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index.c

#include <assert.h>
#include <ctype.h>
#include <sys/stat.h>
#include "bam_endian.h"
#include "kstring.h"
#include "bcf.h"
#ifdef _USE_KNETFILE
#include "knetfile.h"
#endif

#define TAD_LIDX_SHIFT 13

typedef struct {
      int32_t n, m;
      uint64_t *offset;
} bcf_lidx_t;

struct __bcf_idx_t {
      int32_t n;
      bcf_lidx_t *index2;
};

/************
 * indexing *
 ************/

static inline void insert_offset2(bcf_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;
}

bcf_idx_t *bcf_idx_core(bcf_t *bp, bcf_hdr_t *h)
{
      bcf_idx_t *idx;
      int32_t last_coor, last_tid;
      uint64_t last_off;
      kstring_t *str;
      BGZF *fp = bp->fp;
      bcf1_t *b;
      int ret;

      b = calloc(1, sizeof(bcf1_t));
      str = calloc(1, sizeof(kstring_t));
      idx = (bcf_idx_t*)calloc(1, sizeof(bcf_idx_t));
      idx->n = h->n_ref;
      idx->index2 = calloc(h->n_ref, sizeof(bcf_lidx_t));

      last_tid = 0xffffffffu;
      last_off = bgzf_tell(fp); last_coor = 0xffffffffu;
      while ((ret = bcf_read(bp, h, b)) > 0) {
            int end, tmp;
            if (last_tid != b->tid) { // change of chromosomes
                  last_tid = b->tid;
            } else if (last_coor > b->pos) {
                  fprintf(stderr, "[bcf_idx_core] the input is out of order\n");
                  free(str->s); free(str); free(idx); bcf_destroy(b);
                  return 0;
            }
            tmp = strlen(b->ref);
            end = b->pos + (tmp > 0? tmp : 1);
            insert_offset2(&idx->index2[b->tid], b->pos, end, last_off);
            last_off = bgzf_tell(fp);
            last_coor = b->pos;
      }
      free(str->s); free(str); bcf_destroy(b);
      return idx;
}

void bcf_idx_destroy(bcf_idx_t *idx)
{
      int i;
      if (idx == 0) return;
      for (i = 0; i < idx->n; ++i) free(idx->index2[i].offset);
      free(idx->index2);
      free(idx);
}

/******************
 * index file I/O *
 ******************/

void bcf_idx_save(const bcf_idx_t *idx, BGZF *fp)
{
      int32_t i, ti_is_be;
      ti_is_be = bam_is_big_endian();
      bgzf_write(fp, "BCI\4", 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);
      for (i = 0; i < idx->n; ++i) {
            bcf_lidx_t *index2 = idx->index2 + i;
            // 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 bcf_idx_t *bcf_idx_load_core(BGZF *fp)
{
      int i, ti_is_be;
      char magic[4];
      bcf_idx_t *idx;
      ti_is_be = bam_is_big_endian();
      if (fp == 0) {
            fprintf(stderr, "[%s] fail to load index.\n", __func__);
            return 0;
      }
      bgzf_read(fp, magic, 4);
      if (strncmp(magic, "BCI\4", 4)) {
            fprintf(stderr, "[%s] wrong magic number.\n", __func__);
            return 0;
      }
      idx = (bcf_idx_t*)calloc(1, sizeof(bcf_idx_t)); 
      bgzf_read(fp, &idx->n, 4);
      if (ti_is_be) bam_swap_endian_4p(&idx->n);
      idx->index2 = (bcf_lidx_t*)calloc(idx->n, sizeof(bcf_lidx_t));
      for (i = 0; i < idx->n; ++i) {
            bcf_lidx_t *index2 = idx->index2 + i;
            int j;
            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;
}

bcf_idx_t *bcf_idx_load_local(const char *fnidx)
{
      BGZF *fp;
      fp = bgzf_open(fnidx, "r");
      if (fp) {
            bcf_idx_t *idx = bcf_idx_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), ".bci");
      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;
}

bcf_idx_t *bcf_idx_load(const char *fn)
{
      bcf_idx_t *idx;
    char *fname = get_local_version(fn);
      if (fname == 0) return 0;
      idx = bcf_idx_load_local(fname);
    free(fname);
      return idx;
}

int bcf_idx_build2(const char *fn, const char *_fnidx)
{
      char *fnidx;
      BGZF *fpidx;
      bcf_t *bp;
      bcf_idx_t *idx;
      bcf_hdr_t *h;
      if ((bp = bcf_open(fn, "r")) == 0) {
            fprintf(stderr, "[bcf_idx_build2] fail to open the BAM file.\n");
            return -1;
      }
      h = bcf_hdr_read(bp);
      idx = bcf_idx_core(bp, h);
      bcf_close(bp);
      if (_fnidx == 0) {
            fnidx = (char*)calloc(strlen(fn) + 5, 1);
            strcpy(fnidx, fn); strcat(fnidx, ".bci");
      } else fnidx = strdup(_fnidx);
      fpidx = bgzf_open(fnidx, "w");
      if (fpidx == 0) {
            fprintf(stderr, "[bcf_idx_build2] fail to create the index file.\n");
            free(fnidx);
            return -1;
      }
      bcf_idx_save(idx, fpidx);
      bcf_idx_destroy(idx);
      bgzf_close(fpidx);
      free(fnidx);
      return 0;
}

int bcf_idx_build(const char *fn)
{
      return bcf_idx_build2(fn, 0);
}

/********************************************
 * parse a region in the format chr:beg-end *
 ********************************************/

int bcf_parse_region(void *str2id, 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 = bcf_str2id(str2id, 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 *
 *******************************/

uint64_t bcf_idx_query(const bcf_idx_t *idx, int tid, int beg)
{
      uint64_t min_off, *offset;
      int i;
      if (beg < 0) beg = 0;
      offset = idx->index2[tid].offset;
      for (i = beg>>TAD_LIDX_SHIFT; i < idx->index2[tid].n && offset[i] == 0; ++i);
      min_off = (i == idx->index2[tid].n)? offset[idx->index2[tid].n-1] : offset[i];
      return min_off;
}

int bcf_main_index(int argc, char *argv[])
{
      if (argc == 1) {
            fprintf(stderr, "Usage: bcftools index <in.bcf>\n");
            return 1;
      }
      bcf_idx_build(argv[1]);
      return 0;
}

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