7 #include "bam_endian.h"
13 #define TAD_MIN_CHUNK_GAP 32768
14 // 1<<14 is the size of minimum bin.
15 #define TAD_LIDX_SHIFT 14
21 #define pair64_lt(a,b) ((a).u < (b).u)
22 KSORT_INIT(offt, pair64_t, pair64_lt)
34 KHASH_MAP_INIT_INT(i, ti_binlist_t)
35 KHASH_MAP_INIT_STR(s, int)
46 int from_first; // read from the first record; no random access
47 int tid, beg, end, n_off, i, finished;
50 const ti_index_t *idx;
55 int tid, beg, end, bin;
58 ti_conf_t ti_conf_gff = { 0, 1, 4, 5, '#', 0 };
59 ti_conf_t ti_conf_bed = { TI_FLAG_UCSC, 1, 2, 3, '#', 0 };
60 ti_conf_t ti_conf_psltbl = { TI_FLAG_UCSC, 15, 17, 18, '#', 0 };
61 ti_conf_t ti_conf_sam = { TI_PRESET_SAM, 3, 4, 0, '@', 0 };
62 ti_conf_t ti_conf_vcf = { TI_PRESET_VCF, 1, 2, 0, '#', 0 };
69 int ti_readline(BGZF *fp, kstring_t *str)
73 while ((c = bgzf_getc(fp)) >= 0 && c != '\n') {
75 if (c != '\r') kputc(c, str);
77 if (c < 0 && l == 0) return -1; // end of file
82 /* Below is a faster implementation largely equivalent to the one
83 * commented out above. */
84 int ti_readline(BGZF *fp, kstring_t *str)
87 unsigned char *buf = (unsigned char*)fp->uncompressed_block;
90 if (fp->block_offset >= fp->block_length) {
91 if (bgzf_read_block(fp) != 0) { state = -2; break; }
92 if (fp->block_length == 0) { state = -1; break; }
94 for (l = fp->block_offset; l < fp->block_length && buf[l] != '\n'; ++l);
95 if (l < fp->block_length) state = 1;
96 l -= fp->block_offset;
97 if (str->l + l + 1 >= str->m) {
98 str->m = str->l + l + 2;
100 str->s = (char*)realloc(str->s, str->m);
102 memcpy(str->s + str->l, buf + fp->block_offset, l);
104 fp->block_offset += l + 1;
105 if (fp->block_offset >= fp->block_length) {
107 fp->block_address = knet_tell(fp->x.fpr);
109 fp->block_address = ftello(fp->file);
111 fp->block_offset = 0;
112 fp->block_length = 0;
114 } while (state == 0);
115 if (str->l == 0 && state < 0) return state;
120 /*************************************
121 * get the interval from a data line *
122 *************************************/
124 static inline int ti_reg2bin(uint32_t beg, uint32_t end)
127 if (beg>>14 == end>>14) return 4681 + (beg>>14);
128 if (beg>>17 == end>>17) return 585 + (beg>>17);
129 if (beg>>20 == end>>20) return 73 + (beg>>20);
130 if (beg>>23 == end>>23) return 9 + (beg>>23);
131 if (beg>>26 == end>>26) return 1 + (beg>>26);
135 static int get_tid(ti_index_t *idx, const char *ss)
139 k = kh_get(s, idx->tname, ss);
140 if (k == kh_end(idx->tname)) { // a new target sequence
142 // update idx->n, ->max, ->index and ->index2
143 if (idx->n == idx->max) {
144 idx->max = idx->max? idx->max<<1 : 8;
145 idx->index = realloc(idx->index, idx->max * sizeof(void*));
146 idx->index2 = realloc(idx->index2, idx->max * sizeof(ti_lidx_t));
148 memset(&idx->index2[idx->n], 0, sizeof(ti_lidx_t));
149 idx->index[idx->n++] = kh_init(i);
151 tid = size = kh_size(idx->tname);
152 k = kh_put(s, idx->tname, strdup(ss), &ret);
153 kh_value(idx->tname, k) = size;
154 assert(idx->n == kh_size(idx->tname));
155 } else tid = kh_value(idx->tname, k);
159 static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
161 int i, b = 0, id = 1;
163 intv->tid = intv->beg = intv->end = intv->bin = -1;
164 for (i = 0; i <= str->l; ++i) {
165 if (str->s[i] == '\t' || str->s[i] == 0) {
166 if (id == idx->conf.sc) {
168 intv->tid = get_tid(idx, str->s + b);
169 if (i != str->l) str->s[i] = '\t';
170 } else if (id == idx->conf.bc) {
171 // here ->beg is 0-based.
172 intv->beg = intv->end = strtol(str->s + b, &s, 0);
173 if (!(idx->conf.preset&TI_FLAG_UCSC)) --intv->beg;
175 if (intv->beg < 0) intv->beg = 0;
176 if (intv->end < 1) intv->end = 1;
178 if ((idx->conf.preset&0xffff) == TI_PRESET_GENERIC) {
179 if (id == idx->conf.ec) intv->end = strtol(str->s + b, &s, 0);
180 } else if ((idx->conf.preset&0xffff) == TI_PRESET_SAM) {
181 if (id == 6) { // CIGAR
184 for (s = str->s + b; s < str->s + i;) {
185 long x = strtol(s, &t, 10);
187 if (op == 'M' || op == 'D' || op == 'N') l += x;
191 intv->end = intv->beg + l;
193 } else if ((idx->conf.preset&0xffff) == TI_PRESET_VCF) {
194 // FIXME: the following is NOT tested and is likely to be buggy
196 if (b < i) intv->end = intv->beg + (i - b);
197 } else if (id == 8) { // look for "END="
200 s = strstr(str->s + b, "END=");
201 if (s == str->s + b) s += 4;
203 s = strstr(str->s + b, ";END=");
206 if (s) intv->end = strtol(s, &s, 0);
215 if (intv->tid < 0 || intv->beg < 0 || intv->end < 0) return -1;
216 intv->bin = ti_reg2bin(intv->beg, intv->end);
224 // requirement: len <= LEN_MASK
225 static inline void insert_offset(khash_t(i) *h, int bin, uint64_t beg, uint64_t end)
230 k = kh_put(i, h, bin, &ret);
232 if (ret) { // not present
234 l->list = (pair64_t*)calloc(l->m, 16);
238 l->list = (pair64_t*)realloc(l->list, l->m * 16);
240 l->list[l->n].u = beg; l->list[l->n++].v = end;
243 static inline void insert_offset2(ti_lidx_t *index2, int _beg, int _end, uint64_t offset)
246 beg = _beg >> TAD_LIDX_SHIFT;
247 end = (_end - 1) >> TAD_LIDX_SHIFT;
248 if (index2->m < end + 1) {
249 int old_m = index2->m;
251 kroundup32(index2->m);
252 index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8);
253 memset(index2->offset + old_m, 0, 8 * (index2->m - old_m));
256 if (index2->offset[beg] == 0) index2->offset[beg] = offset;
258 for (i = beg; i <= end; ++i)
259 if (index2->offset[i] == 0) index2->offset[i] = offset;
261 if (index2->n < end + 1) index2->n = end + 1;
264 static void merge_chunks(ti_index_t *idx)
269 for (i = 0; i < idx->n; ++i) {
270 index = idx->index[i];
271 for (k = kh_begin(index); k != kh_end(index); ++k) {
273 if (!kh_exist(index, k)) continue;
274 p = &kh_value(index, k);
276 for (l = 1; l < p->n; ++l) {
277 if (p->list[m].v>>16 == p->list[l].u>>16) p->list[m].v = p->list[l].v;
278 else p->list[++m] = p->list[l];
285 static void fill_missing(ti_index_t *idx)
288 for (i = 0; i < idx->n; ++i) {
289 ti_lidx_t *idx2 = &idx->index2[i];
290 for (j = 1; j < idx2->n; ++j)
291 if (idx2->offset[j] == 0)
292 idx2->offset[j] = idx2->offset[j-1];
296 ti_index_t *ti_index_core(BGZF *fp, const ti_conf_t *conf)
300 uint32_t last_bin, save_bin;
301 int32_t last_coor, last_tid, save_tid;
302 uint64_t save_off, last_off, lineno = 0;
305 str = calloc(1, sizeof(kstring_t));
307 idx = (ti_index_t*)calloc(1, sizeof(ti_index_t));
309 idx->n = idx->max = 0;
310 idx->tname = kh_init(s);
314 save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
315 save_off = last_off = bgzf_tell(fp); last_coor = 0xffffffffu;
316 while ((ret = ti_readline(fp, str)) >= 0) {
319 if (lineno <= idx->conf.line_skip || str->s[0] == idx->conf.meta_char) {
320 last_off = bgzf_tell(fp);
323 get_intv(idx, str, &intv);
324 if (last_tid != intv.tid) { // change of chromosomes
326 last_bin = 0xffffffffu;
327 } else if (last_coor > intv.beg) {
328 fprintf(stderr, "[ti_index_core] the file out of order at line %llu\n", (unsigned long long)lineno);
331 insert_offset2(&idx->index2[intv.tid], intv.beg, intv.end, last_off);
332 if (intv.bin != last_bin) { // then possibly write the binning index
333 if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record
334 insert_offset(idx->index[save_tid], save_bin, save_off, last_off);
336 save_bin = last_bin = intv.bin;
338 if (save_tid < 0) break;
340 if (bgzf_tell(fp) <= last_off) {
341 fprintf(stderr, "[ti_index_core] bug in BGZF: %llx < %llx\n",
342 (unsigned long long)bgzf_tell(fp), (unsigned long long)last_off);
345 last_off = bgzf_tell(fp);
346 last_coor = intv.beg;
348 if (save_tid >= 0) insert_offset(idx->index[save_tid], save_bin, save_off, bgzf_tell(fp));
352 free(str->s); free(str);
356 void ti_index_destroy(ti_index_t *idx)
360 if (idx == 0) return;
361 // destroy the name hash table
362 for (k = kh_begin(idx->tname); k != kh_end(idx->tname); ++k) {
363 if (kh_exist(idx->tname, k))
364 free((char*)kh_key(idx->tname, k));
366 kh_destroy(s, idx->tname);
367 // destroy the binning index
368 for (i = 0; i < idx->n; ++i) {
369 khash_t(i) *index = idx->index[i];
370 ti_lidx_t *index2 = idx->index2 + i;
371 for (k = kh_begin(index); k != kh_end(index); ++k) {
372 if (kh_exist(index, k))
373 free(kh_value(index, k).list);
375 kh_destroy(i, index);
376 free(index2->offset);
379 // destroy the linear index
388 void ti_index_save(const ti_index_t *idx, BGZF *fp)
390 int32_t i, size, ti_is_be;
392 ti_is_be = bam_is_big_endian();
393 bgzf_write(fp, "TBI\1", 4);
396 bgzf_write(fp, bam_swap_endian_4p(&x), 4);
397 } else bgzf_write(fp, &idx->n, 4);
398 assert(sizeof(ti_conf_t) == 24);
399 if (ti_is_be) { // write ti_conf_t;
401 memcpy(x, &idx->conf, 24);
402 for (i = 0; i < 6; ++i) bgzf_write(fp, bam_swap_endian_4p(&x[i]), 4);
403 } else bgzf_write(fp, &idx->conf, sizeof(ti_conf_t));
404 { // write target names
407 name = calloc(kh_size(idx->tname), sizeof(void*));
408 for (k = kh_begin(idx->tname); k != kh_end(idx->tname); ++k)
409 if (kh_exist(idx->tname, k))
410 name[kh_value(idx->tname, k)] = (char*)kh_key(idx->tname, k);
411 for (i = 0; i < kh_size(idx->tname); ++i)
412 l += strlen(name[i]) + 1;
413 if (ti_is_be) bgzf_write(fp, bam_swap_endian_4p(&l), 4);
414 else bgzf_write(fp, &l, 4);
415 for (i = 0; i < kh_size(idx->tname); ++i)
416 bgzf_write(fp, name[i], strlen(name[i]) + 1);
419 for (i = 0; i < idx->n; ++i) {
420 khash_t(i) *index = idx->index[i];
421 ti_lidx_t *index2 = idx->index2 + i;
422 // write binning index
423 size = kh_size(index);
424 if (ti_is_be) { // big endian
426 bgzf_write(fp, bam_swap_endian_4p(&x), 4);
427 } else bgzf_write(fp, &size, 4);
428 for (k = kh_begin(index); k != kh_end(index); ++k) {
429 if (kh_exist(index, k)) {
430 ti_binlist_t *p = &kh_value(index, k);
431 if (ti_is_be) { // big endian
433 x = kh_key(index, k); bgzf_write(fp, bam_swap_endian_4p(&x), 4);
434 x = p->n; bgzf_write(fp, bam_swap_endian_4p(&x), 4);
435 for (x = 0; (int)x < p->n; ++x) {
436 bam_swap_endian_8p(&p->list[x].u);
437 bam_swap_endian_8p(&p->list[x].v);
439 bgzf_write(fp, p->list, 16 * p->n);
440 for (x = 0; (int)x < p->n; ++x) {
441 bam_swap_endian_8p(&p->list[x].u);
442 bam_swap_endian_8p(&p->list[x].v);
445 bgzf_write(fp, &kh_key(index, k), 4);
446 bgzf_write(fp, &p->n, 4);
447 bgzf_write(fp, p->list, 16 * p->n);
451 // write linear index (index2)
454 bgzf_write(fp, bam_swap_endian_4p(&x), 4);
455 } else bgzf_write(fp, &index2->n, 4);
456 if (ti_is_be) { // big endian
458 for (x = 0; (int)x < index2->n; ++x)
459 bam_swap_endian_8p(&index2->offset[x]);
460 bgzf_write(fp, index2->offset, 8 * index2->n);
461 for (x = 0; (int)x < index2->n; ++x)
462 bam_swap_endian_8p(&index2->offset[x]);
463 } else bgzf_write(fp, index2->offset, 8 * index2->n);
467 static ti_index_t *ti_index_load_core(BGZF *fp)
472 ti_is_be = bam_is_big_endian();
474 fprintf(stderr, "[ti_index_load_core] fail to load index.\n");
477 bgzf_read(fp, magic, 4);
478 if (strncmp(magic, "TBI\1", 4)) {
479 fprintf(stderr, "[ti_index_load] wrong magic number.\n");
482 idx = (ti_index_t*)calloc(1, sizeof(ti_index_t));
483 bgzf_read(fp, &idx->n, 4);
484 if (ti_is_be) bam_swap_endian_4p(&idx->n);
485 idx->tname = kh_init(s);
486 idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
487 idx->index2 = (ti_lidx_t*)calloc(idx->n, sizeof(ti_lidx_t));
489 bgzf_read(fp, &idx->conf, sizeof(ti_conf_t));
491 bam_swap_endian_4p(&idx->conf.preset);
492 bam_swap_endian_4p(&idx->conf.sc);
493 bam_swap_endian_4p(&idx->conf.bc);
494 bam_swap_endian_4p(&idx->conf.ec);
495 bam_swap_endian_4p(&idx->conf.meta_char);
496 bam_swap_endian_4p(&idx->conf.line_skip);
498 { // read target names
503 bgzf_read(fp, &l, 4);
504 if (ti_is_be) bam_swap_endian_4p(&l);
506 bgzf_read(fp, buf, l);
507 str = calloc(1, sizeof(kstring_t));
508 for (i = j = 0; i < l; ++i) {
510 khint_t k = kh_put(s, idx->tname, strdup(str->s), &ret);
511 kh_value(idx->tname, k) = j++;
513 } else kputc(buf[i], str);
515 free(str->s); free(str); free(buf);
517 for (i = 0; i < idx->n; ++i) {
519 ti_lidx_t *index2 = idx->index2 + i;
524 index = idx->index[i] = kh_init(i);
525 // load binning index
526 bgzf_read(fp, &size, 4);
527 if (ti_is_be) bam_swap_endian_4p(&size);
528 for (j = 0; j < (int)size; ++j) {
529 bgzf_read(fp, &key, 4);
530 if (ti_is_be) bam_swap_endian_4p(&key);
531 k = kh_put(i, index, key, &ret);
532 p = &kh_value(index, k);
533 bgzf_read(fp, &p->n, 4);
534 if (ti_is_be) bam_swap_endian_4p(&p->n);
536 p->list = (pair64_t*)malloc(p->m * 16);
537 bgzf_read(fp, p->list, 16 * p->n);
540 for (x = 0; x < p->n; ++x) {
541 bam_swap_endian_8p(&p->list[x].u);
542 bam_swap_endian_8p(&p->list[x].v);
547 bgzf_read(fp, &index2->n, 4);
548 if (ti_is_be) bam_swap_endian_4p(&index2->n);
549 index2->m = index2->n;
550 index2->offset = (uint64_t*)calloc(index2->m, 8);
551 bgzf_read(fp, index2->offset, index2->n * 8);
553 for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]);
558 ti_index_t *ti_index_load_local(const char *fnidx)
561 fp = bgzf_open(fnidx, "r");
563 ti_index_t *idx = ti_index_load_core(fp);
570 static void download_from_remote(const char *url)
572 const int buf_size = 1 * 1024 * 1024;
578 if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return;
580 for (fn = (char*)url + l - 1; fn >= url; --fn)
581 if (*fn == '/') break;
582 ++fn; // fn now points to the file name
583 fp_remote = knet_open(url, "r");
584 if (fp_remote == 0) {
585 fprintf(stderr, "[download_from_remote] fail to open remote file.\n");
588 if ((fp = fopen(fn, "w")) == 0) {
589 fprintf(stderr, "[download_from_remote] fail to create file in the working directory.\n");
590 knet_close(fp_remote);
593 buf = (uint8_t*)calloc(buf_size, 1);
594 while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
595 fwrite(buf, 1, l, fp);
598 knet_close(fp_remote);
601 static void download_from_remote(const char *url)
607 static char *get_local_version(const char *fn)
610 char *fnidx = (char*)calloc(strlen(fn) + 5, 1);
611 strcat(strcpy(fnidx, fn), ".tbi");
612 if ((strstr(fnidx, "ftp://") == fnidx || strstr(fnidx, "http://") == fnidx)) {
614 int l = strlen(fnidx);
615 for (p = fnidx + l - 1; p >= fnidx; --p)
616 if (*p == '/') break;
617 url = fnidx; fnidx = strdup(p + 1);
618 if (stat(fnidx, &sbuf) == 0) {
622 fprintf(stderr, "[%s] downloading the index file...\n", __func__);
623 download_from_remote(url);
626 if (stat(fnidx, &sbuf) == 0) return fnidx;
627 free(fnidx); return 0;
630 const char **ti_seqname(const ti_index_t *idx, int *n)
635 names = calloc(idx->n, sizeof(void*));
636 for (k = kh_begin(idx->tname); k < kh_end(idx->tname); ++k)
637 if (kh_exist(idx->tname, k))
638 names[kh_val(idx->tname, k)] = kh_key(idx->tname, k);
642 ti_index_t *ti_index_load(const char *fn)
645 char *fname = get_local_version(fn);
646 if (fname == 0) return 0;
647 idx = ti_index_load_local(fname);
649 if (idx == 0) fprintf(stderr, "[ti_index_load] fail to load BAM index.\n");
653 int ti_index_build2(const char *fn, const ti_conf_t *conf, const char *_fnidx)
658 if ((fp = bgzf_open(fn, "r")) == 0) {
659 fprintf(stderr, "[ti_index_build2] fail to open the BAM file.\n");
662 idx = ti_index_core(fp, conf);
665 fnidx = (char*)calloc(strlen(fn) + 5, 1);
666 strcpy(fnidx, fn); strcat(fnidx, ".tbi");
667 } else fnidx = strdup(_fnidx);
668 fpidx = bgzf_open(fnidx, "w");
670 fprintf(stderr, "[ti_index_build2] fail to create the index file.\n");
674 ti_index_save(idx, fpidx);
675 ti_index_destroy(idx);
681 int ti_index_build(const char *fn, const ti_conf_t *conf)
683 return ti_index_build2(fn, conf, 0);
686 /********************************************
687 * parse a region in the format chr:beg-end *
688 ********************************************/
690 int ti_get_tid(const ti_index_t *idx, const char *name)
693 const khash_t(s) *h = idx->tname;
694 iter = kh_get(s, h, name); /* get the tid */
695 if (iter == kh_end(h)) return -1;
696 return kh_value(h, iter);
699 int ti_parse_region(const ti_index_t *idx, const char *str, int *tid, int *begin, int *end)
704 p = s = (char*)malloc(l+1);
705 /* squeeze out "," */
706 for (i = k = 0; i != l; ++i)
707 if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i];
709 for (i = 0; i != k; ++i) if (s[i] == ':') break;
711 if ((*tid = ti_get_tid(idx, s)) < 0) {
715 if (i == k) { /* dump the whole sequence */
716 *begin = 0; *end = 1<<29; free(s);
719 for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
725 if (*begin > 0) --*begin;
727 if (*begin > *end) return -1;
731 /*******************************
732 * retrieve a specified region *
733 *******************************/
735 #define MAX_BIN 37450 // =(8^6-1)/7+1
737 static inline int reg2bins(uint32_t beg, uint32_t end, uint16_t list[MAX_BIN])
740 if (beg >= end) return 0;
741 if (end >= 1u<<29) end = 1u<<29;
744 for (k = 1 + (beg>>26); k <= 1 + (end>>26); ++k) list[i++] = k;
745 for (k = 9 + (beg>>23); k <= 9 + (end>>23); ++k) list[i++] = k;
746 for (k = 73 + (beg>>20); k <= 73 + (end>>20); ++k) list[i++] = k;
747 for (k = 585 + (beg>>17); k <= 585 + (end>>17); ++k) list[i++] = k;
748 for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) list[i++] = k;
752 ti_iter_t ti_iter_first()
755 iter = calloc(1, sizeof(struct __ti_iter_t));
756 iter->from_first = 1;
760 ti_iter_t ti_iter_query(const ti_index_t *idx, int tid, int beg, int end)
763 int i, n_bins, n_off;
770 if (beg < 0) beg = 0;
771 if (end < beg) return 0;
772 // initialize the iterator
773 iter = calloc(1, sizeof(struct __ti_iter_t));
774 iter->idx = idx; iter->tid = tid; iter->beg = beg; iter->end = end; iter->i = -1;
776 bins = (uint16_t*)calloc(MAX_BIN, 2);
777 n_bins = reg2bins(beg, end, bins);
778 index = idx->index[tid];
779 if (idx->index2[tid].n > 0) {
780 min_off = (beg>>TAD_LIDX_SHIFT >= idx->index2[tid].n)? idx->index2[tid].offset[idx->index2[tid].n-1]
781 : idx->index2[tid].offset[beg>>TAD_LIDX_SHIFT];
782 if (min_off == 0) { // improvement for index files built by tabix prior to 0.1.4
783 int n = beg>>TAD_LIDX_SHIFT;
784 if (n > idx->index2[tid].n) n = idx->index2[tid].n;
785 for (i = n - 1; i >= 0; --i)
786 if (idx->index2[tid].offset[i] != 0) break;
787 if (i >= 0) min_off = idx->index2[tid].offset[i];
789 } else min_off = 0; // tabix 0.1.2 may produce such index files
790 for (i = n_off = 0; i < n_bins; ++i) {
791 if ((k = kh_get(i, index, bins[i])) != kh_end(index))
792 n_off += kh_value(index, k).n;
795 free(bins); return iter;
797 off = (pair64_t*)calloc(n_off, 16);
798 for (i = n_off = 0; i < n_bins; ++i) {
799 if ((k = kh_get(i, index, bins[i])) != kh_end(index)) {
801 ti_binlist_t *p = &kh_value(index, k);
802 for (j = 0; j < p->n; ++j)
803 if (p->list[j].v > min_off) off[n_off++] = p->list[j];
809 ks_introsort(offt, n_off, off);
810 // resolve completely contained adjacent blocks
811 for (i = 1, l = 0; i < n_off; ++i)
812 if (off[l].v < off[i].v)
815 // resolve overlaps between adjacent blocks; this may happen due to the merge in indexing
816 for (i = 1; i < n_off; ++i)
817 if (off[i-1].v >= off[i].u) off[i-1].v = off[i].u;
818 { // merge adjacent blocks
819 for (i = 1, l = 0; i < n_off; ++i) {
820 if (off[l].v>>16 == off[i].u>>16) off[l].v = off[i].v;
821 else off[++l] = off[i];
826 iter->n_off = n_off; iter->off = off;
830 const char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
832 if (iter->finished) return 0;
833 if (iter->from_first) {
835 if ((ret = ti_readline(fp, &iter->str)) < 0) {
839 if (len) *len = iter->str.l;
843 if (iter->n_off == 0) return 0;
846 if (iter->curr_off == 0 || iter->curr_off >= iter->off[iter->i].v) { // then jump to the next chunk
847 if (iter->i == iter->n_off - 1) break; // no more chunks
848 if (iter->i >= 0) assert(iter->curr_off == iter->off[iter->i].v); // otherwise bug
849 if (iter->i < 0 || iter->off[iter->i].v != iter->off[iter->i+1].u) { // not adjacent chunks; then seek
850 bgzf_seek(fp, iter->off[iter->i+1].u, SEEK_SET);
851 iter->curr_off = bgzf_tell(fp);
855 if ((ret = ti_readline(fp, &iter->str)) >= 0) {
857 iter->curr_off = bgzf_tell(fp);
858 if (iter->str.s[0] == iter->idx->conf.meta_char) continue;
859 get_intv((ti_index_t*)iter->idx, &iter->str, &intv);
860 if (intv.tid != iter->tid || intv.beg >= iter->end) break; // no need to proceed
861 else if (intv.end > iter->beg && iter->end > intv.beg) {
862 if (len) *len = iter->str.l;
865 } else break; // end of file
871 void ti_iter_destroy(ti_iter_t iter)
874 free(iter->str.s); free(iter->off);
879 int ti_fetch(BGZF *fp, const ti_index_t *idx, int tid, int beg, int end, void *data, ti_fetch_f func)
884 iter = ti_iter_query(idx, tid, beg, end);
885 while ((s = ti_iter_read(fp, iter, &len)) != 0)
887 ti_iter_destroy(iter);
895 tabix_t *ti_open(const char *fn, const char *fnidx)
899 if ((fp = bgzf_open(fn, "r")) == 0) return 0;
900 t = calloc(1, sizeof(tabix_t));
902 if (fnidx) t->fnidx = strdup(fnidx);
907 void ti_close(tabix_t *t)
911 if (t->idx) ti_index_destroy(t->idx);
912 free(t->fn); free(t->fnidx);
917 int ti_lazy_index_load(tabix_t *t)
919 if (t->idx == 0) { // load index
920 if (t->fnidx) t->idx = ti_index_load_local(t->fnidx);
921 else t->idx = ti_index_load(t->fn);
922 if (t->idx == 0) return -1; // fail to load index
927 ti_iter_t ti_queryi(tabix_t *t, int tid, int beg, int end)
929 if (tid < 0) return ti_iter_first();
930 if (ti_lazy_index_load(t) != 0) return 0;
931 return ti_iter_query(t->idx, tid, beg, end);
934 ti_iter_t ti_querys(tabix_t *t, const char *reg)
937 if (reg == 0) return ti_iter_first();
938 if (ti_lazy_index_load(t) != 0) return 0;
939 if (ti_parse_region(t->idx, reg, &tid, &beg, &end) < 0) return 0;
940 return ti_iter_query(t->idx, tid, beg, end);
943 ti_iter_t ti_query(tabix_t *t, const char *name, int beg, int end)
946 if (name == 0) return ti_iter_first();
947 // then need to load the index
948 if (ti_lazy_index_load(t) != 0) return 0;
949 if ((tid = ti_get_tid(t->idx, name)) < 0) return 0;
950 return ti_iter_query(t->idx, tid, beg, end);
953 const char *ti_read(tabix_t *t, ti_iter_t iter, int *len)
955 return ti_iter_read(t->fp, iter, len);