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(off, 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
195 if (id == 5) { // ALT
198 for (s = str->s + b; s < str->s + i;) {
200 long x = strtol(s + 1, &t, 10);
201 if (x > max) max = x;
205 intv->end = intv->beg + max;
213 if (intv->tid < 0 || intv->beg < 0 || intv->end < 0) return -1;
214 intv->bin = ti_reg2bin(intv->beg, intv->end);
222 // requirement: len <= LEN_MASK
223 static inline void insert_offset(khash_t(i) *h, int bin, uint64_t beg, uint64_t end)
228 k = kh_put(i, h, bin, &ret);
230 if (ret) { // not present
232 l->list = (pair64_t*)calloc(l->m, 16);
236 l->list = (pair64_t*)realloc(l->list, l->m * 16);
238 l->list[l->n].u = beg; l->list[l->n++].v = end;
241 static inline void insert_offset2(ti_lidx_t *index2, int _beg, int _end, uint64_t offset)
244 beg = _beg >> TAD_LIDX_SHIFT;
245 end = (_end - 1) >> TAD_LIDX_SHIFT;
246 if (index2->m < end + 1) {
247 int old_m = index2->m;
249 kroundup32(index2->m);
250 index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8);
251 memset(index2->offset + old_m, 0, 8 * (index2->m - old_m));
254 if (index2->offset[beg] == 0) index2->offset[beg] = offset;
256 for (i = beg; i <= end; ++i)
257 if (index2->offset[i] == 0) index2->offset[i] = offset;
259 if (index2->n < end + 1) index2->n = end + 1;
262 static void merge_chunks(ti_index_t *idx)
267 for (i = 0; i < idx->n; ++i) {
268 index = idx->index[i];
269 for (k = kh_begin(index); k != kh_end(index); ++k) {
271 if (!kh_exist(index, k)) continue;
272 p = &kh_value(index, k);
274 for (l = 1; l < p->n; ++l) {
275 if (p->list[m].v>>16 == p->list[l].u>>16) p->list[m].v = p->list[l].v;
276 else p->list[++m] = p->list[l];
283 static void fill_missing(ti_index_t *idx)
286 for (i = 0; i < idx->n; ++i) {
287 ti_lidx_t *idx2 = &idx->index2[i];
288 for (j = 1; j < idx2->n; ++j)
289 if (idx2->offset[j] == 0)
290 idx2->offset[j] = idx2->offset[j-1];
294 ti_index_t *ti_index_core(BGZF *fp, const ti_conf_t *conf)
298 uint32_t last_bin, save_bin;
299 int32_t last_coor, last_tid, save_tid;
300 uint64_t save_off, last_off, lineno = 0;
303 str = calloc(1, sizeof(kstring_t));
305 idx = (ti_index_t*)calloc(1, sizeof(ti_index_t));
307 idx->n = idx->max = 0;
308 idx->tname = kh_init(s);
312 save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
313 save_off = last_off = bgzf_tell(fp); last_coor = 0xffffffffu;
314 while ((ret = ti_readline(fp, str)) >= 0) {
317 if (lineno <= idx->conf.line_skip || str->s[0] == idx->conf.meta_char) {
318 last_off = bgzf_tell(fp);
321 get_intv(idx, str, &intv);
322 if (last_tid != intv.tid) { // change of chromosomes
324 last_bin = 0xffffffffu;
325 } else if (last_coor > intv.beg) {
326 fprintf(stderr, "[ti_index_core] the file out of order at line %llu\n", (unsigned long long)lineno);
329 insert_offset2(&idx->index2[intv.tid], intv.beg, intv.end, last_off);
330 if (intv.bin != last_bin) { // then possibly write the binning index
331 if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record
332 insert_offset(idx->index[save_tid], save_bin, save_off, last_off);
334 save_bin = last_bin = intv.bin;
336 if (save_tid < 0) break;
338 if (bgzf_tell(fp) <= last_off) {
339 fprintf(stderr, "[ti_index_core] bug in BGZF: %llx < %llx\n",
340 (unsigned long long)bgzf_tell(fp), (unsigned long long)last_off);
343 last_off = bgzf_tell(fp);
344 last_coor = intv.beg;
346 if (save_tid >= 0) insert_offset(idx->index[save_tid], save_bin, save_off, bgzf_tell(fp));
350 free(str->s); free(str);
354 void ti_index_destroy(ti_index_t *idx)
358 if (idx == 0) return;
359 // destroy the name hash table
360 for (k = kh_begin(idx->tname); k != kh_end(idx->tname); ++k) {
361 if (kh_exist(idx->tname, k))
362 free((char*)kh_key(idx->tname, k));
364 kh_destroy(s, idx->tname);
365 // destroy the binning index
366 for (i = 0; i < idx->n; ++i) {
367 khash_t(i) *index = idx->index[i];
368 ti_lidx_t *index2 = idx->index2 + i;
369 for (k = kh_begin(index); k != kh_end(index); ++k) {
370 if (kh_exist(index, k))
371 free(kh_value(index, k).list);
373 kh_destroy(i, index);
374 free(index2->offset);
377 // destroy the linear index
386 void ti_index_save(const ti_index_t *idx, BGZF *fp)
388 int32_t i, size, ti_is_be;
390 ti_is_be = bam_is_big_endian();
391 bgzf_write(fp, "TBI\1", 4);
394 bgzf_write(fp, bam_swap_endian_4p(&x), 4);
395 } else bgzf_write(fp, &idx->n, 4);
396 assert(sizeof(ti_conf_t) == 24);
397 if (ti_is_be) { // write ti_conf_t;
399 memcpy(x, &idx->conf, 24);
400 for (i = 0; i < 6; ++i) bgzf_write(fp, bam_swap_endian_4p(&x[i]), 4);
401 } else bgzf_write(fp, &idx->conf, sizeof(ti_conf_t));
402 { // write target names
405 name = calloc(kh_size(idx->tname), sizeof(void*));
406 for (k = kh_begin(idx->tname); k != kh_end(idx->tname); ++k)
407 if (kh_exist(idx->tname, k))
408 name[kh_value(idx->tname, k)] = (char*)kh_key(idx->tname, k);
409 for (i = 0; i < kh_size(idx->tname); ++i)
410 l += strlen(name[i]) + 1;
411 if (ti_is_be) bgzf_write(fp, bam_swap_endian_4p(&l), 4);
412 else bgzf_write(fp, &l, 4);
413 for (i = 0; i < kh_size(idx->tname); ++i)
414 bgzf_write(fp, name[i], strlen(name[i]) + 1);
417 for (i = 0; i < idx->n; ++i) {
418 khash_t(i) *index = idx->index[i];
419 ti_lidx_t *index2 = idx->index2 + i;
420 // write binning index
421 size = kh_size(index);
422 if (ti_is_be) { // big endian
424 bgzf_write(fp, bam_swap_endian_4p(&x), 4);
425 } else bgzf_write(fp, &size, 4);
426 for (k = kh_begin(index); k != kh_end(index); ++k) {
427 if (kh_exist(index, k)) {
428 ti_binlist_t *p = &kh_value(index, k);
429 if (ti_is_be) { // big endian
431 x = kh_key(index, k); bgzf_write(fp, bam_swap_endian_4p(&x), 4);
432 x = p->n; bgzf_write(fp, bam_swap_endian_4p(&x), 4);
433 for (x = 0; (int)x < p->n; ++x) {
434 bam_swap_endian_8p(&p->list[x].u);
435 bam_swap_endian_8p(&p->list[x].v);
437 bgzf_write(fp, p->list, 16 * p->n);
438 for (x = 0; (int)x < p->n; ++x) {
439 bam_swap_endian_8p(&p->list[x].u);
440 bam_swap_endian_8p(&p->list[x].v);
443 bgzf_write(fp, &kh_key(index, k), 4);
444 bgzf_write(fp, &p->n, 4);
445 bgzf_write(fp, p->list, 16 * p->n);
449 // write linear index (index2)
452 bgzf_write(fp, bam_swap_endian_4p(&x), 4);
453 } else bgzf_write(fp, &index2->n, 4);
454 if (ti_is_be) { // big endian
456 for (x = 0; (int)x < index2->n; ++x)
457 bam_swap_endian_8p(&index2->offset[x]);
458 bgzf_write(fp, index2->offset, 8 * index2->n);
459 for (x = 0; (int)x < index2->n; ++x)
460 bam_swap_endian_8p(&index2->offset[x]);
461 } else bgzf_write(fp, index2->offset, 8 * index2->n);
465 static ti_index_t *ti_index_load_core(BGZF *fp)
470 ti_is_be = bam_is_big_endian();
472 fprintf(stderr, "[ti_index_load_core] fail to load index.\n");
475 bgzf_read(fp, magic, 4);
476 if (strncmp(magic, "TBI\1", 4)) {
477 fprintf(stderr, "[ti_index_load] wrong magic number.\n");
480 idx = (ti_index_t*)calloc(1, sizeof(ti_index_t));
481 bgzf_read(fp, &idx->n, 4);
482 if (ti_is_be) bam_swap_endian_4p(&idx->n);
483 idx->tname = kh_init(s);
484 idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
485 idx->index2 = (ti_lidx_t*)calloc(idx->n, sizeof(ti_lidx_t));
487 bgzf_read(fp, &idx->conf, sizeof(ti_conf_t));
489 bam_swap_endian_4p(&idx->conf.preset);
490 bam_swap_endian_4p(&idx->conf.sc);
491 bam_swap_endian_4p(&idx->conf.bc);
492 bam_swap_endian_4p(&idx->conf.ec);
493 bam_swap_endian_4p(&idx->conf.meta_char);
494 bam_swap_endian_4p(&idx->conf.line_skip);
496 { // read target names
501 bgzf_read(fp, &l, 4);
502 if (ti_is_be) bam_swap_endian_4p(&l);
504 bgzf_read(fp, buf, l);
505 str = calloc(1, sizeof(kstring_t));
506 for (i = j = 0; i < l; ++i) {
508 khint_t k = kh_put(s, idx->tname, strdup(str->s), &ret);
509 kh_value(idx->tname, k) = j++;
511 } else kputc(buf[i], str);
513 free(str->s); free(str); free(buf);
515 for (i = 0; i < idx->n; ++i) {
517 ti_lidx_t *index2 = idx->index2 + i;
522 index = idx->index[i] = kh_init(i);
523 // load binning index
524 bgzf_read(fp, &size, 4);
525 if (ti_is_be) bam_swap_endian_4p(&size);
526 for (j = 0; j < (int)size; ++j) {
527 bgzf_read(fp, &key, 4);
528 if (ti_is_be) bam_swap_endian_4p(&key);
529 k = kh_put(i, index, key, &ret);
530 p = &kh_value(index, k);
531 bgzf_read(fp, &p->n, 4);
532 if (ti_is_be) bam_swap_endian_4p(&p->n);
534 p->list = (pair64_t*)malloc(p->m * 16);
535 bgzf_read(fp, p->list, 16 * p->n);
538 for (x = 0; x < p->n; ++x) {
539 bam_swap_endian_8p(&p->list[x].u);
540 bam_swap_endian_8p(&p->list[x].v);
545 bgzf_read(fp, &index2->n, 4);
546 if (ti_is_be) bam_swap_endian_4p(&index2->n);
547 index2->m = index2->n;
548 index2->offset = (uint64_t*)calloc(index2->m, 8);
549 bgzf_read(fp, index2->offset, index2->n * 8);
551 for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]);
556 ti_index_t *ti_index_load_local(const char *fnidx)
559 fp = bgzf_open(fnidx, "r");
561 ti_index_t *idx = ti_index_load_core(fp);
568 static void download_from_remote(const char *url)
570 const int buf_size = 1 * 1024 * 1024;
576 if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return;
578 for (fn = (char*)url + l - 1; fn >= url; --fn)
579 if (*fn == '/') break;
580 ++fn; // fn now points to the file name
581 fp_remote = knet_open(url, "r");
582 if (fp_remote == 0) {
583 fprintf(stderr, "[download_from_remote] fail to open remote file.\n");
586 if ((fp = fopen(fn, "w")) == 0) {
587 fprintf(stderr, "[download_from_remote] fail to create file in the working directory.\n");
588 knet_close(fp_remote);
591 buf = (uint8_t*)calloc(buf_size, 1);
592 while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
593 fwrite(buf, 1, l, fp);
596 knet_close(fp_remote);
599 static void download_from_remote(const char *url)
605 static char *get_local_version(const char *fn)
608 char *fnidx = (char*)calloc(strlen(fn) + 5, 1);
609 strcat(strcpy(fnidx, fn), ".tbi");
610 if ((strstr(fnidx, "ftp://") == fnidx || strstr(fnidx, "http://") == fnidx)) {
612 int l = strlen(fnidx);
613 for (p = fnidx + l - 1; p >= fnidx; --p)
614 if (*p == '/') break;
615 url = fnidx; fnidx = strdup(p + 1);
616 if (stat(fnidx, &sbuf) == 0) {
620 fprintf(stderr, "[%s] downloading the index file...\n", __func__);
621 download_from_remote(url);
624 if (stat(fnidx, &sbuf) == 0) return fnidx;
625 free(fnidx); return 0;
628 const char **ti_seqname(const ti_index_t *idx, int *n)
633 names = calloc(idx->n, sizeof(void*));
634 for (k = kh_begin(idx->tname); k < kh_end(idx->tname); ++k)
635 if (kh_exist(idx->tname, k))
636 names[kh_val(idx->tname, k)] = kh_key(idx->tname, k);
640 ti_index_t *ti_index_load(const char *fn)
643 char *fname = get_local_version(fn);
644 if (fname == 0) return 0;
645 idx = ti_index_load_local(fname);
647 if (idx == 0) fprintf(stderr, "[ti_index_load] fail to load BAM index.\n");
651 int ti_index_build2(const char *fn, const ti_conf_t *conf, const char *_fnidx)
656 if ((fp = bgzf_open(fn, "r")) == 0) {
657 fprintf(stderr, "[ti_index_build2] fail to open the BAM file.\n");
660 idx = ti_index_core(fp, conf);
663 fnidx = (char*)calloc(strlen(fn) + 5, 1);
664 strcpy(fnidx, fn); strcat(fnidx, ".tbi");
665 } else fnidx = strdup(_fnidx);
666 fpidx = bgzf_open(fnidx, "w");
668 fprintf(stderr, "[ti_index_build2] fail to create the index file.\n");
672 ti_index_save(idx, fpidx);
673 ti_index_destroy(idx);
679 int ti_index_build(const char *fn, const ti_conf_t *conf)
681 return ti_index_build2(fn, conf, 0);
684 /********************************************
685 * parse a region in the format chr:beg-end *
686 ********************************************/
688 int ti_get_tid(const ti_index_t *idx, const char *name)
691 const khash_t(s) *h = idx->tname;
692 iter = kh_get(s, h, name); /* get the tid */
693 if (iter == kh_end(h)) return -1;
694 return kh_value(h, iter);
697 int ti_parse_region(const ti_index_t *idx, const char *str, int *tid, int *begin, int *end)
702 p = s = (char*)malloc(l+1);
703 /* squeeze out "," */
704 for (i = k = 0; i != l; ++i)
705 if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i];
707 for (i = 0; i != k; ++i) if (s[i] == ':') break;
709 if ((*tid = ti_get_tid(idx, s)) < 0) {
713 if (i == k) { /* dump the whole sequence */
714 *begin = 0; *end = 1<<29; free(s);
717 for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
723 if (*begin > 0) --*begin;
725 if (*begin > *end) return -1;
729 /*******************************
730 * retrieve a specified region *
731 *******************************/
733 #define MAX_BIN 37450 // =(8^6-1)/7+1
735 static inline int reg2bins(uint32_t beg, uint32_t end, uint16_t list[MAX_BIN])
738 if (beg >= end) return 0;
739 if (end >= 1u<<29) end = 1u<<29;
742 for (k = 1 + (beg>>26); k <= 1 + (end>>26); ++k) list[i++] = k;
743 for (k = 9 + (beg>>23); k <= 9 + (end>>23); ++k) list[i++] = k;
744 for (k = 73 + (beg>>20); k <= 73 + (end>>20); ++k) list[i++] = k;
745 for (k = 585 + (beg>>17); k <= 585 + (end>>17); ++k) list[i++] = k;
746 for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) list[i++] = k;
750 ti_iter_t ti_iter_first()
753 iter = calloc(1, sizeof(struct __ti_iter_t));
754 iter->from_first = 1;
758 ti_iter_t ti_iter_query(const ti_index_t *idx, int tid, int beg, int end)
761 int i, n_bins, n_off;
768 if (beg < 0) beg = 0;
769 if (end < beg) return 0;
770 // initialize the iterator
771 iter = calloc(1, sizeof(struct __ti_iter_t));
772 iter->idx = idx; iter->tid = tid; iter->beg = beg; iter->end = end; iter->i = -1;
774 bins = (uint16_t*)calloc(MAX_BIN, 2);
775 n_bins = reg2bins(beg, end, bins);
776 index = idx->index[tid];
777 if (idx->index2[tid].n > 0) {
778 min_off = (beg>>TAD_LIDX_SHIFT >= idx->index2[tid].n)? idx->index2[tid].offset[idx->index2[tid].n-1]
779 : idx->index2[tid].offset[beg>>TAD_LIDX_SHIFT];
780 if (min_off == 0) { // improvement for index files built by tabix prior to 0.1.4
781 int n = beg>>TAD_LIDX_SHIFT;
782 if (n > idx->index2[tid].n) n = idx->index2[tid].n;
783 for (i = n - 1; i >= 0; --i)
784 if (idx->index2[tid].offset[i] != 0) break;
785 if (i >= 0) min_off = idx->index2[tid].offset[i];
787 } else min_off = 0; // tabix 0.1.2 may produce such index files
788 for (i = n_off = 0; i < n_bins; ++i) {
789 if ((k = kh_get(i, index, bins[i])) != kh_end(index))
790 n_off += kh_value(index, k).n;
793 free(bins); return iter;
795 off = (pair64_t*)calloc(n_off, 16);
796 for (i = n_off = 0; i < n_bins; ++i) {
797 if ((k = kh_get(i, index, bins[i])) != kh_end(index)) {
799 ti_binlist_t *p = &kh_value(index, k);
800 for (j = 0; j < p->n; ++j)
801 if (p->list[j].v > min_off) off[n_off++] = p->list[j];
807 ks_introsort(off, n_off, off);
808 // resolve completely contained adjacent blocks
809 for (i = 1, l = 0; i < n_off; ++i)
810 if (off[l].v < off[i].v)
813 // resolve overlaps between adjacent blocks; this may happen due to the merge in indexing
814 for (i = 1; i < n_off; ++i)
815 if (off[i-1].v >= off[i].u) off[i-1].v = off[i].u;
816 { // merge adjacent blocks
817 for (i = 1, l = 0; i < n_off; ++i) {
818 if (off[l].v>>16 == off[i].u>>16) off[l].v = off[i].v;
819 else off[++l] = off[i];
824 iter->n_off = n_off; iter->off = off;
828 const char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
830 if (iter->finished) return 0;
831 if (iter->from_first) {
833 if ((ret = ti_readline(fp, &iter->str)) < 0) {
837 if (len) *len = iter->str.l;
841 if (iter->n_off == 0) return 0;
844 if (iter->curr_off == 0 || iter->curr_off >= iter->off[iter->i].v) { // then jump to the next chunk
845 if (iter->i == iter->n_off - 1) break; // no more chunks
846 if (iter->i >= 0) assert(iter->curr_off == iter->off[iter->i].v); // otherwise bug
847 if (iter->i < 0 || iter->off[iter->i].v != iter->off[iter->i+1].u) { // not adjacent chunks; then seek
848 bgzf_seek(fp, iter->off[iter->i+1].u, SEEK_SET);
849 iter->curr_off = bgzf_tell(fp);
853 if ((ret = ti_readline(fp, &iter->str)) >= 0) {
855 iter->curr_off = bgzf_tell(fp);
856 if (iter->str.s[0] == iter->idx->conf.meta_char) continue;
857 get_intv((ti_index_t*)iter->idx, &iter->str, &intv);
858 if (intv.tid != iter->tid || intv.beg >= iter->end) break; // no need to proceed
859 else if (intv.end > iter->beg && iter->end > intv.beg) {
860 if (len) *len = iter->str.l;
863 } else break; // end of file
869 void ti_iter_destroy(ti_iter_t iter)
872 free(iter->str.s); free(iter->off);
877 int ti_fetch(BGZF *fp, const ti_index_t *idx, int tid, int beg, int end, void *data, ti_fetch_f func)
882 iter = ti_iter_query(idx, tid, beg, end);
883 while ((s = ti_iter_read(fp, iter, &len)) != 0)
885 ti_iter_destroy(iter);
893 tabix_t *ti_open(const char *fn, const char *fnidx)
897 if ((fp = bgzf_open(fn, "r")) == 0) return 0;
898 t = calloc(1, sizeof(tabix_t));
900 if (fnidx) t->fnidx = strdup(fnidx);
905 void ti_close(tabix_t *t)
909 if (t->idx) ti_index_destroy(t->idx);
910 free(t->fn); free(t->fnidx);
915 int ti_lazy_index_load(tabix_t *t)
917 if (t->idx == 0) { // load index
918 if (t->fnidx) t->idx = ti_index_load_local(t->fnidx);
919 else t->idx = ti_index_load(t->fn);
920 if (t->idx == 0) return -1; // fail to load index
925 ti_iter_t ti_queryi(tabix_t *t, int tid, int beg, int end)
927 if (tid < 0) return ti_iter_first();
928 if (ti_lazy_index_load(t) != 0) return 0;
929 return ti_iter_query(t->idx, tid, beg, end);
932 ti_iter_t ti_querys(tabix_t *t, const char *reg)
935 if (reg == 0) return ti_iter_first();
936 if (ti_lazy_index_load(t) != 0) return 0;
937 if (ti_parse_region(t->idx, reg, &tid, &beg, &end) < 0) return 0;
938 return ti_iter_query(t->idx, tid, beg, end);
941 ti_iter_t ti_query(tabix_t *t, const char *name, int beg, int end)
944 if (name == 0) return ti_iter_first();
945 // then need to load the index
946 if (ti_lazy_index_load(t) != 0) return 0;
947 if ((tid = ti_get_tid(t->idx, name)) < 0) return 0;
948 return ti_iter_query(t->idx, tid, beg, end);
951 const char *ti_read(tabix_t *t, ti_iter_t iter, int *len)
953 return ti_iter_read(t->fp, iter, len);