9 #include "bam_endian.h"
15 #define TAD_MIN_CHUNK_GAP 32768
16 // 1<<14 is the size of minimum bin.
17 #define TAD_LIDX_SHIFT 14
23 #define pair64_lt(a,b) ((a).u < (b).u)
24 KSORT_INIT(offt, pair64_t, pair64_lt)
36 KHASH_MAP_INIT_INT(i, ti_binlist_t)
37 KHASH_MAP_INIT_STR(s, int)
48 int from_first; // read from the first record; no random access
49 int tid, beg, end, n_off, i, finished;
52 const ti_index_t *idx;
57 int tid, beg, end, bin;
60 ti_conf_t ti_conf_gff = { 0, 1, 4, 5, '#', 0 };
61 ti_conf_t ti_conf_bed = { TI_FLAG_UCSC, 1, 2, 3, '#', 0 };
62 ti_conf_t ti_conf_psltbl = { TI_FLAG_UCSC, 15, 17, 18, '#', 0 };
63 ti_conf_t ti_conf_sam = { TI_PRESET_SAM, 3, 4, 0, '@', 0 };
64 ti_conf_t ti_conf_vcf = { TI_PRESET_VCF, 1, 2, 0, '#', 0 };
71 int ti_readline(BGZF *fp, kstring_t *str)
75 while ((c = bgzf_getc(fp)) >= 0 && c != '\n') {
77 if (c != '\r') kputc(c, str);
79 if (c < 0 && l == 0) return -1; // end of file
84 /* Below is a faster implementation largely equivalent to the one
85 * commented out above. */
86 int ti_readline(BGZF *fp, kstring_t *str)
88 return bgzf_getline(fp, '\n', str);
91 /*************************************
92 * get the interval from a data line *
93 *************************************/
95 static inline int ti_reg2bin(uint32_t beg, uint32_t end)
98 if (beg>>14 == end>>14) return 4681 + (beg>>14);
99 if (beg>>17 == end>>17) return 585 + (beg>>17);
100 if (beg>>20 == end>>20) return 73 + (beg>>20);
101 if (beg>>23 == end>>23) return 9 + (beg>>23);
102 if (beg>>26 == end>>26) return 1 + (beg>>26);
106 static int get_tid(ti_index_t *idx, const char *ss)
110 k = kh_get(s, idx->tname, ss);
111 if (k == kh_end(idx->tname)) { // a new target sequence
113 // update idx->n, ->max, ->index and ->index2
114 if (idx->n == idx->max) {
115 idx->max = idx->max? idx->max<<1 : 8;
116 idx->index = realloc(idx->index, idx->max * sizeof(void*));
117 idx->index2 = realloc(idx->index2, idx->max * sizeof(ti_lidx_t));
119 memset(&idx->index2[idx->n], 0, sizeof(ti_lidx_t));
120 idx->index[idx->n++] = kh_init(i);
122 tid = size = kh_size(idx->tname);
123 k = kh_put(s, idx->tname, strdup(ss), &ret);
124 kh_value(idx->tname, k) = size;
125 assert(idx->n == kh_size(idx->tname));
126 } else tid = kh_value(idx->tname, k);
130 int ti_get_intv(const ti_conf_t *conf, int len, char *line, ti_interval_t *intv)
132 int i, b = 0, id = 1, ncols = 0;
134 intv->ss = intv->se = 0; intv->beg = intv->end = -1;
135 for (i = 0; i <= len; ++i) {
136 if (line[i] == '\t' || line[i] == 0) {
138 if (id == conf->sc) {
139 intv->ss = line + b; intv->se = line + i;
140 } else if (id == conf->bc) {
141 // here ->beg is 0-based.
142 intv->beg = intv->end = strtol(line + b, &s, 0);
143 if (!(conf->preset&TI_FLAG_UCSC)) --intv->beg;
145 if (intv->beg < 0) intv->beg = 0;
146 if (intv->end < 1) intv->end = 1;
148 if ((conf->preset&0xffff) == TI_PRESET_GENERIC) {
149 if (id == conf->ec) intv->end = strtol(line + b, &s, 0);
150 } else if ((conf->preset&0xffff) == TI_PRESET_SAM) {
151 if (id == 6) { // CIGAR
154 for (s = line + b; s < line + i;) {
155 long x = strtol(s, &t, 10);
157 if (op == 'M' || op == 'D' || op == 'N') l += x;
161 intv->end = intv->beg + l;
163 } else if ((conf->preset&0xffff) == TI_PRESET_VCF) {
164 // FIXME: the following is NOT tested and is likely to be buggy
166 if (b < i) intv->end = intv->beg + (i - b);
167 } else if (id == 8) { // look for "END="
170 s = strstr(line + b, "END=");
171 if (s == line + b) s += 4;
173 s = strstr(line + b, ";END=");
176 if (s) intv->end = strtol(s, &s, 0);
186 if (ncols < conf->sc || ncols < conf->bc || ncols < conf->ec) {
187 if (ncols == 1) fprintf(pysamerr,"[get_intv] Is the file tab-delimited? The line has %d field only: %s\n", ncols, line);
188 else fprintf(pysamerr,"[get_intv] The line has %d field(s) only: %s\n", ncols, line);
192 if (intv->ss == 0 || intv->se == 0 || intv->beg < 0 || intv->end < 0) return -1;
196 static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
199 intv->tid = intv->beg = intv->end = intv->bin = -1;
200 if (ti_get_intv(&idx->conf, str->l, str->s, &x) == 0) {
202 *x.se = '\0'; intv->tid = get_tid(idx, x.ss); *x.se = c;
203 intv->beg = x.beg; intv->end = x.end;
204 intv->bin = ti_reg2bin(intv->beg, intv->end);
205 return (intv->tid >= 0 && intv->beg >= 0 && intv->end >= 0)? 0 : -1;
207 fprintf(pysamerr, "[%s] the following line cannot be parsed and skipped: %s\n", __func__, str->s);
216 // requirement: len <= LEN_MASK
217 static inline void insert_offset(khash_t(i) *h, int bin, uint64_t beg, uint64_t end)
222 k = kh_put(i, h, bin, &ret);
224 if (ret) { // not present
226 l->list = (pair64_t*)calloc(l->m, 16);
230 l->list = (pair64_t*)realloc(l->list, l->m * 16);
232 l->list[l->n].u = beg; l->list[l->n++].v = end;
235 static inline uint64_t insert_offset2(ti_lidx_t *index2, int _beg, int _end, uint64_t offset)
238 beg = _beg >> TAD_LIDX_SHIFT;
239 end = (_end - 1) >> TAD_LIDX_SHIFT;
240 if (index2->m < end + 1) {
241 int old_m = index2->m;
243 kroundup32(index2->m);
244 index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8);
245 memset(index2->offset + old_m, 0, 8 * (index2->m - old_m));
248 if (index2->offset[beg] == 0) index2->offset[beg] = offset;
250 for (i = beg; i <= end; ++i)
251 if (index2->offset[i] == 0) index2->offset[i] = offset;
253 if (index2->n < end + 1) index2->n = end + 1;
254 return (uint64_t)beg<<32 | end;
257 static void merge_chunks(ti_index_t *idx)
262 for (i = 0; i < idx->n; ++i) {
263 index = idx->index[i];
264 for (k = kh_begin(index); k != kh_end(index); ++k) {
266 if (!kh_exist(index, k)) continue;
267 p = &kh_value(index, k);
269 for (l = 1; l < p->n; ++l) {
270 if (p->list[m].v>>16 == p->list[l].u>>16) p->list[m].v = p->list[l].v;
271 else p->list[++m] = p->list[l];
278 static void fill_missing(ti_index_t *idx)
281 for (i = 0; i < idx->n; ++i) {
282 ti_lidx_t *idx2 = &idx->index2[i];
283 for (j = 1; j < idx2->n; ++j)
284 if (idx2->offset[j] == 0)
285 idx2->offset[j] = idx2->offset[j-1];
289 ti_index_t *ti_index_core(BGZF *fp, const ti_conf_t *conf)
293 uint32_t last_bin, save_bin;
294 int32_t last_coor, last_tid, save_tid;
295 uint64_t save_off, last_off, lineno = 0, offset0 = (uint64_t)-1, tmp;
298 str = calloc(1, sizeof(kstring_t));
300 idx = (ti_index_t*)calloc(1, sizeof(ti_index_t));
302 idx->n = idx->max = 0;
303 idx->tname = kh_init(s);
307 save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
308 save_off = last_off = bgzf_tell(fp); last_coor = 0xffffffffu;
309 while ((ret = ti_readline(fp, str)) >= 0) {
312 if (lineno <= idx->conf.line_skip || str->s[0] == idx->conf.meta_char) {
313 last_off = bgzf_tell(fp);
316 get_intv(idx, str, &intv);
317 if ( intv.beg<0 || intv.end<0 )
319 fprintf(pysamerr,"[ti_index_core] the indexes overlap or are out of bounds\n");
322 if (last_tid != intv.tid) { // change of chromosomes
323 if (last_tid>intv.tid )
325 fprintf(pysamerr,"[ti_index_core] the chromosome blocks not continuous at line %llu, is the file sorted? [pos %d]\n",(unsigned long long)lineno,intv.beg+1);
329 last_bin = 0xffffffffu;
330 } else if (last_coor > intv.beg) {
331 fprintf(pysamerr, "[ti_index_core] the file out of order at line %llu\n", (unsigned long long)lineno);
334 tmp = insert_offset2(&idx->index2[intv.tid], intv.beg, intv.end, last_off);
335 if (last_off == 0) offset0 = tmp;
336 if (intv.bin != last_bin) { // then possibly write the binning index
337 if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record
338 insert_offset(idx->index[save_tid], save_bin, save_off, last_off);
340 save_bin = last_bin = intv.bin;
342 if (save_tid < 0) break;
344 if (bgzf_tell(fp) <= last_off) {
345 fprintf(pysamerr, "[ti_index_core] bug in BGZF: %llx < %llx\n",
346 (unsigned long long)bgzf_tell(fp), (unsigned long long)last_off);
349 last_off = bgzf_tell(fp);
350 last_coor = intv.beg;
352 if (save_tid >= 0) insert_offset(idx->index[save_tid], save_bin, save_off, bgzf_tell(fp));
355 if (offset0 != (uint64_t)-1 && idx->n && idx->index2[0].offset) {
356 int i, beg = offset0>>32, end = offset0&0xffffffffu;
357 for (i = beg; i <= end; ++i) idx->index2[0].offset[i] = 0;
360 free(str->s); free(str);
364 void ti_index_destroy(ti_index_t *idx)
368 if (idx == 0) return;
369 // destroy the name hash table
370 for (k = kh_begin(idx->tname); k != kh_end(idx->tname); ++k) {
371 if (kh_exist(idx->tname, k))
372 free((char*)kh_key(idx->tname, k));
374 kh_destroy(s, idx->tname);
375 // destroy the binning index
376 for (i = 0; i < idx->n; ++i) {
377 khash_t(i) *index = idx->index[i];
378 ti_lidx_t *index2 = idx->index2 + i;
379 for (k = kh_begin(index); k != kh_end(index); ++k) {
380 if (kh_exist(index, k))
381 free(kh_value(index, k).list);
383 kh_destroy(i, index);
384 free(index2->offset);
387 // destroy the linear index
396 void ti_index_save(const ti_index_t *idx, BGZF *fp)
398 int32_t i, size, ti_is_be;
400 ti_is_be = bam_is_big_endian();
401 bgzf_write(fp, "TBI\1", 4);
404 bgzf_write(fp, bam_swap_endian_4p(&x), 4);
405 } else bgzf_write(fp, &idx->n, 4);
406 assert(sizeof(ti_conf_t) == 24);
407 if (ti_is_be) { // write ti_conf_t;
409 memcpy(x, &idx->conf, 24);
410 for (i = 0; i < 6; ++i) bgzf_write(fp, bam_swap_endian_4p(&x[i]), 4);
411 } else bgzf_write(fp, &idx->conf, sizeof(ti_conf_t));
412 { // write target names
415 name = calloc(kh_size(idx->tname), sizeof(void*));
416 for (k = kh_begin(idx->tname); k != kh_end(idx->tname); ++k)
417 if (kh_exist(idx->tname, k))
418 name[kh_value(idx->tname, k)] = (char*)kh_key(idx->tname, k);
419 for (i = 0; i < kh_size(idx->tname); ++i)
420 l += strlen(name[i]) + 1;
421 if (ti_is_be) bgzf_write(fp, bam_swap_endian_4p(&l), 4);
422 else bgzf_write(fp, &l, 4);
423 for (i = 0; i < kh_size(idx->tname); ++i)
424 bgzf_write(fp, name[i], strlen(name[i]) + 1);
427 for (i = 0; i < idx->n; ++i) {
428 khash_t(i) *index = idx->index[i];
429 ti_lidx_t *index2 = idx->index2 + i;
430 // write binning index
431 size = kh_size(index);
432 if (ti_is_be) { // big endian
434 bgzf_write(fp, bam_swap_endian_4p(&x), 4);
435 } else bgzf_write(fp, &size, 4);
436 for (k = kh_begin(index); k != kh_end(index); ++k) {
437 if (kh_exist(index, k)) {
438 ti_binlist_t *p = &kh_value(index, k);
439 if (ti_is_be) { // big endian
441 x = kh_key(index, k); bgzf_write(fp, bam_swap_endian_4p(&x), 4);
442 x = p->n; bgzf_write(fp, bam_swap_endian_4p(&x), 4);
443 for (x = 0; (int)x < p->n; ++x) {
444 bam_swap_endian_8p(&p->list[x].u);
445 bam_swap_endian_8p(&p->list[x].v);
447 bgzf_write(fp, p->list, 16 * p->n);
448 for (x = 0; (int)x < p->n; ++x) {
449 bam_swap_endian_8p(&p->list[x].u);
450 bam_swap_endian_8p(&p->list[x].v);
453 bgzf_write(fp, &kh_key(index, k), 4);
454 bgzf_write(fp, &p->n, 4);
455 bgzf_write(fp, p->list, 16 * p->n);
459 // write linear index (index2)
462 bgzf_write(fp, bam_swap_endian_4p(&x), 4);
463 } else bgzf_write(fp, &index2->n, 4);
464 if (ti_is_be) { // big endian
466 for (x = 0; (int)x < index2->n; ++x)
467 bam_swap_endian_8p(&index2->offset[x]);
468 bgzf_write(fp, index2->offset, 8 * index2->n);
469 for (x = 0; (int)x < index2->n; ++x)
470 bam_swap_endian_8p(&index2->offset[x]);
471 } else bgzf_write(fp, index2->offset, 8 * index2->n);
475 static ti_index_t *ti_index_load_core(BGZF *fp)
480 ti_is_be = bam_is_big_endian();
482 fprintf(pysamerr, "[ti_index_load_core] fail to load index.\n");
485 bgzf_read(fp, magic, 4);
486 if (strncmp(magic, "TBI\1", 4)) {
487 fprintf(pysamerr, "[ti_index_load] wrong magic number.\n");
490 idx = (ti_index_t*)calloc(1, sizeof(ti_index_t));
491 bgzf_read(fp, &idx->n, 4);
492 if (ti_is_be) bam_swap_endian_4p(&idx->n);
493 idx->tname = kh_init(s);
494 idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
495 idx->index2 = (ti_lidx_t*)calloc(idx->n, sizeof(ti_lidx_t));
497 bgzf_read(fp, &idx->conf, sizeof(ti_conf_t));
499 bam_swap_endian_4p(&idx->conf.preset);
500 bam_swap_endian_4p(&idx->conf.sc);
501 bam_swap_endian_4p(&idx->conf.bc);
502 bam_swap_endian_4p(&idx->conf.ec);
503 bam_swap_endian_4p(&idx->conf.meta_char);
504 bam_swap_endian_4p(&idx->conf.line_skip);
506 { // read target names
511 bgzf_read(fp, &l, 4);
512 if (ti_is_be) bam_swap_endian_4p(&l);
514 bgzf_read(fp, buf, l);
515 str = calloc(1, sizeof(kstring_t));
516 for (i = j = 0; i < l; ++i) {
518 khint_t k = kh_put(s, idx->tname, strdup(str->s), &ret);
519 kh_value(idx->tname, k) = j++;
521 } else kputc(buf[i], str);
523 free(str->s); free(str); free(buf);
525 for (i = 0; i < idx->n; ++i) {
527 ti_lidx_t *index2 = idx->index2 + i;
532 index = idx->index[i] = kh_init(i);
533 // load binning index
534 bgzf_read(fp, &size, 4);
535 if (ti_is_be) bam_swap_endian_4p(&size);
536 for (j = 0; j < (int)size; ++j) {
537 bgzf_read(fp, &key, 4);
538 if (ti_is_be) bam_swap_endian_4p(&key);
539 k = kh_put(i, index, key, &ret);
540 p = &kh_value(index, k);
541 bgzf_read(fp, &p->n, 4);
542 if (ti_is_be) bam_swap_endian_4p(&p->n);
544 p->list = (pair64_t*)malloc(p->m * 16);
545 bgzf_read(fp, p->list, 16 * p->n);
548 for (x = 0; x < p->n; ++x) {
549 bam_swap_endian_8p(&p->list[x].u);
550 bam_swap_endian_8p(&p->list[x].v);
555 bgzf_read(fp, &index2->n, 4);
556 if (ti_is_be) bam_swap_endian_4p(&index2->n);
557 index2->m = index2->n;
558 index2->offset = (uint64_t*)calloc(index2->m, 8);
559 bgzf_read(fp, index2->offset, index2->n * 8);
561 for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]);
566 ti_index_t *ti_index_load_local(const char *fnidx)
569 fp = bgzf_open(fnidx, "r");
571 ti_index_t *idx = ti_index_load_core(fp);
578 static void download_from_remote(const char *url)
580 const int buf_size = 1 * 1024 * 1024;
586 if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return;
588 for (fn = (char*)url + l - 1; fn >= url; --fn)
589 if (*fn == '/') break;
590 ++fn; // fn now points to the file name
591 fp_remote = knet_open(url, "r");
592 if (fp_remote == 0) {
593 fprintf(pysamerr, "[download_from_remote] fail to open remote file.\n");
596 if ((fp = fopen(fn, "w")) == 0) {
597 fprintf(pysamerr, "[download_from_remote] fail to create file in the working directory.\n");
598 knet_close(fp_remote);
601 buf = (uint8_t*)calloc(buf_size, 1);
602 while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
603 fwrite(buf, 1, l, fp);
606 knet_close(fp_remote);
609 static void download_from_remote(const char *url)
615 static char *get_local_version(const char *fn)
618 char *fnidx = (char*)calloc(strlen(fn) + 5, 1);
619 strcat(strcpy(fnidx, fn), ".tbi");
620 if ((strstr(fnidx, "ftp://") == fnidx || strstr(fnidx, "http://") == fnidx)) {
622 int l = strlen(fnidx);
623 for (p = fnidx + l - 1; p >= fnidx; --p)
624 if (*p == '/') break;
625 url = fnidx; fnidx = strdup(p + 1);
626 if (stat(fnidx, &sbuf) == 0) {
630 fprintf(pysamerr, "[%s] downloading the index file...\n", __func__);
631 download_from_remote(url);
634 if (stat(fnidx, &sbuf) == 0) return fnidx;
635 free(fnidx); return 0;
638 const char **ti_seqname(const ti_index_t *idx, int *n)
643 names = calloc(idx->n, sizeof(void*));
644 for (k = kh_begin(idx->tname); k < kh_end(idx->tname); ++k)
645 if (kh_exist(idx->tname, k))
646 names[kh_val(idx->tname, k)] = kh_key(idx->tname, k);
650 ti_index_t *ti_index_load(const char *fn)
653 char *fname = get_local_version(fn);
654 if (fname == 0) return 0;
655 idx = ti_index_load_local(fname);
656 if (idx == 0) fprintf(pysamerr, "[ti_index_load] fail to load the index: %s\n", fname);
661 int ti_index_build2(const char *fn, const ti_conf_t *conf, const char *_fnidx)
666 if ((fp = bgzf_open(fn, "r")) == 0) {
667 fprintf(pysamerr, "[ti_index_build2] fail to open the file: %s\n", fn);
670 idx = ti_index_core(fp, conf);
673 fnidx = (char*)calloc(strlen(fn) + 5, 1);
674 strcpy(fnidx, fn); strcat(fnidx, ".tbi");
675 } else fnidx = strdup(_fnidx);
676 fpidx = bgzf_open(fnidx, "w");
678 fprintf(pysamerr, "[ti_index_build2] fail to create the index file.\n");
682 ti_index_save(idx, fpidx);
683 ti_index_destroy(idx);
689 int ti_index_build(const char *fn, const ti_conf_t *conf)
691 return ti_index_build2(fn, conf, 0);
694 /********************************************
695 * parse a region in the format chr:beg-end *
696 ********************************************/
698 int ti_get_tid(const ti_index_t *idx, const char *name)
701 const khash_t(s) *h = idx->tname;
702 iter = kh_get(s, h, name); /* get the tid */
703 if (iter == kh_end(h)) return -1;
704 return kh_value(h, iter);
707 int ti_parse_region(const ti_index_t *idx, const char *str, int *tid, int *begin, int *end)
712 p = s = (char*)malloc(l+1);
713 /* squeeze out "," */
714 for (i = k = 0; i != l; ++i)
715 if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i];
717 for (i = 0; i != k; ++i) if (s[i] == ':') break;
719 if ((*tid = ti_get_tid(idx, s)) < 0) {
723 if (i == k) { /* dump the whole sequence */
724 *begin = 0; *end = 1<<29; free(s);
727 for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
733 if (*begin > 0) --*begin;
735 if (*begin > *end) return -1;
739 /*******************************
740 * retrieve a specified region *
741 *******************************/
743 #define MAX_BIN 37450 // =(8^6-1)/7+1
745 static inline int reg2bins(uint32_t beg, uint32_t end, uint16_t list[MAX_BIN])
748 if (beg >= end) return 0;
749 if (end >= 1u<<29) end = 1u<<29;
752 for (k = 1 + (beg>>26); k <= 1 + (end>>26); ++k) list[i++] = k;
753 for (k = 9 + (beg>>23); k <= 9 + (end>>23); ++k) list[i++] = k;
754 for (k = 73 + (beg>>20); k <= 73 + (end>>20); ++k) list[i++] = k;
755 for (k = 585 + (beg>>17); k <= 585 + (end>>17); ++k) list[i++] = k;
756 for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) list[i++] = k;
760 ti_iter_t ti_iter_first()
763 iter = calloc(1, sizeof(struct __ti_iter_t));
764 iter->from_first = 1;
768 ti_iter_t ti_iter_query(const ti_index_t *idx, int tid, int beg, int end)
771 int i, n_bins, n_off;
778 if (beg < 0) beg = 0;
779 if (end < beg) return 0;
780 // initialize the iterator
781 iter = calloc(1, sizeof(struct __ti_iter_t));
782 iter->idx = idx; iter->tid = tid; iter->beg = beg; iter->end = end; iter->i = -1;
784 bins = (uint16_t*)calloc(MAX_BIN, 2);
785 n_bins = reg2bins(beg, end, bins);
786 index = idx->index[tid];
787 if (idx->index2[tid].n > 0) {
788 min_off = (beg>>TAD_LIDX_SHIFT >= idx->index2[tid].n)? idx->index2[tid].offset[idx->index2[tid].n-1]
789 : idx->index2[tid].offset[beg>>TAD_LIDX_SHIFT];
790 if (min_off == 0) { // improvement for index files built by tabix prior to 0.1.4
791 int n = beg>>TAD_LIDX_SHIFT;
792 if (n > idx->index2[tid].n) n = idx->index2[tid].n;
793 for (i = n - 1; i >= 0; --i)
794 if (idx->index2[tid].offset[i] != 0) break;
795 if (i >= 0) min_off = idx->index2[tid].offset[i];
797 } else min_off = 0; // tabix 0.1.2 may produce such index files
798 for (i = n_off = 0; i < n_bins; ++i) {
799 if ((k = kh_get(i, index, bins[i])) != kh_end(index))
800 n_off += kh_value(index, k).n;
803 free(bins); return iter;
805 off = (pair64_t*)calloc(n_off, 16);
806 for (i = n_off = 0; i < n_bins; ++i) {
807 if ((k = kh_get(i, index, bins[i])) != kh_end(index)) {
809 ti_binlist_t *p = &kh_value(index, k);
810 for (j = 0; j < p->n; ++j)
811 if (p->list[j].v > min_off) off[n_off++] = p->list[j];
815 free(bins); free(off); return iter;
820 ks_introsort(offt, n_off, off);
821 // resolve completely contained adjacent blocks
822 for (i = 1, l = 0; i < n_off; ++i)
823 if (off[l].v < off[i].v)
826 // resolve overlaps between adjacent blocks; this may happen due to the merge in indexing
827 for (i = 1; i < n_off; ++i)
828 if (off[i-1].v >= off[i].u) off[i-1].v = off[i].u;
829 { // merge adjacent blocks
830 for (i = 1, l = 0; i < n_off; ++i) {
831 if (off[l].v>>16 == off[i].u>>16) off[l].v = off[i].v;
832 else off[++l] = off[i];
837 iter->n_off = n_off; iter->off = off;
841 const char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
843 if (iter->finished) return 0;
844 if (iter->from_first) {
846 if ((ret = ti_readline(fp, &iter->str)) < 0) {
850 if (len) *len = iter->str.l;
854 if (iter->n_off == 0) return 0;
857 if (iter->curr_off == 0 || iter->curr_off >= iter->off[iter->i].v) { // then jump to the next chunk
858 if (iter->i == iter->n_off - 1) break; // no more chunks
859 if (iter->i >= 0) assert(iter->curr_off == iter->off[iter->i].v); // otherwise bug
860 if (iter->i < 0 || iter->off[iter->i].v != iter->off[iter->i+1].u) { // not adjacent chunks; then seek
861 bgzf_seek(fp, iter->off[iter->i+1].u, SEEK_SET);
862 iter->curr_off = bgzf_tell(fp);
866 if ((ret = ti_readline(fp, &iter->str)) >= 0) {
868 iter->curr_off = bgzf_tell(fp);
869 if (iter->str.s[0] == iter->idx->conf.meta_char) continue;
870 get_intv((ti_index_t*)iter->idx, &iter->str, &intv);
871 if (intv.tid != iter->tid || intv.beg >= iter->end) break; // no need to proceed
872 else if (intv.end > iter->beg && iter->end > intv.beg) {
873 if (len) *len = iter->str.l;
876 } else break; // end of file
882 void ti_iter_destroy(ti_iter_t iter)
885 free(iter->str.s); free(iter->off);
890 int ti_fetch(BGZF *fp, const ti_index_t *idx, int tid, int beg, int end, void *data, ti_fetch_f func)
895 iter = ti_iter_query(idx, tid, beg, end);
896 while ((s = ti_iter_read(fp, iter, &len)) != 0)
898 ti_iter_destroy(iter);
902 const ti_conf_t *ti_get_conf(ti_index_t *idx) { return idx? &idx->conf : 0; }
908 tabix_t *ti_open(const char *fn, const char *fnidx)
912 if ((fp = bgzf_open(fn, "r")) == 0) return 0;
913 t = calloc(1, sizeof(tabix_t));
915 if (fnidx) t->fnidx = strdup(fnidx);
920 void ti_close(tabix_t *t)
924 if (t->idx) ti_index_destroy(t->idx);
925 free(t->fn); free(t->fnidx);
930 int ti_lazy_index_load(tabix_t *t)
932 if (t->idx == 0) { // load index
933 if (t->fnidx) t->idx = ti_index_load_local(t->fnidx);
934 else t->idx = ti_index_load(t->fn);
935 if (t->idx == 0) return -1; // fail to load index
940 ti_iter_t ti_queryi(tabix_t *t, int tid, int beg, int end)
942 if (tid < 0) return ti_iter_first();
943 if (ti_lazy_index_load(t) != 0) return 0;
944 return ti_iter_query(t->idx, tid, beg, end);
947 ti_iter_t ti_querys(tabix_t *t, const char *reg)
950 if (reg == 0) return ti_iter_first();
951 if (ti_lazy_index_load(t) != 0) return 0;
952 if (ti_parse_region(t->idx, reg, &tid, &beg, &end) < 0) return 0;
953 return ti_iter_query(t->idx, tid, beg, end);
956 ti_iter_t ti_query(tabix_t *t, const char *name, int beg, int end)
959 if (name == 0) return ti_iter_first();
960 // then need to load the index
961 if (ti_lazy_index_load(t) != 0) return 0;
962 if ((tid = ti_get_tid(t->idx, name)) < 0) return 0;
963 return ti_iter_query(t->idx, tid, beg, end);
966 const char *ti_read(tabix_t *t, ti_iter_t iter, int *len)
968 return ti_iter_read(t->fp, iter, len);