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index.c

#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

00017 typedef struct {
      uint64_t u, v;
} pair64_t;

#define pair64_lt(a,b) ((a).u < (b).u)
KSORT_INIT(offt, pair64_t, pair64_lt)

00024 typedef struct {
      uint32_t m, n;
      pair64_t *list;
} ti_binlist_t;

00029 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)

00037 struct __ti_index_t {
      ti_conf_t conf;
      int32_t n, max;
      khash_t(s) *tname;
      khash_t(i) **index;
      ti_lidx_t *index2;
};

00045 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;
};

00054 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;
}

int ti_get_intv(const ti_conf_t *conf, int len, char *line, ti_interval_t *intv)
{
      int i, b = 0, id = 1, ncols = 0;
      char *s;
      intv->ss = intv->se = 0; intv->beg = intv->end = -1;
      for (i = 0; i <= len; ++i) {
            if (line[i] == '\t' || line[i] == 0) {
            ++ncols;
                  if (id == conf->sc) {
                        intv->ss = line + b; intv->se = line + i;
                  } else if (id == conf->bc) {
                        // here ->beg is 0-based.
                        intv->beg = intv->end = strtol(line + b, &s, 0);
                        if (!(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 ((conf->preset&0xffff) == TI_PRESET_GENERIC) {
                              if (id == conf->ec) intv->end = strtol(line + b, &s, 0);
                        } else if ((conf->preset&0xffff) == TI_PRESET_SAM) {
                              if (id == 6) { // CIGAR
                                    int l = 0, op;
                                    char *t;
                                    for (s = line + b; s < line + 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 ((conf->preset&0xffff) == TI_PRESET_VCF) {
                              // FIXME: the following is NOT tested and is likely to be buggy
                              if (id == 4) {
                                    if (b < i) intv->end = intv->beg + (i - b);
                              } else if (id == 8) { // look for "END="
                                    int c = line[i];
                                    line[i] = 0;
                                    s = strstr(line + b, "END=");
                                    if (s == line + b) s += 4;
                                    else if (s) {
                                          s = strstr(line + b, ";END=");
                                          if (s) s += 5;
                                    }
                                    if (s) intv->end = strtol(s, &s, 0);
                                    line[i] = c;
                              }
                        }
                  }
                  b = i + 1;
                  ++id;
            }
      }
/*
      if (ncols < conf->sc || ncols < conf->bc || ncols < conf->ec) {
            if (ncols == 1) fprintf(stderr,"[get_intv] Is the file tab-delimited? The line has %d field only: %s\n", ncols, line);
            else fprintf(stderr,"[get_intv] The line has %d field(s) only: %s\n", ncols, line);
            exit(1);
      }
*/
      if (intv->ss == 0 || intv->se == 0 || intv->beg < 0 || intv->end < 0) return -1;
      return 0;
}

static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
{
      ti_interval_t x;
      intv->tid = intv->beg = intv->end = intv->bin = -1;
      if (ti_get_intv(&idx->conf, str->l, str->s, &x) == 0) {
            int c = *x.se;
            *x.se = '\0'; intv->tid = get_tid(idx, x.ss); *x.se = c;
            intv->beg = x.beg; intv->end = x.end;
            intv->bin = ti_reg2bin(intv->beg, intv->end);
            return (intv->tid >= 0 && intv->beg >= 0 && intv->end >= 0)? 0 : -1;
      } else {
            fprintf(stderr, "[%s] the following line cannot be parsed and skipped: %s\n", __func__, str->s);
            return -1;
      }
}

/************
 * 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 uint64_t 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;
      return (uint64_t)beg<<32 | end;
}

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, offset0 = (uint64_t)-1, tmp;
      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 ( intv.beg<0 || intv.end<0 )
        {
            fprintf(stderr,"[ti_index_core] the indexes overlap or are out of bounds\n");
            exit(1);
        }
            if (last_tid != intv.tid) { // change of chromosomes
            if (last_tid>intv.tid )
            {
                fprintf(stderr,"[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);
                exit(1);
            }
                  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);
            }
            tmp = insert_offset2(&idx->index2[intv.tid], intv.beg, intv.end, last_off);
            if (last_off == 0) offset0 = tmp;
            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);
      if (offset0 != (uint64_t)-1 && idx->n && idx->index2[0].offset) {
            int i, beg = offset0>>32, end = offset0&0xffffffffu;
            for (i = beg; i <= end; ++i) idx->index2[0].offset[i] = 0;
      }

      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);
      if (idx == 0) fprintf(stderr, "[ti_index_load] fail to load the index: %s\n", fname);
    free(fname);
      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 file: %s\n", fn);
            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];
            }
      }
      if (n_off == 0) {
            free(bins); free(off); return iter;
      }
      free(bins);
      {
            int l;
            ks_introsort(offt, 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;
}

const ti_conf_t *ti_get_conf(ti_index_t *idx) { return idx? &idx->conf : 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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