+++ /dev/null
-#include <ctype.h>
-#include <assert.h>
-#include <sys/stat.h>
-#include "khash.h"
-#include "ksort.h"
-#include "kstring.h"
-#include "bam_endian.h"
-#ifdef _USE_KNETFILE
-#include "knetfile.h"
-#endif
-#include "tabix.h"
-
-#define TAD_MIN_CHUNK_GAP 32768
-// 1<<14 is the size of minimum bin.
-#define TAD_LIDX_SHIFT 14
-
-typedef struct {
- uint64_t u, v;
-} pair64_t;
-
-#define pair64_lt(a,b) ((a).u < (b).u)
-KSORT_INIT(off, pair64_t, pair64_lt)
-
-typedef struct {
- uint32_t m, n;
- pair64_t *list;
-} ti_binlist_t;
-
-typedef struct {
- int32_t n, m;
- uint64_t *offset;
-} ti_lidx_t;
-
-KHASH_MAP_INIT_INT(i, ti_binlist_t)
-KHASH_MAP_INIT_STR(s, int)
-
-struct __ti_index_t {
- ti_conf_t conf;
- int32_t n, max;
- khash_t(s) *tname;
- khash_t(i) **index;
- ti_lidx_t *index2;
-};
-
-struct __ti_iter_t {
- int from_first; // read from the first record; no random access
- int tid, beg, end, n_off, i, finished;
- uint64_t curr_off;
- kstring_t str;
- const ti_index_t *idx;
- pair64_t *off;
-};
-
-typedef struct {
- int tid, beg, end, bin;
-} ti_intv_t;
-
-ti_conf_t ti_conf_gff = { 0, 1, 4, 5, '#', 0 };
-ti_conf_t ti_conf_bed = { TI_FLAG_UCSC, 1, 2, 3, '#', 0 };
-ti_conf_t ti_conf_psltbl = { TI_FLAG_UCSC, 15, 17, 18, '#', 0 };
-ti_conf_t ti_conf_sam = { TI_PRESET_SAM, 3, 4, 0, '@', 0 };
-ti_conf_t ti_conf_vcf = { TI_PRESET_VCF, 1, 2, 0, '#', 0 };
-
-/***************
- * read a line *
- ***************/
-
-/*
-int ti_readline(BGZF *fp, kstring_t *str)
-{
- int c, l = 0;
- str->l = 0;
- while ((c = bgzf_getc(fp)) >= 0 && c != '\n') {
- ++l;
- if (c != '\r') kputc(c, str);
- }
- if (c < 0 && l == 0) return -1; // end of file
- return str->l;
-}
-*/
-
-/* Below is a faster implementation largely equivalent to the one
- * commented out above. */
-int ti_readline(BGZF *fp, kstring_t *str)
-{
- int l, state = 0;
- unsigned char *buf = (unsigned char*)fp->uncompressed_block;
- str->l = 0;
- do {
- if (fp->block_offset >= fp->block_length) {
- if (bgzf_read_block(fp) != 0) { state = -2; break; }
- if (fp->block_length == 0) { state = -1; break; }
- }
- for (l = fp->block_offset; l < fp->block_length && buf[l] != '\n'; ++l);
- if (l < fp->block_length) state = 1;
- l -= fp->block_offset;
- if (str->l + l + 1 >= str->m) {
- str->m = str->l + l + 2;
- kroundup32(str->m);
- str->s = (char*)realloc(str->s, str->m);
- }
- memcpy(str->s + str->l, buf + fp->block_offset, l);
- str->l += l;
- fp->block_offset += l + 1;
- if (fp->block_offset >= fp->block_length) {
-#ifdef _USE_KNETFILE
- fp->block_address = knet_tell(fp->x.fpr);
-#else
- fp->block_address = ftello(fp->file);
-#endif
- fp->block_offset = 0;
- fp->block_length = 0;
- }
- } while (state == 0);
- if (str->l == 0 && state < 0) return state;
- str->s[str->l] = 0;
- return str->l;
-}
-
-/*************************************
- * get the interval from a data line *
- *************************************/
-
-static inline int ti_reg2bin(uint32_t beg, uint32_t end)
-{
- --end;
- if (beg>>14 == end>>14) return 4681 + (beg>>14);
- if (beg>>17 == end>>17) return 585 + (beg>>17);
- if (beg>>20 == end>>20) return 73 + (beg>>20);
- if (beg>>23 == end>>23) return 9 + (beg>>23);
- if (beg>>26 == end>>26) return 1 + (beg>>26);
- return 0;
-}
-
-static int get_tid(ti_index_t *idx, const char *ss)
-{
- khint_t k;
- int tid;
- k = kh_get(s, idx->tname, ss);
- if (k == kh_end(idx->tname)) { // a new target sequence
- int ret, size;
- // update idx->n, ->max, ->index and ->index2
- if (idx->n == idx->max) {
- idx->max = idx->max? idx->max<<1 : 8;
- idx->index = realloc(idx->index, idx->max * sizeof(void*));
- idx->index2 = realloc(idx->index2, idx->max * sizeof(ti_lidx_t));
- }
- memset(&idx->index2[idx->n], 0, sizeof(ti_lidx_t));
- idx->index[idx->n++] = kh_init(i);
- // update ->tname
- tid = size = kh_size(idx->tname);
- k = kh_put(s, idx->tname, strdup(ss), &ret);
- kh_value(idx->tname, k) = size;
- assert(idx->n == kh_size(idx->tname));
- } else tid = kh_value(idx->tname, k);
- return tid;
-}
-
-static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
-{
- int i, b = 0, id = 1;
- char *s;
- intv->tid = intv->beg = intv->end = intv->bin = -1;
- for (i = 0; i <= str->l; ++i) {
- if (str->s[i] == '\t' || str->s[i] == 0) {
- if (id == idx->conf.sc) {
- str->s[i] = 0;
- intv->tid = get_tid(idx, str->s + b);
- if (i != str->l) str->s[i] = '\t';
- } else if (id == idx->conf.bc) {
- // here ->beg is 0-based.
- intv->beg = intv->end = strtol(str->s + b, &s, 0);
- if (!(idx->conf.preset&TI_FLAG_UCSC)) --intv->beg;
- else ++intv->end;
- if (intv->beg < 0) intv->beg = 0;
- if (intv->end < 1) intv->end = 1;
- } else {
- if ((idx->conf.preset&0xffff) == TI_PRESET_GENERIC) {
- if (id == idx->conf.ec) intv->end = strtol(str->s + b, &s, 0);
- } else if ((idx->conf.preset&0xffff) == TI_PRESET_SAM) {
- if (id == 6) { // CIGAR
- int l = 0, op;
- char *t;
- for (s = str->s + b; s < str->s + i;) {
- long x = strtol(s, &t, 10);
- op = toupper(*t);
- if (op == 'M' || op == 'D' || op == 'N') l += x;
- s = t + 1;
- }
- if (l == 0) l = 1;
- intv->end = intv->beg + l;
- }
- } else if ((idx->conf.preset&0xffff) == TI_PRESET_VCF) {
- // FIXME: the following is NOT tested and is likely to be buggy
- if (id == 5) { // ALT
- char *t;
- int max = 1;
- for (s = str->s + b; s < str->s + i;) {
- if (s[i] == 'D') {
- long x = strtol(s + 1, &t, 10);
- if (x > max) max = x;
- s = t + 1;
- } else ++s;
- }
- intv->end = intv->beg + max;
- }
- }
- }
- b = i + 1;
- ++id;
- }
- }
- if (intv->tid < 0 || intv->beg < 0 || intv->end < 0) return -1;
- intv->bin = ti_reg2bin(intv->beg, intv->end);
- return 0;
-}
-
-/************
- * indexing *
- ************/
-
-// requirement: len <= LEN_MASK
-static inline void insert_offset(khash_t(i) *h, int bin, uint64_t beg, uint64_t end)
-{
- khint_t k;
- ti_binlist_t *l;
- int ret;
- k = kh_put(i, h, bin, &ret);
- l = &kh_value(h, k);
- if (ret) { // not present
- l->m = 1; l->n = 0;
- l->list = (pair64_t*)calloc(l->m, 16);
- }
- if (l->n == l->m) {
- l->m <<= 1;
- l->list = (pair64_t*)realloc(l->list, l->m * 16);
- }
- l->list[l->n].u = beg; l->list[l->n++].v = end;
-}
-
-static inline void insert_offset2(ti_lidx_t *index2, int _beg, int _end, uint64_t offset)
-{
- int i, beg, end;
- beg = _beg >> TAD_LIDX_SHIFT;
- end = (_end - 1) >> TAD_LIDX_SHIFT;
- if (index2->m < end + 1) {
- int old_m = index2->m;
- index2->m = end + 1;
- kroundup32(index2->m);
- index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8);
- memset(index2->offset + old_m, 0, 8 * (index2->m - old_m));
- }
- if (beg == end) {
- if (index2->offset[beg] == 0) index2->offset[beg] = offset;
- } else {
- for (i = beg; i <= end; ++i)
- if (index2->offset[i] == 0) index2->offset[i] = offset;
- }
- if (index2->n < end + 1) index2->n = end + 1;
-}
-
-static void merge_chunks(ti_index_t *idx)
-{
- khash_t(i) *index;
- int i, l, m;
- khint_t k;
- for (i = 0; i < idx->n; ++i) {
- index = idx->index[i];
- for (k = kh_begin(index); k != kh_end(index); ++k) {
- ti_binlist_t *p;
- if (!kh_exist(index, k)) continue;
- p = &kh_value(index, k);
- m = 0;
- for (l = 1; l < p->n; ++l) {
- if (p->list[m].v>>16 == p->list[l].u>>16) p->list[m].v = p->list[l].v;
- else p->list[++m] = p->list[l];
- } // ~for(l)
- p->n = m + 1;
- } // ~for(k)
- } // ~for(i)
-}
-
-static void fill_missing(ti_index_t *idx)
-{
- int i, j;
- for (i = 0; i < idx->n; ++i) {
- ti_lidx_t *idx2 = &idx->index2[i];
- for (j = 1; j < idx2->n; ++j)
- if (idx2->offset[j] == 0)
- idx2->offset[j] = idx2->offset[j-1];
- }
-}
-
-ti_index_t *ti_index_core(BGZF *fp, const ti_conf_t *conf)
-{
- int ret;
- ti_index_t *idx;
- uint32_t last_bin, save_bin;
- int32_t last_coor, last_tid, save_tid;
- uint64_t save_off, last_off, lineno = 0;
- kstring_t *str;
-
- str = calloc(1, sizeof(kstring_t));
-
- idx = (ti_index_t*)calloc(1, sizeof(ti_index_t));
- idx->conf = *conf;
- idx->n = idx->max = 0;
- idx->tname = kh_init(s);
- idx->index = 0;
- idx->index2 = 0;
-
- save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
- save_off = last_off = bgzf_tell(fp); last_coor = 0xffffffffu;
- while ((ret = ti_readline(fp, str)) >= 0) {
- ti_intv_t intv;
- ++lineno;
- if (lineno <= idx->conf.line_skip || str->s[0] == idx->conf.meta_char) {
- last_off = bgzf_tell(fp);
- continue;
- }
- get_intv(idx, str, &intv);
- if (last_tid != intv.tid) { // change of chromosomes
- last_tid = intv.tid;
- last_bin = 0xffffffffu;
- } else if (last_coor > intv.beg) {
- fprintf(stderr, "[ti_index_core] the file out of order at line %llu\n", (unsigned long long)lineno);
- exit(1);
- }
- insert_offset2(&idx->index2[intv.tid], intv.beg, intv.end, last_off);
- if (intv.bin != last_bin) { // then possibly write the binning index
- if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record
- insert_offset(idx->index[save_tid], save_bin, save_off, last_off);
- save_off = last_off;
- save_bin = last_bin = intv.bin;
- save_tid = intv.tid;
- if (save_tid < 0) break;
- }
- if (bgzf_tell(fp) <= last_off) {
- fprintf(stderr, "[ti_index_core] bug in BGZF: %llx < %llx\n",
- (unsigned long long)bgzf_tell(fp), (unsigned long long)last_off);
- exit(1);
- }
- last_off = bgzf_tell(fp);
- last_coor = intv.beg;
- }
- if (save_tid >= 0) insert_offset(idx->index[save_tid], save_bin, save_off, bgzf_tell(fp));
- merge_chunks(idx);
- fill_missing(idx);
-
- free(str->s); free(str);
- return idx;
-}
-
-void ti_index_destroy(ti_index_t *idx)
-{
- khint_t k;
- int i;
- if (idx == 0) return;
- // destroy the name hash table
- for (k = kh_begin(idx->tname); k != kh_end(idx->tname); ++k) {
- if (kh_exist(idx->tname, k))
- free((char*)kh_key(idx->tname, k));
- }
- kh_destroy(s, idx->tname);
- // destroy the binning index
- for (i = 0; i < idx->n; ++i) {
- khash_t(i) *index = idx->index[i];
- ti_lidx_t *index2 = idx->index2 + i;
- for (k = kh_begin(index); k != kh_end(index); ++k) {
- if (kh_exist(index, k))
- free(kh_value(index, k).list);
- }
- kh_destroy(i, index);
- free(index2->offset);
- }
- free(idx->index);
- // destroy the linear index
- free(idx->index2);
- free(idx);
-}
-
-/******************
- * index file I/O *
- ******************/
-
-void ti_index_save(const ti_index_t *idx, BGZF *fp)
-{
- int32_t i, size, ti_is_be;
- khint_t k;
- ti_is_be = bam_is_big_endian();
- bgzf_write(fp, "TBI\1", 4);
- if (ti_is_be) {
- uint32_t x = idx->n;
- bgzf_write(fp, bam_swap_endian_4p(&x), 4);
- } else bgzf_write(fp, &idx->n, 4);
- assert(sizeof(ti_conf_t) == 24);
- if (ti_is_be) { // write ti_conf_t;
- uint32_t x[6];
- memcpy(x, &idx->conf, 24);
- for (i = 0; i < 6; ++i) bgzf_write(fp, bam_swap_endian_4p(&x[i]), 4);
- } else bgzf_write(fp, &idx->conf, sizeof(ti_conf_t));
- { // write target names
- char **name;
- int32_t l = 0;
- name = calloc(kh_size(idx->tname), sizeof(void*));
- for (k = kh_begin(idx->tname); k != kh_end(idx->tname); ++k)
- if (kh_exist(idx->tname, k))
- name[kh_value(idx->tname, k)] = (char*)kh_key(idx->tname, k);
- for (i = 0; i < kh_size(idx->tname); ++i)
- l += strlen(name[i]) + 1;
- if (ti_is_be) bgzf_write(fp, bam_swap_endian_4p(&l), 4);
- else bgzf_write(fp, &l, 4);
- for (i = 0; i < kh_size(idx->tname); ++i)
- bgzf_write(fp, name[i], strlen(name[i]) + 1);
- free(name);
- }
- for (i = 0; i < idx->n; ++i) {
- khash_t(i) *index = idx->index[i];
- ti_lidx_t *index2 = idx->index2 + i;
- // write binning index
- size = kh_size(index);
- if (ti_is_be) { // big endian
- uint32_t x = size;
- bgzf_write(fp, bam_swap_endian_4p(&x), 4);
- } else bgzf_write(fp, &size, 4);
- for (k = kh_begin(index); k != kh_end(index); ++k) {
- if (kh_exist(index, k)) {
- ti_binlist_t *p = &kh_value(index, k);
- if (ti_is_be) { // big endian
- uint32_t x;
- x = kh_key(index, k); bgzf_write(fp, bam_swap_endian_4p(&x), 4);
- x = p->n; bgzf_write(fp, bam_swap_endian_4p(&x), 4);
- for (x = 0; (int)x < p->n; ++x) {
- bam_swap_endian_8p(&p->list[x].u);
- bam_swap_endian_8p(&p->list[x].v);
- }
- bgzf_write(fp, p->list, 16 * p->n);
- for (x = 0; (int)x < p->n; ++x) {
- bam_swap_endian_8p(&p->list[x].u);
- bam_swap_endian_8p(&p->list[x].v);
- }
- } else {
- bgzf_write(fp, &kh_key(index, k), 4);
- bgzf_write(fp, &p->n, 4);
- bgzf_write(fp, p->list, 16 * p->n);
- }
- }
- }
- // write linear index (index2)
- if (ti_is_be) {
- int x = index2->n;
- bgzf_write(fp, bam_swap_endian_4p(&x), 4);
- } else bgzf_write(fp, &index2->n, 4);
- if (ti_is_be) { // big endian
- int x;
- for (x = 0; (int)x < index2->n; ++x)
- bam_swap_endian_8p(&index2->offset[x]);
- bgzf_write(fp, index2->offset, 8 * index2->n);
- for (x = 0; (int)x < index2->n; ++x)
- bam_swap_endian_8p(&index2->offset[x]);
- } else bgzf_write(fp, index2->offset, 8 * index2->n);
- }
-}
-
-static ti_index_t *ti_index_load_core(BGZF *fp)
-{
- int i, ti_is_be;
- char magic[4];
- ti_index_t *idx;
- ti_is_be = bam_is_big_endian();
- if (fp == 0) {
- fprintf(stderr, "[ti_index_load_core] fail to load index.\n");
- return 0;
- }
- bgzf_read(fp, magic, 4);
- if (strncmp(magic, "TBI\1", 4)) {
- fprintf(stderr, "[ti_index_load] wrong magic number.\n");
- return 0;
- }
- idx = (ti_index_t*)calloc(1, sizeof(ti_index_t));
- bgzf_read(fp, &idx->n, 4);
- if (ti_is_be) bam_swap_endian_4p(&idx->n);
- idx->tname = kh_init(s);
- idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
- idx->index2 = (ti_lidx_t*)calloc(idx->n, sizeof(ti_lidx_t));
- // read idx->conf
- bgzf_read(fp, &idx->conf, sizeof(ti_conf_t));
- if (ti_is_be) {
- bam_swap_endian_4p(&idx->conf.preset);
- bam_swap_endian_4p(&idx->conf.sc);
- bam_swap_endian_4p(&idx->conf.bc);
- bam_swap_endian_4p(&idx->conf.ec);
- bam_swap_endian_4p(&idx->conf.meta_char);
- bam_swap_endian_4p(&idx->conf.line_skip);
- }
- { // read target names
- int j, ret;
- kstring_t *str;
- int32_t l;
- uint8_t *buf;
- bgzf_read(fp, &l, 4);
- if (ti_is_be) bam_swap_endian_4p(&l);
- buf = calloc(l, 1);
- bgzf_read(fp, buf, l);
- str = calloc(1, sizeof(kstring_t));
- for (i = j = 0; i < l; ++i) {
- if (buf[i] == 0) {
- khint_t k = kh_put(s, idx->tname, strdup(str->s), &ret);
- kh_value(idx->tname, k) = j++;
- str->l = 0;
- } else kputc(buf[i], str);
- }
- free(str->s); free(str); free(buf);
- }
- for (i = 0; i < idx->n; ++i) {
- khash_t(i) *index;
- ti_lidx_t *index2 = idx->index2 + i;
- uint32_t key, size;
- khint_t k;
- int j, ret;
- ti_binlist_t *p;
- index = idx->index[i] = kh_init(i);
- // load binning index
- bgzf_read(fp, &size, 4);
- if (ti_is_be) bam_swap_endian_4p(&size);
- for (j = 0; j < (int)size; ++j) {
- bgzf_read(fp, &key, 4);
- if (ti_is_be) bam_swap_endian_4p(&key);
- k = kh_put(i, index, key, &ret);
- p = &kh_value(index, k);
- bgzf_read(fp, &p->n, 4);
- if (ti_is_be) bam_swap_endian_4p(&p->n);
- p->m = p->n;
- p->list = (pair64_t*)malloc(p->m * 16);
- bgzf_read(fp, p->list, 16 * p->n);
- if (ti_is_be) {
- int x;
- for (x = 0; x < p->n; ++x) {
- bam_swap_endian_8p(&p->list[x].u);
- bam_swap_endian_8p(&p->list[x].v);
- }
- }
- }
- // load linear index
- bgzf_read(fp, &index2->n, 4);
- if (ti_is_be) bam_swap_endian_4p(&index2->n);
- index2->m = index2->n;
- index2->offset = (uint64_t*)calloc(index2->m, 8);
- bgzf_read(fp, index2->offset, index2->n * 8);
- if (ti_is_be)
- for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]);
- }
- return idx;
-}
-
-ti_index_t *ti_index_load_local(const char *fnidx)
-{
- BGZF *fp;
- fp = bgzf_open(fnidx, "r");
- if (fp) {
- ti_index_t *idx = ti_index_load_core(fp);
- bgzf_close(fp);
- return idx;
- } else return 0;
-}
-
-#ifdef _USE_KNETFILE
-static void download_from_remote(const char *url)
-{
- const int buf_size = 1 * 1024 * 1024;
- char *fn;
- FILE *fp;
- uint8_t *buf;
- knetFile *fp_remote;
- int l;
- if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return;
- l = strlen(url);
- for (fn = (char*)url + l - 1; fn >= url; --fn)
- if (*fn == '/') break;
- ++fn; // fn now points to the file name
- fp_remote = knet_open(url, "r");
- if (fp_remote == 0) {
- fprintf(stderr, "[download_from_remote] fail to open remote file.\n");
- return;
- }
- if ((fp = fopen(fn, "w")) == 0) {
- fprintf(stderr, "[download_from_remote] fail to create file in the working directory.\n");
- knet_close(fp_remote);
- return;
- }
- buf = (uint8_t*)calloc(buf_size, 1);
- while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
- fwrite(buf, 1, l, fp);
- free(buf);
- fclose(fp);
- knet_close(fp_remote);
-}
-#else
-static void download_from_remote(const char *url)
-{
- return;
-}
-#endif
-
-static char *get_local_version(const char *fn)
-{
- struct stat sbuf;
- char *fnidx = (char*)calloc(strlen(fn) + 5, 1);
- strcat(strcpy(fnidx, fn), ".tbi");
- if ((strstr(fnidx, "ftp://") == fnidx || strstr(fnidx, "http://") == fnidx)) {
- char *p, *url;
- int l = strlen(fnidx);
- for (p = fnidx + l - 1; p >= fnidx; --p)
- if (*p == '/') break;
- url = fnidx; fnidx = strdup(p + 1);
- if (stat(fnidx, &sbuf) == 0) {
- free(url);
- return fnidx;
- }
- fprintf(stderr, "[%s] downloading the index file...\n", __func__);
- download_from_remote(url);
- free(url);
- }
- if (stat(fnidx, &sbuf) == 0) return fnidx;
- free(fnidx); return 0;
-}
-
-const char **ti_seqname(const ti_index_t *idx, int *n)
-{
- const char **names;
- khint_t k;
- *n = idx->n;
- names = calloc(idx->n, sizeof(void*));
- for (k = kh_begin(idx->tname); k < kh_end(idx->tname); ++k)
- if (kh_exist(idx->tname, k))
- names[kh_val(idx->tname, k)] = kh_key(idx->tname, k);
- return names;
-}
-
-ti_index_t *ti_index_load(const char *fn)
-{
- ti_index_t *idx;
- char *fname = get_local_version(fn);
- if (fname == 0) return 0;
- idx = ti_index_load_local(fname);
- free(fname);
- if (idx == 0) fprintf(stderr, "[ti_index_load] fail to load BAM index.\n");
- return idx;
-}
-
-int ti_index_build2(const char *fn, const ti_conf_t *conf, const char *_fnidx)
-{
- char *fnidx;
- BGZF *fp, *fpidx;
- ti_index_t *idx;
- if ((fp = bgzf_open(fn, "r")) == 0) {
- fprintf(stderr, "[ti_index_build2] fail to open the BAM file.\n");
- return -1;
- }
- idx = ti_index_core(fp, conf);
- bgzf_close(fp);
- if (_fnidx == 0) {
- fnidx = (char*)calloc(strlen(fn) + 5, 1);
- strcpy(fnidx, fn); strcat(fnidx, ".tbi");
- } else fnidx = strdup(_fnidx);
- fpidx = bgzf_open(fnidx, "w");
- if (fpidx == 0) {
- fprintf(stderr, "[ti_index_build2] fail to create the index file.\n");
- free(fnidx);
- return -1;
- }
- ti_index_save(idx, fpidx);
- ti_index_destroy(idx);
- bgzf_close(fpidx);
- free(fnidx);
- return 0;
-}
-
-int ti_index_build(const char *fn, const ti_conf_t *conf)
-{
- return ti_index_build2(fn, conf, 0);
-}
-
-/********************************************
- * parse a region in the format chr:beg-end *
- ********************************************/
-
-int ti_get_tid(const ti_index_t *idx, const char *name)
-{
- khiter_t iter;
- const khash_t(s) *h = idx->tname;
- iter = kh_get(s, h, name); /* get the tid */
- if (iter == kh_end(h)) return -1;
- return kh_value(h, iter);
-}
-
-int ti_parse_region(const ti_index_t *idx, const char *str, int *tid, int *begin, int *end)
-{
- char *s, *p;
- int i, l, k;
- l = strlen(str);
- p = s = (char*)malloc(l+1);
- /* squeeze out "," */
- for (i = k = 0; i != l; ++i)
- if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i];
- s[k] = 0;
- for (i = 0; i != k; ++i) if (s[i] == ':') break;
- s[i] = 0;
- if ((*tid = ti_get_tid(idx, s)) < 0) {
- free(s);
- return -1;
- }
- if (i == k) { /* dump the whole sequence */
- *begin = 0; *end = 1<<29; free(s);
- return 0;
- }
- for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
- *begin = atoi(p);
- if (i < k) {
- p = s + i + 1;
- *end = atoi(p);
- } else *end = 1<<29;
- if (*begin > 0) --*begin;
- free(s);
- if (*begin > *end) return -1;
- return 0;
-}
-
-/*******************************
- * retrieve a specified region *
- *******************************/
-
-#define MAX_BIN 37450 // =(8^6-1)/7+1
-
-static inline int reg2bins(uint32_t beg, uint32_t end, uint16_t list[MAX_BIN])
-{
- int i = 0, k;
- if (beg >= end) return 0;
- if (end >= 1u<<29) end = 1u<<29;
- --end;
- list[i++] = 0;
- for (k = 1 + (beg>>26); k <= 1 + (end>>26); ++k) list[i++] = k;
- for (k = 9 + (beg>>23); k <= 9 + (end>>23); ++k) list[i++] = k;
- for (k = 73 + (beg>>20); k <= 73 + (end>>20); ++k) list[i++] = k;
- for (k = 585 + (beg>>17); k <= 585 + (end>>17); ++k) list[i++] = k;
- for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) list[i++] = k;
- return i;
-}
-
-ti_iter_t ti_iter_first()
-{
- ti_iter_t iter;
- iter = calloc(1, sizeof(struct __ti_iter_t));
- iter->from_first = 1;
- return iter;
-}
-
-ti_iter_t ti_iter_query(const ti_index_t *idx, int tid, int beg, int end)
-{
- uint16_t *bins;
- int i, n_bins, n_off;
- pair64_t *off;
- khint_t k;
- khash_t(i) *index;
- uint64_t min_off;
- ti_iter_t iter = 0;
-
- if (beg < 0) beg = 0;
- if (end < beg) return 0;
- // initialize the iterator
- iter = calloc(1, sizeof(struct __ti_iter_t));
- iter->idx = idx; iter->tid = tid; iter->beg = beg; iter->end = end; iter->i = -1;
- // random access
- bins = (uint16_t*)calloc(MAX_BIN, 2);
- n_bins = reg2bins(beg, end, bins);
- index = idx->index[tid];
- if (idx->index2[tid].n > 0) {
- min_off = (beg>>TAD_LIDX_SHIFT >= idx->index2[tid].n)? idx->index2[tid].offset[idx->index2[tid].n-1]
- : idx->index2[tid].offset[beg>>TAD_LIDX_SHIFT];
- if (min_off == 0) { // improvement for index files built by tabix prior to 0.1.4
- int n = beg>>TAD_LIDX_SHIFT;
- if (n > idx->index2[tid].n) n = idx->index2[tid].n;
- for (i = n - 1; i >= 0; --i)
- if (idx->index2[tid].offset[i] != 0) break;
- if (i >= 0) min_off = idx->index2[tid].offset[i];
- }
- } else min_off = 0; // tabix 0.1.2 may produce such index files
- for (i = n_off = 0; i < n_bins; ++i) {
- if ((k = kh_get(i, index, bins[i])) != kh_end(index))
- n_off += kh_value(index, k).n;
- }
- if (n_off == 0) {
- free(bins); return iter;
- }
- off = (pair64_t*)calloc(n_off, 16);
- for (i = n_off = 0; i < n_bins; ++i) {
- if ((k = kh_get(i, index, bins[i])) != kh_end(index)) {
- int j;
- ti_binlist_t *p = &kh_value(index, k);
- for (j = 0; j < p->n; ++j)
- if (p->list[j].v > min_off) off[n_off++] = p->list[j];
- }
- }
- free(bins);
- {
- int l;
- ks_introsort(off, n_off, off);
- // resolve completely contained adjacent blocks
- for (i = 1, l = 0; i < n_off; ++i)
- if (off[l].v < off[i].v)
- off[++l] = off[i];
- n_off = l + 1;
- // resolve overlaps between adjacent blocks; this may happen due to the merge in indexing
- for (i = 1; i < n_off; ++i)
- if (off[i-1].v >= off[i].u) off[i-1].v = off[i].u;
- { // merge adjacent blocks
- for (i = 1, l = 0; i < n_off; ++i) {
- if (off[l].v>>16 == off[i].u>>16) off[l].v = off[i].v;
- else off[++l] = off[i];
- }
- n_off = l + 1;
- }
- }
- iter->n_off = n_off; iter->off = off;
- return iter;
-}
-
-const char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
-{
- if (iter->finished) return 0;
- if (iter->from_first) {
- int ret;
- if ((ret = ti_readline(fp, &iter->str)) < 0) {
- iter->finished = 1;
- return 0;
- } else {
- if (len) *len = iter->str.l;
- return iter->str.s;
- }
- }
- if (iter->n_off == 0) return 0;
- while (1) {
- int ret;
- if (iter->curr_off == 0 || iter->curr_off >= iter->off[iter->i].v) { // then jump to the next chunk
- if (iter->i == iter->n_off - 1) break; // no more chunks
- if (iter->i >= 0) assert(iter->curr_off == iter->off[iter->i].v); // otherwise bug
- if (iter->i < 0 || iter->off[iter->i].v != iter->off[iter->i+1].u) { // not adjacent chunks; then seek
- bgzf_seek(fp, iter->off[iter->i+1].u, SEEK_SET);
- iter->curr_off = bgzf_tell(fp);
- }
- ++iter->i;
- }
- if ((ret = ti_readline(fp, &iter->str)) >= 0) {
- ti_intv_t intv;
- iter->curr_off = bgzf_tell(fp);
- if (iter->str.s[0] == iter->idx->conf.meta_char) continue;
- get_intv((ti_index_t*)iter->idx, &iter->str, &intv);
- if (intv.tid != iter->tid || intv.beg >= iter->end) break; // no need to proceed
- else if (intv.end > iter->beg && iter->end > intv.beg) {
- if (len) *len = iter->str.l;
- return iter->str.s;
- }
- } else break; // end of file
- }
- iter->finished = 1;
- return 0;
-}
-
-void ti_iter_destroy(ti_iter_t iter)
-{
- if (iter) {
- free(iter->str.s); free(iter->off);
- free(iter);
- }
-}
-
-int ti_fetch(BGZF *fp, const ti_index_t *idx, int tid, int beg, int end, void *data, ti_fetch_f func)
-{
- ti_iter_t iter;
- const char *s;
- int len;
- iter = ti_iter_query(idx, tid, beg, end);
- while ((s = ti_iter_read(fp, iter, &len)) != 0)
- func(len, s, data);
- ti_iter_destroy(iter);
- return 0;
-}
-
-/*******************
- * High-level APIs *
- *******************/
-
-tabix_t *ti_open(const char *fn, const char *fnidx)
-{
- tabix_t *t;
- BGZF *fp;
- if ((fp = bgzf_open(fn, "r")) == 0) return 0;
- t = calloc(1, sizeof(tabix_t));
- t->fn = strdup(fn);
- if (fnidx) t->fnidx = strdup(fnidx);
- t->fp = fp;
- return t;
-}
-
-void ti_close(tabix_t *t)
-{
- if (t) {
- bgzf_close(t->fp);
- if (t->idx) ti_index_destroy(t->idx);
- free(t->fn); free(t->fnidx);
- free(t);
- }
-}
-
-int ti_lazy_index_load(tabix_t *t)
-{
- if (t->idx == 0) { // load index
- if (t->fnidx) t->idx = ti_index_load_local(t->fnidx);
- else t->idx = ti_index_load(t->fn);
- if (t->idx == 0) return -1; // fail to load index
- }
- return 0;
-}
-
-ti_iter_t ti_queryi(tabix_t *t, int tid, int beg, int end)
-{
- if (tid < 0) return ti_iter_first();
- if (ti_lazy_index_load(t) != 0) return 0;
- return ti_iter_query(t->idx, tid, beg, end);
-}
-
-ti_iter_t ti_querys(tabix_t *t, const char *reg)
-{
- int tid, beg, end;
- if (reg == 0) return ti_iter_first();
- if (ti_lazy_index_load(t) != 0) return 0;
- if (ti_parse_region(t->idx, reg, &tid, &beg, &end) < 0) return 0;
- return ti_iter_query(t->idx, tid, beg, end);
-}
-
-ti_iter_t ti_query(tabix_t *t, const char *name, int beg, int end)
-{
- int tid;
- if (name == 0) return ti_iter_first();
- // then need to load the index
- if (ti_lazy_index_load(t) != 0) return 0;
- if ((tid = ti_get_tid(t->idx, name)) < 0) return 0;
- return ti_iter_query(t->idx, tid, beg, end);
-}
-
-const char *ti_read(tabix_t *t, ti_iter_t iter, int *len)
-{
- return ti_iter_read(t->fp, iter, len);
-}
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