Mercurial > repos > ryanmorin > nextgen_variant_identification
comparison SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/bam_index.c @ 0:74f5ea818cea
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author | ryanmorin |
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date | Wed, 12 Oct 2011 19:50:38 -0400 |
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1 #include <ctype.h> | |
2 #include <assert.h> | |
3 #include "bam.h" | |
4 #include "khash.h" | |
5 #include "ksort.h" | |
6 #include "bam_endian.h" | |
7 #ifdef _USE_KNETFILE | |
8 #include "knetfile.h" | |
9 #endif | |
10 | |
11 /*! | |
12 @header | |
13 | |
14 Alignment indexing. Before indexing, BAM must be sorted based on the | |
15 leftmost coordinate of alignments. In indexing, BAM uses two indices: | |
16 a UCSC binning index and a simple linear index. The binning index is | |
17 efficient for alignments spanning long distance, while the auxiliary | |
18 linear index helps to reduce unnecessary seek calls especially for | |
19 short alignments. | |
20 | |
21 The UCSC binning scheme was suggested by Richard Durbin and Lincoln | |
22 Stein and is explained by Kent et al. (2002). In this scheme, each bin | |
23 represents a contiguous genomic region which can be fully contained in | |
24 another bin; each alignment is associated with a bin which represents | |
25 the smallest region containing the entire alignment. The binning | |
26 scheme is essentially another representation of R-tree. A distinct bin | |
27 uniquely corresponds to a distinct internal node in a R-tree. Bin A is | |
28 a child of Bin B if region A is contained in B. | |
29 | |
30 In BAM, each bin may span 2^29, 2^26, 2^23, 2^20, 2^17 or 2^14 bp. Bin | |
31 0 spans a 512Mbp region, bins 1-8 span 64Mbp, 9-72 8Mbp, 73-584 1Mbp, | |
32 585-4680 128Kbp and bins 4681-37449 span 16Kbp regions. If we want to | |
33 find the alignments overlapped with a region [rbeg,rend), we need to | |
34 calculate the list of bins that may be overlapped the region and test | |
35 the alignments in the bins to confirm the overlaps. If the specified | |
36 region is short, typically only a few alignments in six bins need to | |
37 be retrieved. The overlapping alignments can be quickly fetched. | |
38 | |
39 */ | |
40 | |
41 #define BAM_MIN_CHUNK_GAP 32768 | |
42 // 1<<14 is the size of minimum bin. | |
43 #define BAM_LIDX_SHIFT 14 | |
44 | |
45 typedef struct { | |
46 uint64_t u, v; | |
47 } pair64_t; | |
48 | |
49 #define pair64_lt(a,b) ((a).u < (b).u) | |
50 KSORT_INIT(off, pair64_t, pair64_lt) | |
51 | |
52 typedef struct { | |
53 uint32_t m, n; | |
54 pair64_t *list; | |
55 } bam_binlist_t; | |
56 | |
57 typedef struct { | |
58 int32_t n, m; | |
59 uint64_t *offset; | |
60 } bam_lidx_t; | |
61 | |
62 KHASH_MAP_INIT_INT(i, bam_binlist_t) | |
63 | |
64 struct __bam_index_t { | |
65 int32_t n; | |
66 khash_t(i) **index; | |
67 bam_lidx_t *index2; | |
68 }; | |
69 | |
70 // requirement: len <= LEN_MASK | |
71 static inline void insert_offset(khash_t(i) *h, int bin, uint64_t beg, uint64_t end) | |
72 { | |
73 khint_t k; | |
74 bam_binlist_t *l; | |
75 int ret; | |
76 k = kh_put(i, h, bin, &ret); | |
77 l = &kh_value(h, k); | |
78 if (ret) { // not present | |
79 l->m = 1; l->n = 0; | |
80 l->list = (pair64_t*)calloc(l->m, 16); | |
81 } | |
82 if (l->n == l->m) { | |
83 l->m <<= 1; | |
84 l->list = (pair64_t*)realloc(l->list, l->m * 16); | |
85 } | |
86 l->list[l->n].u = beg; l->list[l->n++].v = end; | |
87 } | |
88 | |
89 static inline void insert_offset2(bam_lidx_t *index2, bam1_t *b, uint64_t offset) | |
90 { | |
91 int i, beg, end; | |
92 beg = b->core.pos >> BAM_LIDX_SHIFT; | |
93 end = (bam_calend(&b->core, bam1_cigar(b)) - 1) >> BAM_LIDX_SHIFT; | |
94 if (index2->m < end + 1) { | |
95 int old_m = index2->m; | |
96 index2->m = end + 1; | |
97 kroundup32(index2->m); | |
98 index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8); | |
99 memset(index2->offset + old_m, 0, 8 * (index2->m - old_m)); | |
100 } | |
101 for (i = beg + 1; i <= end; ++i) | |
102 if (index2->offset[i] == 0) index2->offset[i] = offset; | |
103 index2->n = end + 1; | |
104 } | |
105 | |
106 static void merge_chunks(bam_index_t *idx) | |
107 { | |
108 #if defined(BAM_TRUE_OFFSET) || defined(BAM_VIRTUAL_OFFSET16) | |
109 khash_t(i) *index; | |
110 int i, l, m; | |
111 khint_t k; | |
112 for (i = 0; i < idx->n; ++i) { | |
113 index = idx->index[i]; | |
114 for (k = kh_begin(index); k != kh_end(index); ++k) { | |
115 bam_binlist_t *p; | |
116 if (!kh_exist(index, k)) continue; | |
117 p = &kh_value(index, k); | |
118 m = 0; | |
119 for (l = 1; l < p->n; ++l) { | |
120 #ifdef BAM_TRUE_OFFSET | |
121 if (p->list[m].v + BAM_MIN_CHUNK_GAP > p->list[l].u) p->list[m].v = p->list[l].v; | |
122 #else | |
123 if (p->list[m].v>>16 == p->list[l].u>>16) p->list[m].v = p->list[l].v; | |
124 #endif | |
125 else p->list[++m] = p->list[l]; | |
126 } // ~for(l) | |
127 p->n = m + 1; | |
128 } // ~for(k) | |
129 } // ~for(i) | |
130 #endif // defined(BAM_TRUE_OFFSET) || defined(BAM_BGZF) | |
131 } | |
132 | |
133 bam_index_t *bam_index_core(bamFile fp) | |
134 { | |
135 bam1_t *b; | |
136 bam_header_t *h; | |
137 int i, ret; | |
138 bam_index_t *idx; | |
139 uint32_t last_bin, save_bin; | |
140 int32_t last_coor, last_tid, save_tid; | |
141 bam1_core_t *c; | |
142 uint64_t save_off, last_off; | |
143 | |
144 idx = (bam_index_t*)calloc(1, sizeof(bam_index_t)); | |
145 b = (bam1_t*)calloc(1, sizeof(bam1_t)); | |
146 h = bam_header_read(fp); | |
147 c = &b->core; | |
148 | |
149 idx->n = h->n_targets; | |
150 bam_header_destroy(h); | |
151 idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*)); | |
152 for (i = 0; i < idx->n; ++i) idx->index[i] = kh_init(i); | |
153 idx->index2 = (bam_lidx_t*)calloc(idx->n, sizeof(bam_lidx_t)); | |
154 | |
155 save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | |
156 save_off = last_off = bam_tell(fp); last_coor = 0xffffffffu; | |
157 while ((ret = bam_read1(fp, b)) >= 0) { | |
158 if (last_tid != c->tid) { // change of chromosomes | |
159 last_tid = c->tid; | |
160 last_bin = 0xffffffffu; | |
161 } else if (last_coor > c->pos) { | |
162 fprintf(stderr, "[bam_index_core] the alignment is not sorted (%s): %u > %u in %d-th chr\n", | |
163 bam1_qname(b), last_coor, c->pos, c->tid+1); | |
164 exit(1); | |
165 } | |
166 if (b->core.tid >= 0 && b->core.bin < 4681) insert_offset2(&idx->index2[b->core.tid], b, last_off); | |
167 if (c->bin != last_bin) { // then possibly write the binning index | |
168 if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record | |
169 insert_offset(idx->index[save_tid], save_bin, save_off, last_off); | |
170 save_off = last_off; | |
171 save_bin = last_bin = c->bin; | |
172 save_tid = c->tid; | |
173 if (save_tid < 0) break; | |
174 } | |
175 if (bam_tell(fp) <= last_off) { | |
176 fprintf(stderr, "[bam_index_core] bug in BGZF/RAZF: %llx < %llx\n", | |
177 (unsigned long long)bam_tell(fp), (unsigned long long)last_off); | |
178 exit(1); | |
179 } | |
180 last_off = bam_tell(fp); | |
181 last_coor = b->core.pos; | |
182 } | |
183 if (save_tid >= 0) insert_offset(idx->index[save_tid], save_bin, save_off, bam_tell(fp)); | |
184 merge_chunks(idx); | |
185 if (ret < -1) fprintf(stderr, "[bam_index_core] truncated file? Continue anyway. (%d)\n", ret); | |
186 free(b->data); free(b); | |
187 return idx; | |
188 } | |
189 | |
190 void bam_index_destroy(bam_index_t *idx) | |
191 { | |
192 khint_t k; | |
193 int i; | |
194 if (idx == 0) return; | |
195 for (i = 0; i < idx->n; ++i) { | |
196 khash_t(i) *index = idx->index[i]; | |
197 bam_lidx_t *index2 = idx->index2 + i; | |
198 for (k = kh_begin(index); k != kh_end(index); ++k) { | |
199 if (kh_exist(index, k)) | |
200 free(kh_value(index, k).list); | |
201 } | |
202 kh_destroy(i, index); | |
203 free(index2->offset); | |
204 } | |
205 free(idx->index); free(idx->index2); | |
206 free(idx); | |
207 } | |
208 | |
209 void bam_index_save(const bam_index_t *idx, FILE *fp) | |
210 { | |
211 int32_t i, size; | |
212 khint_t k; | |
213 fwrite("BAI\1", 1, 4, fp); | |
214 if (bam_is_be) { | |
215 uint32_t x = idx->n; | |
216 fwrite(bam_swap_endian_4p(&x), 4, 1, fp); | |
217 } else fwrite(&idx->n, 4, 1, fp); | |
218 for (i = 0; i < idx->n; ++i) { | |
219 khash_t(i) *index = idx->index[i]; | |
220 bam_lidx_t *index2 = idx->index2 + i; | |
221 // write binning index | |
222 size = kh_size(index); | |
223 if (bam_is_be) { // big endian | |
224 uint32_t x = size; | |
225 fwrite(bam_swap_endian_4p(&x), 4, 1, fp); | |
226 } else fwrite(&size, 4, 1, fp); | |
227 for (k = kh_begin(index); k != kh_end(index); ++k) { | |
228 if (kh_exist(index, k)) { | |
229 bam_binlist_t *p = &kh_value(index, k); | |
230 if (bam_is_be) { // big endian | |
231 uint32_t x; | |
232 x = kh_key(index, k); fwrite(bam_swap_endian_4p(&x), 4, 1, fp); | |
233 x = p->n; fwrite(bam_swap_endian_4p(&x), 4, 1, fp); | |
234 for (x = 0; (int)x < p->n; ++x) { | |
235 bam_swap_endian_8p(&p->list[x].u); | |
236 bam_swap_endian_8p(&p->list[x].v); | |
237 } | |
238 fwrite(p->list, 16, p->n, fp); | |
239 for (x = 0; (int)x < p->n; ++x) { | |
240 bam_swap_endian_8p(&p->list[x].u); | |
241 bam_swap_endian_8p(&p->list[x].v); | |
242 } | |
243 } else { | |
244 fwrite(&kh_key(index, k), 4, 1, fp); | |
245 fwrite(&p->n, 4, 1, fp); | |
246 fwrite(p->list, 16, p->n, fp); | |
247 } | |
248 } | |
249 } | |
250 // write linear index (index2) | |
251 if (bam_is_be) { | |
252 int x = index2->n; | |
253 fwrite(bam_swap_endian_4p(&x), 4, 1, fp); | |
254 } else fwrite(&index2->n, 4, 1, fp); | |
255 if (bam_is_be) { // big endian | |
256 int x; | |
257 for (x = 0; (int)x < index2->n; ++x) | |
258 bam_swap_endian_8p(&index2->offset[x]); | |
259 fwrite(index2->offset, 8, index2->n, fp); | |
260 for (x = 0; (int)x < index2->n; ++x) | |
261 bam_swap_endian_8p(&index2->offset[x]); | |
262 } else fwrite(index2->offset, 8, index2->n, fp); | |
263 } | |
264 fflush(fp); | |
265 } | |
266 | |
267 static bam_index_t *bam_index_load_core(FILE *fp) | |
268 { | |
269 int i; | |
270 char magic[4]; | |
271 bam_index_t *idx; | |
272 if (fp == 0) { | |
273 fprintf(stderr, "[bam_index_load_core] fail to load index.\n"); | |
274 return 0; | |
275 } | |
276 fread(magic, 1, 4, fp); | |
277 if (strncmp(magic, "BAI\1", 4)) { | |
278 fprintf(stderr, "[bam_index_load] wrong magic number.\n"); | |
279 fclose(fp); | |
280 return 0; | |
281 } | |
282 idx = (bam_index_t*)calloc(1, sizeof(bam_index_t)); | |
283 fread(&idx->n, 4, 1, fp); | |
284 if (bam_is_be) bam_swap_endian_4p(&idx->n); | |
285 idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*)); | |
286 idx->index2 = (bam_lidx_t*)calloc(idx->n, sizeof(bam_lidx_t)); | |
287 for (i = 0; i < idx->n; ++i) { | |
288 khash_t(i) *index; | |
289 bam_lidx_t *index2 = idx->index2 + i; | |
290 uint32_t key, size; | |
291 khint_t k; | |
292 int j, ret; | |
293 bam_binlist_t *p; | |
294 index = idx->index[i] = kh_init(i); | |
295 // load binning index | |
296 fread(&size, 4, 1, fp); | |
297 if (bam_is_be) bam_swap_endian_4p(&size); | |
298 for (j = 0; j < (int)size; ++j) { | |
299 fread(&key, 4, 1, fp); | |
300 if (bam_is_be) bam_swap_endian_4p(&key); | |
301 k = kh_put(i, index, key, &ret); | |
302 p = &kh_value(index, k); | |
303 fread(&p->n, 4, 1, fp); | |
304 if (bam_is_be) bam_swap_endian_4p(&p->n); | |
305 p->m = p->n; | |
306 p->list = (pair64_t*)malloc(p->m * 16); | |
307 fread(p->list, 16, p->n, fp); | |
308 if (bam_is_be) { | |
309 int x; | |
310 for (x = 0; x < p->n; ++x) { | |
311 bam_swap_endian_8p(&p->list[x].u); | |
312 bam_swap_endian_8p(&p->list[x].v); | |
313 } | |
314 } | |
315 } | |
316 // load linear index | |
317 fread(&index2->n, 4, 1, fp); | |
318 if (bam_is_be) bam_swap_endian_4p(&index2->n); | |
319 index2->m = index2->n; | |
320 index2->offset = (uint64_t*)calloc(index2->m, 8); | |
321 fread(index2->offset, index2->n, 8, fp); | |
322 if (bam_is_be) | |
323 for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]); | |
324 } | |
325 return idx; | |
326 } | |
327 | |
328 bam_index_t *bam_index_load_local(const char *_fn) | |
329 { | |
330 FILE *fp; | |
331 char *fnidx, *fn; | |
332 | |
333 if (strstr(_fn, "ftp://") == _fn || strstr(_fn, "http://") == _fn) { | |
334 const char *p; | |
335 int l = strlen(_fn); | |
336 for (p = _fn + l - 1; p >= _fn; --p) | |
337 if (*p == '/') break; | |
338 fn = strdup(p + 1); | |
339 } else fn = strdup(_fn); | |
340 fnidx = (char*)calloc(strlen(fn) + 5, 1); | |
341 strcpy(fnidx, fn); strcat(fnidx, ".bai"); | |
342 fp = fopen(fnidx, "r"); | |
343 if (fp == 0) { // try "{base}.bai" | |
344 char *s = strstr(fn, "bam"); | |
345 if (s == fn + strlen(fn) - 3) { | |
346 strcpy(fnidx, fn); | |
347 fnidx[strlen(fn)-1] = 'i'; | |
348 fp = fopen(fnidx, "r"); | |
349 } | |
350 } | |
351 free(fnidx); free(fn); | |
352 if (fp) { | |
353 bam_index_t *idx = bam_index_load_core(fp); | |
354 fclose(fp); | |
355 return idx; | |
356 } else return 0; | |
357 } | |
358 | |
359 #ifdef _USE_KNETFILE | |
360 static void download_from_remote(const char *url) | |
361 { | |
362 const int buf_size = 1 * 1024 * 1024; | |
363 char *fn; | |
364 FILE *fp; | |
365 uint8_t *buf; | |
366 knetFile *fp_remote; | |
367 int l; | |
368 if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return; | |
369 l = strlen(url); | |
370 for (fn = (char*)url + l - 1; fn >= url; --fn) | |
371 if (*fn == '/') break; | |
372 ++fn; // fn now points to the file name | |
373 fp_remote = knet_open(url, "r"); | |
374 if (fp_remote == 0) { | |
375 fprintf(stderr, "[download_from_remote] fail to open remote file.\n"); | |
376 return; | |
377 } | |
378 if ((fp = fopen(fn, "w")) == 0) { | |
379 fprintf(stderr, "[download_from_remote] fail to create file in the working directory.\n"); | |
380 knet_close(fp_remote); | |
381 return; | |
382 } | |
383 buf = (uint8_t*)calloc(buf_size, 1); | |
384 while ((l = knet_read(fp_remote, buf, buf_size)) != 0) | |
385 fwrite(buf, 1, l, fp); | |
386 free(buf); | |
387 fclose(fp); | |
388 knet_close(fp_remote); | |
389 } | |
390 #else | |
391 static void download_from_remote(const char *url) | |
392 { | |
393 return; | |
394 } | |
395 #endif | |
396 | |
397 bam_index_t *bam_index_load(const char *fn) | |
398 { | |
399 bam_index_t *idx; | |
400 idx = bam_index_load_local(fn); | |
401 if (idx == 0 && (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)) { | |
402 char *fnidx = calloc(strlen(fn) + 5, 1); | |
403 strcat(strcpy(fnidx, fn), ".bai"); | |
404 fprintf(stderr, "[bam_index_load] attempting to download the remote index file.\n"); | |
405 download_from_remote(fnidx); | |
406 idx = bam_index_load_local(fn); | |
407 } | |
408 if (idx == 0) fprintf(stderr, "[bam_index_load] fail to load BAM index.\n"); | |
409 return idx; | |
410 } | |
411 | |
412 int bam_index_build2(const char *fn, const char *_fnidx) | |
413 { | |
414 char *fnidx; | |
415 FILE *fpidx; | |
416 bamFile fp; | |
417 bam_index_t *idx; | |
418 if ((fp = bam_open(fn, "r")) == 0) { | |
419 fprintf(stderr, "[bam_index_build2] fail to open the BAM file.\n"); | |
420 return -1; | |
421 } | |
422 idx = bam_index_core(fp); | |
423 bam_close(fp); | |
424 if (_fnidx == 0) { | |
425 fnidx = (char*)calloc(strlen(fn) + 5, 1); | |
426 strcpy(fnidx, fn); strcat(fnidx, ".bai"); | |
427 } else fnidx = strdup(_fnidx); | |
428 fpidx = fopen(fnidx, "w"); | |
429 if (fpidx == 0) { | |
430 fprintf(stderr, "[bam_index_build2] fail to create the index file.\n"); | |
431 free(fnidx); | |
432 return -1; | |
433 } | |
434 bam_index_save(idx, fpidx); | |
435 bam_index_destroy(idx); | |
436 fclose(fpidx); | |
437 free(fnidx); | |
438 return 0; | |
439 } | |
440 | |
441 int bam_index_build(const char *fn) | |
442 { | |
443 return bam_index_build2(fn, 0); | |
444 } | |
445 | |
446 int bam_index(int argc, char *argv[]) | |
447 { | |
448 if (argc < 2) { | |
449 fprintf(stderr, "Usage: samtools index <in.bam> [<out.index>]\n"); | |
450 return 1; | |
451 } | |
452 if (argc >= 3) bam_index_build2(argv[1], argv[2]); | |
453 else bam_index_build(argv[1]); | |
454 return 0; | |
455 } | |
456 | |
457 #define MAX_BIN 37450 // =(8^6-1)/7+1 | |
458 | |
459 static inline int reg2bins(uint32_t beg, uint32_t end, uint16_t list[MAX_BIN]) | |
460 { | |
461 int i = 0, k; | |
462 --end; | |
463 list[i++] = 0; | |
464 for (k = 1 + (beg>>26); k <= 1 + (end>>26); ++k) list[i++] = k; | |
465 for (k = 9 + (beg>>23); k <= 9 + (end>>23); ++k) list[i++] = k; | |
466 for (k = 73 + (beg>>20); k <= 73 + (end>>20); ++k) list[i++] = k; | |
467 for (k = 585 + (beg>>17); k <= 585 + (end>>17); ++k) list[i++] = k; | |
468 for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) list[i++] = k; | |
469 return i; | |
470 } | |
471 | |
472 static inline int is_overlap(uint32_t beg, uint32_t end, const bam1_t *b) | |
473 { | |
474 uint32_t rbeg = b->core.pos; | |
475 uint32_t rend = b->core.n_cigar? bam_calend(&b->core, bam1_cigar(b)) : b->core.pos + 1; | |
476 return (rend > beg && rbeg < end); | |
477 } | |
478 | |
479 int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func) | |
480 { | |
481 uint16_t *bins; | |
482 int i, n_bins, n_off; | |
483 pair64_t *off; | |
484 khint_t k; | |
485 khash_t(i) *index; | |
486 uint64_t min_off; | |
487 | |
488 bins = (uint16_t*)calloc(MAX_BIN, 2); | |
489 n_bins = reg2bins(beg, end, bins); | |
490 index = idx->index[tid]; | |
491 min_off = (beg>>BAM_LIDX_SHIFT >= idx->index2[tid].n)? 0 : idx->index2[tid].offset[beg>>BAM_LIDX_SHIFT]; | |
492 for (i = n_off = 0; i < n_bins; ++i) { | |
493 if ((k = kh_get(i, index, bins[i])) != kh_end(index)) | |
494 n_off += kh_value(index, k).n; | |
495 } | |
496 if (n_off == 0) { | |
497 free(bins); return 0; | |
498 } | |
499 off = (pair64_t*)calloc(n_off, 16); | |
500 for (i = n_off = 0; i < n_bins; ++i) { | |
501 if ((k = kh_get(i, index, bins[i])) != kh_end(index)) { | |
502 int j; | |
503 bam_binlist_t *p = &kh_value(index, k); | |
504 for (j = 0; j < p->n; ++j) | |
505 if (p->list[j].v > min_off) off[n_off++] = p->list[j]; | |
506 } | |
507 } | |
508 free(bins); | |
509 { | |
510 bam1_t *b; | |
511 int l, ret, n_seeks; | |
512 uint64_t curr_off; | |
513 b = (bam1_t*)calloc(1, sizeof(bam1_t)); | |
514 ks_introsort(off, n_off, off); | |
515 // resolve completely contained adjacent blocks | |
516 for (i = 1, l = 0; i < n_off; ++i) | |
517 if (off[l].v < off[i].v) | |
518 off[++l] = off[i]; | |
519 n_off = l + 1; | |
520 // resolve overlaps between adjacent blocks; this may happen due to the merge in indexing | |
521 for (i = 1; i < n_off; ++i) | |
522 if (off[i-1].v >= off[i].u) off[i-1].v = off[i].u; | |
523 { // merge adjacent blocks | |
524 #if defined(BAM_TRUE_OFFSET) || defined(BAM_VIRTUAL_OFFSET16) | |
525 for (i = 1, l = 0; i < n_off; ++i) { | |
526 #ifdef BAM_TRUE_OFFSET | |
527 if (off[l].v + BAM_MIN_CHUNK_GAP > off[i].u) off[l].v = off[i].v; | |
528 #else | |
529 if (off[l].v>>16 == off[i].u>>16) off[l].v = off[i].v; | |
530 #endif | |
531 else off[++l] = off[i]; | |
532 } | |
533 n_off = l + 1; | |
534 #endif | |
535 } | |
536 // retrive alignments | |
537 n_seeks = 0; i = -1; curr_off = 0; | |
538 for (;;) { | |
539 if (curr_off == 0 || curr_off >= off[i].v) { // then jump to the next chunk | |
540 if (i == n_off - 1) break; // no more chunks | |
541 if (i >= 0) assert(curr_off == off[i].v); // otherwise bug | |
542 if (i < 0 || off[i].v != off[i+1].u) { // not adjacent chunks; then seek | |
543 bam_seek(fp, off[i+1].u, SEEK_SET); | |
544 curr_off = bam_tell(fp); | |
545 ++n_seeks; | |
546 } | |
547 ++i; | |
548 } | |
549 if ((ret = bam_read1(fp, b)) > 0) { | |
550 curr_off = bam_tell(fp); | |
551 if (b->core.tid != tid || b->core.pos >= end) break; // no need to proceed | |
552 else if (is_overlap(beg, end, b)) func(b, data); | |
553 } else break; // end of file | |
554 } | |
555 // fprintf(stderr, "[bam_fetch] # seek calls: %d\n", n_seeks); | |
556 bam_destroy1(b); | |
557 } | |
558 free(off); | |
559 return 0; | |
560 } |