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bam_aux.c

#include <ctype.h>
#include "bam.h"
#include "khash.h"
typedef char *str_p;
KHASH_MAP_INIT_STR(s, int)
KHASH_MAP_INIT_STR(r2l, str_p)

void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data)
{
      int ori_len = b->data_len;
      b->data_len += 3 + len;
      b->l_aux += 3 + len;
      if (b->m_data < b->data_len) {
            b->m_data = b->data_len;
            kroundup32(b->m_data);
            b->data = (uint8_t*)realloc(b->data, b->m_data);
      }
      b->data[ori_len] = tag[0]; b->data[ori_len + 1] = tag[1];
      b->data[ori_len + 2] = type;
      memcpy(b->data + ori_len + 3, data, len);
}

uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2])
{
      return bam_aux_get(b, tag);
}

#define __skip_tag(s) do { \
            int type = toupper(*(s));                                                           \
            ++(s);                                                                                          \
            if (type == 'C' || type == 'A') ++(s);                                        \
            else if (type == 'S') (s) += 2;                                                     \
            else if (type == 'I' || type == 'F') (s) += 4;                          \
            else if (type == 'D') (s) += 8;                                                     \
            else if (type == 'Z' || type == 'H') { while (*(s)) ++(s); ++(s); } \
      } while (0)

uint8_t *bam_aux_get(const bam1_t *b, const char tag[2])
{
      uint8_t *s;
      int y = tag[0]<<8 | tag[1];
      s = bam1_aux(b);
      while (s < b->data + b->data_len) {
            int x = (int)s[0]<<8 | s[1];
            s += 2;
            if (x == y) return s;
            __skip_tag(s);
      }
      return 0;
}
// s MUST BE returned by bam_aux_get()
int bam_aux_del(bam1_t *b, uint8_t *s)
{
      uint8_t *p, *aux;
      aux = bam1_aux(b);
      p = s - 2;
      __skip_tag(s);
      memmove(p, s, b->l_aux - (s - aux));
      b->data_len -= s - p;
      b->l_aux -= s - p;
      return 0;
}

void bam_init_header_hash(bam_header_t *header)
{
      if (header->hash == 0) {
            int ret, i;
            khiter_t iter;
            khash_t(s) *h;
            header->hash = h = kh_init(s);
            for (i = 0; i < header->n_targets; ++i) {
                  iter = kh_put(s, h, header->target_name[i], &ret);
                  kh_value(h, iter) = i;
            }
      }
}

void bam_destroy_header_hash(bam_header_t *header)
{
      if (header->hash)
            kh_destroy(s, (khash_t(s)*)header->hash);
}

int32_t bam_get_tid(const bam_header_t *header, const char *seq_name)
{
      khint_t k;
      khash_t(s) *h = (khash_t(s)*)header->hash;
      k = kh_get(s, h, seq_name);
      return k == kh_end(h)? -1 : kh_value(h, k);
}

int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end)
{
      char *s, *p;
      int i, l, k;
      khiter_t iter;
      khash_t(s) *h;

      bam_init_header_hash(header);
      h = (khash_t(s)*)header->hash;

      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;
      iter = kh_get(s, h, s); /* get the ref_id */
      if (iter == kh_end(h)) { // name not found
            *ref_id = -1; free(s);
            return -1;
      }
      *ref_id = kh_value(h, iter);
      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) {
            fprintf(stderr, "[bam_parse_region] invalid region.\n");
            return -1;
      }
      return 0;
}

int32_t bam_aux2i(const uint8_t *s)
{
      int type;
      if (s == 0) return 0;
      type = *s++;
      if (type == 'c') return (int32_t)*(int8_t*)s;
      else if (type == 'C') return (int32_t)*(uint8_t*)s;
      else if (type == 's') return (int32_t)*(int16_t*)s;
      else if (type == 'S') return (int32_t)*(uint16_t*)s;
      else if (type == 'i' || type == 'I') return *(int32_t*)s;
      else return 0;
}

float bam_aux2f(const uint8_t *s)
{
      int type;
      type = *s++;
      if (s == 0) return 0.0;
      if (type == 'f') return *(float*)s;
      else return 0.0;
}

double bam_aux2d(const uint8_t *s)
{
      int type;
      type = *s++;
      if (s == 0) return 0.0;
      if (type == 'd') return *(double*)s;
      else return 0.0;
}

char bam_aux2A(const uint8_t *s)
{
      int type;
      type = *s++;
      if (s == 0) return 0;
      if (type == 'A') return *(char*)s;
      else return 0;
}

char *bam_aux2Z(const uint8_t *s)
{
      int type;
      type = *s++;
      if (s == 0) return 0;
      if (type == 'Z' || type == 'H') return (char*)s;
      else return 0;
}

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