_len = h1->target_len, h1->target_len = h2->target_len, h2->target_len = t.target_len;
|
|
65 }
|
|
66
|
|
67 static void swap_header_text(bam_header_t *h1, bam_header_t *h2)
|
|
68 {
|
|
69 int tempi;
|
|
70 char *temps;
|
|
71 tempi = h1->l_text, h1->l_text = h2->l_text, h2->l_text = tempi;
|
|
72 temps = h1->text, h1->text = h2->text, h2->text = temps;
|
|
73 }
|
|
74
|
|
75 #define MERGE_RG 1
|
|
76 #define MERGE_UNCOMP 2
|
|
77 #define MERGE_LEVEL1 4
|
|
78 #define MERGE_FORCE 8
|
|
79
|
|
80 /*!
|
|
81 @abstract Merge multiple sorted BAM.
|
|
82 @param is_by_qname whether to sort by query name
|
|
83 @param out output BAM file name
|
|
84 @param headers name of SAM file from which to copy '@' header lines,
|
|
85 or NULL to copy them from the first file to be merged
|
|
86 @param n number of files to be merged
|
|
87 @param fn names of files to be merged
|
|
88
|
|
89 @discussion Padding information may NOT correctly maintained. This
|
|
90 function is NOT thread safe.
|
|
91 */
|
|
92 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)
|
|
93 {
|
|
94 bamFile fpout, *fp;
|
|
95 heap1_t *heap;
|
|
96 bam_header_t *hout = 0;
|
|
97 bam_header_t *hheaders = NULL;
|
|
98 int i, j, *RG_len = 0;
|
|
99 uint64_t idx = 0;
|
|
100 char **RG = 0, mode[8];
|
|
101 bam_iter_t *iter = 0;
|
|
102
|
|
103 if (headers) {
|
|
104 tamFile fpheaders = sam_open(headers);
|
|
105 if (fpheaders == 0) {
|
|
106 const char *message = strerror(errno);
|
|
107 fprintf(stderr, "[bam_merge_core] cannot open '%s': %s\n", headers, message);
|
|
108 return -1;
|
|
109 }
|
|
110 hheaders = sam_header_read(fpheaders);
|
|
111 sam_close(fpheaders);
|
|
112 }
|
|
113
|
|
114 g_is_by_qname = by_qname;
|
|
115 fp = (bamFile*)calloc(n, sizeof(bamFile));
|
|
116 heap = (heap1_t*)calloc(n, sizeof(heap1_t));
|
|
117 iter = (bam_iter_t*)calloc(n, sizeof(bam_iter_t));
|
|
118 // prepare RG tag
|
|
119 if (flag & MERGE_RG) {
|
|
120 RG = (char**)calloc(n, sizeof(void*));
|
|
121 RG_len = (int*)calloc(n, sizeof(int));
|
|
122 for (i = 0; i != n; ++i) {
|
|
123 int l = strlen(fn[i]);
|
|
124 const char *s = fn[i];
|
|
125 if (l > 4 && strcmp(s + l - 4, ".bam") == 0) l -= 4;
|
|
126 for (j = l - 1; j >= 0; --j) if (s[j] == '/') break;
|
|
127 ++j; l -= j;
|
|
128 RG[i] = calloc(l + 1, 1);
|
|
129 RG_len[i] = l;
|
|
130 strncpy(RG[i], s + j, l);
|
|
131 }
|
|
132 }
|
|
133 // read the first
|
|
134 for (i = 0; i != n; ++i) {
|
|
135 bam_header_t *hin;
|
|
136 fp[i] = bam_open(fn[i], "r");
|
|
137 if (fp[i] == 0) {
|
|
138 int j;
|
|
139 fprintf(stderr, "[bam_merge_core] fail to open file %s\n", fn[i]);
|
|
140 for (j = 0; j < i; ++j) bam_close(fp[j]);
|
|
141 free(fp); free(heap);
|
|
142 // FIXME: possible memory leak
|
|
143 return -1;
|
|
144 }
|
|
145 hin = bam_header_read(fp[i]);
|
|
146 if (i == 0) { // the first BAM
|
|
147 hout = hin;
|
|
148 } else { // validate multiple baf
|
|
149 int min_n_targets = hout->n_targets;
|
|
150 if (hin->n_targets < min_n_targets) min_n_targets = hin->n_targets;
|
|
151
|
|
152 for (j = 0; j < min_n_targets; ++j)
|
|
153 if (strcmp(hout->target_name[j], hin->target_name[j]) != 0) {
|
|
154 fprintf(stderr, "[bam_merge_core] different target sequence name: '%s' != '%s' in file '%s'\n",
|
|
155 hout->target_name[j], hin->target_name[j], fn[i]);
|
|
156 return -1;
|
|
157 }
|
|
158
|
|
159 // If this input file has additional target reference sequences,
|
|
160 // add them to the headers to be output
|
|
161 if (hin->n_targets > hout->n_targets) {
|
|
162 swap_header_targets(hout, hin);
|
|
163 // FIXME Possibly we should also create @SQ text headers
|
|
164 // for the newly added reference sequences
|
|
165 }
|
|
166
|
|
167 bam_header_destroy(hin);
|
|
168 }
|
|
169 }
|
|
170
|
|
171 if (hheaders) {
|
|
172 // If the text headers to be swapped in include any @SQ headers,
|
|
173 // check that they are consistent with the existing binary list
|
|
174 // of reference information.
|
|
175 if (hheaders->n_targets > 0) {
|
|
176 if (hout->n_targets != hheaders->n_targets) {
|
|
177 fprintf(stderr, "[bam_merge_core] number of @SQ headers in '%s' differs from number of target sequences\n", headers);
|
|
178 if (!reg) return -1;
|
|
179 }
|
|
180 for (j = 0; j < hout->n_targets; ++j)
|
|
181 if (strcmp(hout->target_name[j], hheaders->target_name[j]) != 0) {
|
|
182 fprintf(stderr, "[bam_merge_core] @SQ header '%s' in '%s' differs from target sequence\n", hheaders->target_name[j], headers);
|
|
183 if (!reg) return -1;
|
|
184 }
|
|
185 }
|
|
186
|
|
187 swap_header_text(hout, hheaders);
|
|
188 bam_header_destroy(hheaders);
|
|
189 }
|
|
190
|
|
191 if (reg) {
|
|
192 int tid, beg, end;
|
|
193 if (bam_parse_region(hout, reg, &tid, &beg, &end) < 0) {
|
|
194 fprintf(stderr, "[%s] Malformated region string or undefined reference name\n", __func__);
|
|
195 return -1;
|
|
196 }
|
|
197 for (i = 0; i < n; ++i) {
|
|
198 bam_index_t *idx;
|
|
199 idx = bam_index_load(fn[i]);
|
|
200 iter[i] = bam_iter_query(idx, tid, beg, end);
|
|
201 bam_index_destroy(idx);
|
|
202 }
|
|
203 }
|
|
204
|
|
205 for (i = 0; i < n; ++i) {
|
|
206 heap1_t *h = heap + i;
|
|
207 h->i = i;
|
|
208 h->b = (bam1_t*)calloc(1, sizeof(bam1_t));
|
|
209 if (bam_iter_read(fp[i], iter[i], h->b) >= 0) {
|
|
210 h->pos = ((uint64_t)h->b->core.tid<<32) | (uint32_t)((int32_t)h->b->core.pos+1)<<1 | bam1_strand(h->b);
|
|
211 h->idx = idx++;
|
|
212 }
|
|
213 else h->pos = HEAP_EMPTY;
|
|
214 }
|
|
215 if (flag & MERGE_UNCOMP) level = 0;
|
|
216 else if (flag & MERGE_LEVEL1) level = 1;
|
|
217 strcpy(mode, "w");
|
|
218 if (level >= 0) sprintf(mode + 1, "%d", level < 9? level : 9);
|
|
219 if ((fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w")) == 0) {
|
|
220 fprintf(stderr, "[%s] fail to create the output file.\n", __func__);
|
|
221 return -1;
|
|
222 }
|
|
223 bam_header_write(fpout, hout);
|
|
224 bam_header_destroy(hout);
|
|
225 if (!(flag & MERGE_UNCOMP)) bgzf_mt(fpout, n_threads, 256);
|
|
226
|
|
227 ks_heapmake(heap, n, heap);
|
|
228 while (heap->pos != HEAP_EMPTY) {
|
|
229 bam1_t *b = heap->b;
|
|
230 if (flag & MERGE_RG) {
|
|
231 uint8_t *rg = bam_aux_get(b, "RG");
|
|
232 if (rg) bam_aux_del(b, rg);
|
|
233 bam_aux_append(b, "RG", 'Z', RG_len[heap->i] + 1, (uint8_t*)RG[heap->i]);
|
|
234 }
|
|
235 bam_write1_core(fpout, &b->core, b->data_len, b->data);
|
|
236 if ((j = bam_iter_read(fp[heap->i], iter[heap->i], b)) >= 0) {
|
|
237 heap->pos = ((uint64_t)b->core.tid<<32) | (uint32_t)((int)b->core.pos+1)<<1 | bam1_strand(b);
|
|
238 heap->idx = idx++;
|
|
239 } else if (j == -1) {
|
|
240 heap->pos = HEAP_EMPTY;
|
|
241 free(heap->b->data); free(heap->b);
|
|
242 heap->b = 0;
|
|
243 } else fprintf(stderr, "[bam_merge_core] '%s' is truncated. Continue anyway.\n", fn[heap->i]);
|
|
244 ks_heapadjust(heap, 0, n, heap);
|
|
245 }
|
|
246
|
|
247 if (flag & MERGE_RG) {
|
|
248 for (i = 0; i != n; ++i) free(RG[i]);
|
|
249 free(RG); free(RG_len);
|
|
250 }
|
|
251 for (i = 0; i != n; ++i) {
|
|
252 bam_iter_destroy(iter[i]);
|
|
253 bam_close(fp[i]);
|
|
254 }
|
|
255 bam_close(fpout);
|
|
256 free(fp); free(heap); free(iter);
|
|
257 return 0;
|
|
258 }
|
|
259
|
|
260 int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg)
|
|
261 {
|
|
262 return bam_merge_core2(by_qname, out, headers, n, fn, flag, reg, 0, -1);
|
|
263 }
|
|
264
|
|
265 int bam_merge(int argc, char *argv[])
|
|
266 {
|
|
267 int c, is_by_qname = 0, flag = 0, ret = 0, n_threads = 0, level = -1;
|
|
268 char *fn_headers = NULL, *reg = 0;
|
|
269
|
|
270 while ((c = getopt(argc, argv, "h:nru1R:f@:l:")) >= 0) {
|
|
271 switch (c) {
|
|
272 case 'r': flag |= MERGE_RG; break;
|
|
273 case 'f': flag |= MERGE_FORCE; break;
|
|
274 case 'h': fn_headers = strdup(optarg); break;
|
|
275 case 'n': is_by_qname = 1; break;
|
|
276 case '1': flag |= MERGE_LEVEL1; break;
|
|
277 case 'u': flag |= MERGE_UNCOMP; break;
|
|
278 case 'R': reg = strdup(optarg); break;
|
|
279 case 'l': level = atoi(optarg); break;
|
|
280 case '@': n_threads = atoi(optarg); break;
|
|
281 }
|
|
282 }
|
|
283 if (optind + 2 >= argc) {
|
|
284 fprintf(stderr, "\n");
|
|
285 fprintf(stderr, "Usage: samtools merge [-nr] [-h inh.sam] <out.bam> <in1.bam> <in2.bam> [...]\n\n");
|
|
286 fprintf(stderr, "Options: -n sort by read names\n");
|
|
287 fprintf(stderr, " -r attach RG tag (inferred from file names)\n");
|
|
288 fprintf(stderr, " -u uncompressed BAM output\n");
|
|
289 fprintf(stderr, " -f overwrite the output BAM if exist\n");
|
|
290 fprintf(stderr, " -1 compress level 1\n");
|
|
291 fprintf(stderr, " -l INT compression level, from 0 to 9 [-1]\n");
|
|
292 fprintf(stderr, " -@ INT number of BAM compression threads [0]\n");
|
|
293 fprintf(stderr, " -R STR merge file in the specified region STR [all]\n");
|
|
294 fprintf(stderr, " -h FILE copy the header in FILE to <out.bam> [in1.bam]\n\n");
|
|
295 fprintf(stderr, "Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users\n");
|
|
296 fprintf(stderr, " must provide the correct header with -h, or uses Picard which properly maintains\n");
|
|
297 fprintf(stderr, " the header dictionary in merging.\n\n");
|
|
298 return 1;
|
|
299 }
|
|
300 if (!(flag & MERGE_FORCE) && strcmp(argv[optind], "-")) {
|
|
301 FILE *fp = fopen(argv[optind], "rb");
|
|
302 if (fp != NULL) {
|
|
303 fclose(fp);
|
|
304 fprintf(stderr, "[%s] File '%s' exists. Please apply '-f' to overwrite. Abort.\n", __func__, argv[optind]);
|
|
305 return 1;
|
|
306 }
|
|
307 }
|
|
308 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;
|
|
309 free(reg);
|
|
310 free(fn_headers);
|
|
311 return ret;
|
|
312 }
|
|
313
|
|
314 /***************
|
|
315 * BAM sorting *
|
|
316 ***************/
|
|
317
|
|
318 #include <pthread.h>
|
|
319
|
|
320 typedef bam1_t *bam1_p;
|
|
321
|
|
322 static int change_SO(bam_header_t *h, const char *so)
|
|
323 {
|
|
324 char *p, *q, *beg = 0, *end = 0, *newtext;
|
|
325 if (h->l_text > 3) {
|
|
326 if (strncmp(h->text, "@HD", 3) == 0) {
|
|
327 if ((p = strchr(h->text, '\n')) == 0) return -1;
|
|
328 *p = '\0';
|
|
329 if ((q = strstr(h->text, "\tSO:")) != 0) {
|
|
330 *p = '\n'; // change back
|
|
331 if (strncmp(q + 4, so, p - q - 4) != 0) {
|
|
332 beg = q;
|
|
333 for (q += 4; *q != '\n' && *q != '\t'; ++q);
|
|
334 end = q;
|
|
335 } else return 0; // no need to change
|
|
336 } else beg = end = p, *p = '\n';
|
|
337 }
|
|
338 }
|
|
339 if (beg == 0) { // no @HD
|
|
340 h->l_text += strlen(so) + 15;
|
|
341 newtext = malloc(h->l_text + 1);
|
|
342 sprintf(newtext, "@HD\tVN:1.3\tSO:%s\n", so);
|
|
343 strcat(newtext, h->text);
|
|
344 } else { // has @HD but different or no SO
|
|
345 h->l_text = (beg - h->text) + (4 + strlen(so)) + (h->text + h->l_text - end);
|
|
346 newtext = malloc(h->l_text + 1);
|
|
347 strncpy(newtext, h->text, beg - h->text);
|
|
348 sprintf(newtext + (beg - h->text), "\tSO:%s", so);
|
|
349 strcat(newtext, end);
|
|
350 }
|
|
351 free(h->text);
|
|
352 h->text = newtext;
|
|
353 return 0;
|
|
354 }
|
|
355
|
|
356 static inline int bam1_lt(const bam1_p a, const bam1_p b)
|
|
357 {
|
|
358 if (g_is_by_qname) {
|
|
359 int t = strnum_cmp(bam1_qname(a), bam1_qname(b));
|
|
360 return (t < 0 || (t == 0 && (a->core.flag&0xc0) < (b->core.flag&0xc0)));
|
|
361 } 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)));
|
|
362 }
|
|
363 KSORT_INIT(sort, bam1_p, bam1_lt)
|
|
364
|
|
365 typedef struct {
|
|
366 size_t buf_len;
|
|
367 const char *prefix;
|
|
368 bam1_p *buf;
|
|
369 const bam_header_t *h;
|
|
370 int index;
|
|
371 } worker_t;
|
|
372
|
|
373 static void write_buffer(const char *fn, const char *mode, size_t l, bam1_p *buf, const bam_header_t *h, int n_threads)
|
|
374 {
|
|
375 size_t i;
|
|
376 bamFile fp;
|
|
377 fp = strcmp(fn, "-")? bam_open(fn, mode) : bam_dopen(fileno(stdout), mode);
|
|
378 if (fp == 0) return;
|
|
379 bam_header_write(fp, h);
|
|
380 if (n_threads > 1) bgzf_mt(fp, n_threads, 256);
|
|
381 for (i = 0; i < l; ++i)
|
|
382 bam_write1_core(fp, &buf[i]->core, buf[i]->data_len, buf[i]->data);
|
|
383 bam_close(fp);
|
|
384 }
|
|
385
|
|
386 static void *worker(void *data)
|
|
387 {
|
|
388 worker_t *w = (worker_t*)data;
|
|
389 char *name;
|
|
390 ks_mergesort(sort, w->buf_len, w->buf, 0);
|
|
391 name = (char*)calloc(strlen(w->prefix) + 20, 1);
|
|
392 sprintf(name, "%s.%.4d.bam", w->prefix, w->index);
|
|
393 write_buffer(name, "w1", w->buf_len, w->buf, w->h, 0);
|
|
394 free(name);
|
|
395 return 0;
|
|
396 }
|
|
397
|
|
398 static int sort_blocks(int n_files, size_t k, bam1_p *buf, const char *prefix, const bam_header_t *h, int n_threads)
|
|
399 {
|
|
400 int i;
|
|
401 size_t rest;
|
|
402 bam1_p *b;
|
|
403 pthread_t *tid;
|
|
404 pthread_attr_t attr;
|
|
405 worker_t *w;
|
|
406
|
|
407 if (n_threads < 1) n_threads = 1;
|
|
408 if (k < n_threads * 64) n_threads = 1; // use a single thread if we only sort a small batch of records
|
|
409 pthread_attr_init(&attr);
|
|
410 pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
|
|
411 w = calloc(n_threads, sizeof(worker_t));
|
|
412 tid = calloc(n_threads, sizeof(pthread_t));
|
|
413 b = buf; rest = k;
|
|
414 for (i = 0; i < n_threads; ++i) {
|
|
415 w[i].buf_len = rest / (n_threads - i);
|
|
416 w[i].buf = b;
|
|
417 w[i].prefix = prefix;
|
|
418 w[i].h = h;
|
|
419 w[i].index = n_files + i;
|
|
420 b += w[i].buf_len; rest -= w[i].buf_len;
|
|
421 pthread_create(&tid[i], &attr, worker, &w[i]);
|
|
422 }
|
|
423 for (i = 0; i < n_threads; ++i) pthread_join(tid[i], 0);
|
|
424 free(tid); free(w);
|
|
425 return n_files + n_threads;
|
|
426 }
|
|
427
|
|
428 /*!
|
|
429 @abstract Sort an unsorted BAM file based on the chromosome order
|
|
430 and the leftmost position of an alignment
|
|
431
|
|
432 @param is_by_qname whether to sort by query name
|
|
433 @param fn name of the file to be sorted
|
|
434 @param prefix prefix of the output and the temporary files; upon
|
|
435 sucessess, prefix.bam will be written.
|
|
436 @param max_mem approxiate maximum memory (very inaccurate)
|
|
437 @param full_path the given output path is the full path and not just the prefix
|
|
438
|
|
439 @discussion It may create multiple temporary subalignment files
|
|
440 and then merge them by calling bam_merge_core(). This function is
|
|
441 NOT thread safe.
|
|
442 */
|
|
443 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)
|
|
444 {
|
|
445 int ret, i, n_files = 0;
|
|
446 size_t mem, max_k, k, max_mem;
|
|
447 bam_header_t *header;
|
|
448 bamFile fp;
|
|
449 bam1_t *b, **buf;
|
|
450 char *fnout = 0;
|
|
451 char const *suffix = ".bam";
|
|
452 if (full_path) suffix += 4;
|
|
453
|
|
454 if (n_threads < 2) n_threads = 1;
|
|
455 g_is_by_qname = is_by_qname;
|
|
456 max_k = k = 0; mem = 0;
|
|
457 max_mem = _max_mem * n_threads;
|
|
458 buf = 0;
|
|
459 fp = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
|
|
460 if (fp == 0) {
|
|
461 fprintf(stderr, "[bam_sort_core] fail to open file %s\n", fn);
|
|
462 return;
|
|
463 }
|
|
464 header = bam_header_read(fp);
|
|
465 if (is_by_qname) change_SO(header, "queryname");
|
|
466 else change_SO(header, "coordinate");
|
|
467 // write sub files
|
|
468 for (;;) {
|
|
469 if (k == max_k) {
|
|
470 size_t old_max = max_k;
|
|
471 max_k = max_k? max_k<<1 : 0x10000;
|
|
472 buf = realloc(buf, max_k * sizeof(void*));
|
|
473 memset(buf + old_max, 0, sizeof(void*) * (max_k - old_max));
|
|
474 }
|
|
475 if (buf[k] == 0) buf[k] = (bam1_t*)calloc(1, sizeof(bam1_t));
|
|
476 b = buf[k];
|
|
477 if ((ret = bam_read1(fp, b)) < 0) break;
|
|
478 if (b->data_len < b->m_data>>2) { // shrink
|
|
479 b->m_data = b->data_len;
|
|
480 kroundup32(b->m_data);
|
|
481 b->data = realloc(b->data, b->m_data);
|
|
482 }
|
|
483 mem += sizeof(bam1_t) + b->m_data + sizeof(void*) + sizeof(void*); // two sizeof(void*) for the data allocated to pointer arrays
|
|
484 ++k;
|
|
485 if (mem >= max_mem) {
|
|
486 n_files = sort_blocks(n_files, k, buf, prefix, header, n_threads);
|
|
487 mem = k = 0;
|
|
488 }
|
|
489 }
|
|
490 if (ret != -1)
|
|
491 fprintf(stderr, "[bam_sort_core] truncated file. Continue anyway.\n");
|
|
492 // output file name
|
|
493 fnout = calloc(strlen(prefix) + 20, 1);
|
|
494 if (is_stdout) sprintf(fnout, "-");
|
|
495 else sprintf(fnout, "%s%s", prefix, suffix);
|
|
496 // write the final output
|
|
497 if (n_files == 0) { // a single block
|
|
498 char mode[8];
|
|
499 strcpy(mode, "w");
|
|
500 if (level >= 0) sprintf(mode + 1, "%d", level < 9? level : 9);
|
|
501 ks_mergesort(sort, k, buf, 0);
|
|
502 write_buffer(fnout, mode, k, buf, header, n_threads);
|
|
503 } else { // then merge
|
|
504 char **fns;
|
|
505 n_files = sort_blocks(n_files, k, buf, prefix, header, n_threads);
|
|
506 fprintf(stderr, "[bam_sort_core] merging from %d files...\n", n_files);
|
|
507 fns = (char**)calloc(n_files, sizeof(char*));
|
|
508 for (i = 0; i < n_files; ++i) {
|
|
509 fns[i] = (char*)calloc(strlen(prefix) + 20, 1);
|
|
510 sprintf(fns[i], "%s.%.4d%s", prefix, i, suffix);
|
|
511 }
|
|
512 bam_merge_core2(is_by_qname, fnout, 0, n_files, fns, 0, 0, n_threads, level);
|
|
513 for (i = 0; i < n_files; ++i) {
|
|
514 unlink(fns[i]);
|
|
515 free(fns[i]);
|
|
516 }
|
|
517 free(fns);
|
|
518 }
|
|
519 free(fnout);
|
|
520 // free
|
|
521 for (k = 0; k < max_k; ++k) {
|
|
522 if (!buf[k]) continue;
|
|
523 free(buf[k]->data);
|
|
524 free(buf[k]);
|
|
525 }
|
|
526 free(buf);
|
|
527 bam_header_destroy(header);
|
|
528 bam_close(fp);
|
|
529 }
|
|
530
|
|
531 void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem)
|
|
532 {
|
|
533 bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0, 0, -1, 0);
|
|
534 }
|
|
535
|
|
536 int bam_sort(int argc, char *argv[])
|
|
537 {
|
|
538 size_t max_mem = 768<<20; // 512MB
|
|
539 int c, is_by_qname = 0, is_stdout = 0, n_threads = 0, level = -1, full_path = 0;
|
|
540 while ((c = getopt(argc, argv, "fnom:@:l:")) >= 0) {
|
|
541 switch (c) {
|
|
542 case 'f': full_path = 1; break;
|
|
543 case 'o': is_stdout = 1; break;
|
|
544 case 'n': is_by_qname = 1; break;
|
|
545 case 'm': {
|
|
546 char *q;
|
|
547 max_mem = strtol(optarg, &q, 0);
|
|
548 if (*q == 'k' || *q == 'K') max_mem <<= 10;
|
|
549 else if (*q == 'm' || *q == 'M') max_mem <<= 20;
|
|
550 else if (*q == 'g' || *q == 'G') max_mem <<= 30;
|
|
551 break;
|
|
552 }
|
|
553 case '@': n_threads = atoi(optarg); break;
|
|
554 case 'l': level = atoi(optarg); break;
|
|
555 }
|
|
556 }
|
|
557 if (optind + 2 > argc) {
|
|
558 fprintf(stderr, "\n");
|
|
559 fprintf(stderr, "Usage: samtools sort [options] <in.bam> <out.prefix>\n\n");
|
|
560 fprintf(stderr, "Options: -n sort by read name\n");
|
|
561 fprintf(stderr, " -f use <out.prefix> as full file name instead of prefix\n");
|
|
562 fprintf(stderr, " -o final output to stdout\n");
|
|
563 fprintf(stderr, " -l INT compression level, from 0 to 9 [-1]\n");
|
|
564 fprintf(stderr, " -@ INT number of sorting and compression threads [1]\n");
|
|
565 fprintf(stderr, " -m INT max memory per thread; suffix K/M/G recognized [768M]\n");
|
|
566 fprintf(stderr, "\n");
|
|
567 return 1;
|
|
568 }
|
|
569 bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout, n_threads, level, full_path);
|
|
570 return 0;
|
|
571 }
|