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#ifndef LH3_MATCH_HH
#define LH3_MATCH_HH
#include <zlib.h>
#include <stdio.h>
#include "maqmap.h"
#include "dword.hh"
#ifdef _FASTMAP
# define SEED_LENGTH 28
# define MAX_MISMATCH 3
#else
# define SEED_LENGTH 24
# define MAX_MISMATCH 4
#endif
#ifdef MAQ_LONGREADS
# define read_t dword_t<dword_t<bit64_t> >
# define matches_t dword_t<bit64_t>
#else
# define read_t dword_t<bit64_t>
# define matches_t bit64_t
#endif
#define MA_NO_MATCH 0xfffffffful
#define MA_NO_INDEX 0xffffffffu
typedef dword_t<bit64_t> bit128_t;
typedef struct __match_info_t
{
read_t s, q, m;
bit32_t i1, p1, i2;
matches_t mm1, mm2, last_mm1, last_mm2;
bit64_t last1, last2;
int seqid1, last_seqid;
bit8_t c[MAX_MISMATCH + 1];
} match_info_t;
typedef struct
{
bit32_t i1, p11, p12;
bit32_t i2;
matches_t m11, m12;
int seqid1;
} pair_info_t;
typedef struct __match_aux_t
{
int n_mismatch;
int size_l, size_r;
int n_filters;
int max_err10;
int max_dist, min_dist;
int RF_max_dist; // for Illumina long insert-size library
int is_quiet, is_color, is_mm, is_p2diff, is_sw;
char methy_mode;
char *adapter, *dump_file;
int max_hits;
gzFile hits_fp;
read_t *masks;
bit64_t *filters;
int *shift_seed;
int log_n[256];
int q_rate; // mutation rate in phred unit
} match_aux_t;
typedef struct
{
read_t mask;
int shift_seed;
bit64_t filter;
bit128_t *sorted;
bit32_t *index;
} match_index_t;
struct __longreads_t;
typedef struct __match_data_t
{
int n_reads, n_lname;
bit32_t sum_len;
match_info_t *match;
pair_info_t *pair;
char **lname;
match_index_t index[4];
bit8_t *index4;
} match_data_t;
match_aux_t *new_match_aux(int size_l, int size_r, int m);
match_data_t *new_match_data();
void delete_match_data(match_data_t *d);
void delete_match_aux(match_aux_t *o);
void match_data2map(gzFile fpout, FILE *fp_bfa, gzFile fp_bfq_l, gzFile fp_bfq_r, const match_aux_t *o, match_data_t *d);
void ma_trim_adapter(const char adaptor[], const match_data_t *d, struct __longreads_t *lr);
#endif
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