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#ifndef MAQMAP_H_
#define MAQMAP_H_

#define MAX_READLEN 64
#define MAX_NAMELEN 36


#define PAIRFLAG_FF      0x01
#define PAIRFLAG_FR      0x02
#define PAIRFLAG_RF      0x04
#define PAIRFLAG_RR      0x08
#define PAIRFLAG_PAIRED  0x10
#define PAIRFLAG_SW      0x80

#include <string.h>
#include <zlib.h>
#include "const.h"

  name: read name
  size: the length of the read
  seq: read sequence (see also below)
  seq[MAX_READLEN-1]: single end mapping quality (equals to map_qual if not paired)
  map_qual: the final mapping quality
  alt_qual: the lower quality of the two ends (equals to map_qual if not paired)
  flag: status of the pair
  dist: offset of the mate (zero if not paired)
  info1: mismatches in the 24bp (higher 4 bits) and mismatches (lower 4 bits)
  info2: sum of errors of the best hit
  c[2]: count of all 0- and 1-mismatch hits on the reference
typedef struct
      bit8_t seq[MAX_READLEN]; /* the last base is the single-end mapping quality. */
      bit8_t size, map_qual, info1, info2, c[2], flag, alt_qual;
      bit32_t seqid, pos;
      int dist;
      char name[MAX_NAMELEN];
} maqmap1_t;

typedef struct
      int format, n_ref;
      char **ref_name;
      bit64_t n_mapped_reads;
      maqmap1_t *mapped_reads;
} maqmap_t;

#define maqmap_read1(fp, m1) gzread((fp), (m1), sizeof(maqmap1_t))

#ifdef __cplusplus
extern "C" {
      maqmap_t *maq_new_maqmap();
      void maq_delete_maqmap(maqmap_t *mm);
      void maqmap_write_header(gzFile fp, const maqmap_t *mm);
      maqmap_t *maqmap_read_header(gzFile fp);
#ifdef __cplusplus


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