/usr/include/minimap.h is in libminimap-dev 0.2-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 | #ifndef MINIMAP_H
#define MINIMAP_H
#include <stdint.h>
#include <stdio.h>
#include <sys/types.h>
#include "bseq.h"
#define MM_IDX_DEF_B 14
#define MM_DEREP_Q50 5.0
#define MM_F_WITH_REP 0x1
#define MM_F_NO_SELF 0x2
#define MM_F_NO_ISO 0x4
#define MM_F_AVA 0x8
typedef struct {
uint64_t x, y;
} mm128_t;
typedef struct { size_t n, m; mm128_t *a; } mm128_v;
typedef struct { size_t n, m; uint64_t *a; } uint64_v;
typedef struct { size_t n, m; uint32_t *a; } uint32_v;
typedef struct {
mm128_v a; // (minimizer, position) array
int32_t n; // size of the _p_ array
uint64_t *p; // position array for minimizers appearing >1 times
void *h; // hash table indexing _p_ and minimizers appearing once
} mm_idx_bucket_t;
typedef struct {
int b, w, k;
uint32_t n; // number of reference sequences
mm_idx_bucket_t *B;
uint32_t max_occ;
float freq_thres;
int32_t *len; // length of each reference sequence
char **name; // TODO: if this uses too much RAM, switch one concatenated string
} mm_idx_t;
typedef struct {
uint32_t cnt:31, rev:1;
uint32_t rid:31, rep:1;
uint32_t len;
int32_t qs, qe, rs, re;
} mm_reg1_t;
typedef struct {
int radius; // bandwidth to cluster hits
int max_gap; // break a chain if there are no minimizers in a max_gap window
int min_cnt; // minimum number of minimizers to start a chain
int min_match;
int sdust_thres; // score threshold for SDUST; 0 to disable
int flag; // see MM_F_* macros
float merge_frac; // merge two chains if merge_frac fraction of minimzers are shared between the chains
} mm_mapopt_t;
extern int mm_verbose;
extern double mm_realtime0;
struct mm_tbuf_s;
typedef struct mm_tbuf_s mm_tbuf_t;
#ifdef __cplusplus
extern "C" {
#endif
// compute minimizers
void mm_sketch(const char *str, int len, int w, int k, uint32_t rid, mm128_v *p);
// minimizer indexing
mm_idx_t *mm_idx_init(int w, int k, int b);
void mm_idx_destroy(mm_idx_t *mi);
mm_idx_t *mm_idx_gen(bseq_file_t *fp, int w, int k, int b, int tbatch_size, int n_threads, uint64_t ibatch_size, int keep_name);
void mm_idx_set_max_occ(mm_idx_t *mi, float f);
const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n);
mm_idx_t *mm_idx_build(const char *fn, int w, int k, int n_threads);
// minimizer index I/O
void mm_idx_dump(FILE *fp, const mm_idx_t *mi);
mm_idx_t *mm_idx_load(FILE *fp);
// mapping
void mm_mapopt_init(mm_mapopt_t *opt);
mm_tbuf_t *mm_tbuf_init(void);
void mm_tbuf_destroy(mm_tbuf_t *b);
const mm_reg1_t *mm_map(const mm_idx_t *mi, int l_seq, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *name);
int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int n_threads, int tbatch_size);
// private functions (may be moved to a "mmpriv.h" in future)
double cputime(void);
double realtime(void);
void radix_sort_128x(mm128_t *beg, mm128_t *end);
void radix_sort_64(uint64_t *beg, uint64_t *end);
uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);
#ifdef __cplusplus
}
#endif
#endif
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