wztarget.h

#ifndef _WZTARGET_H
#define _WZTARGET_H

#include "wvec.h"

/* This file defines target-tid mapping */

typedef struct target_t {
  int tid;
  char *name;
  uint32_t len;
} target_t;

DEFINE_VECTOR(target_v, target_t);

#define target_name(targets, tid) (ref_target_v((targets), (tid))->name)

static inline void destroy_target_v(target_v *targets) {
  unsigned i;
  for (i=0; i<targets->size; ++i) {
    target_t *t = ref_target_v(targets, i);
    if (t->name) free(t->name);
  }
  free_target_v(targets);
}

static inline unsigned locate_or_insert_target_v(target_v *targets, char *chr) {
  unsigned i;
  target_t *t;
  for (i=0; i<targets->size; ++i) {
    t = ref_target_v(targets, i);
    if (strcmp(t->name, chr)==0) return i;
  }
  t = next_ref_target_v(targets);
  t->name = strdup(chr);
  t->tid = ((int) targets->size)-1;
  return t->tid;
}

/* static inline target_v *bamheader2targets(bam_header_t *header) { */
/*   target_v *targets = init_target_v(50); */
/*   target_t *t; */
/*   int i; */
/*   for (i=0; i<header->n_targets; ++i) { */
/*     t = next_ref_target_v(targets); */
/*     t->tid = i; */
/*     t->name = in->header->target_name[i]; */
/*     t->len = in->header->target_len[i]; */
/*   } */
/*   return targets; */
/* } */

static inline target_t *get_target(target_v *targets, char *chr) {
  unsigned i;
  target_t *t;
  for (i=0; i<targets->size; ++i) {
    t = ref_target_v(targets, i);
    if (strcmp(t->name, chr)==0) return t;
  }
  return NULL;
}

#define tid2name(t, tid) (ref_target_v((t), (tid))->name)

#endif /* _WZTARGET_H */