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redesigned indexing and option APIs

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This commit is contained in:
Heng Li
2017-09-14 17:02:01 -04:00
parent 0f7455cefa
commit eb00521d9b
5 changed files with 151 additions and 98 deletions
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minimap.h
+32 -15
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@@ -5,8 +5,6 @@
#include <stdio.h>
#include <sys/types.h>
#define MM_IDX_DEF_B 14
#define MM_F_NO_SELF 0x001
#define MM_F_AVA 0x002
#define MM_F_CIGAR 0x004
@@ -105,46 +103,65 @@ typedef struct {
int min_dp_max;
int min_ksw_len;
int mini_batch_size;
int32_t max_occ, mid_occ;
} mm_mapopt_t;
typedef struct {
short k, w, is_hpc, bucket_bits;
int mini_batch_size;
uint64_t batch_size;
} mm_idxopt_t;
struct mm_bseq_file_s;
typedef struct {
int is_idx, n_parts;
mm_idxopt_t opt;
union {
struct mm_bseq_file_s *seq;
FILE *idx;
} fp;
} mm_idx_reader_t;
extern int mm_verbose, mm_dbg_flag;
extern double mm_realtime0;
struct mm_tbuf_s;
typedef struct mm_tbuf_s mm_tbuf_t;
struct mm_bseq_file_s;
#define mm_seq4_set(s, i, c) ((s)[(i)>>3] |= (uint32_t)(c) << (((i)&7)<<2))
#define mm_seq4_get(s, i) ((s)[(i)>>3] >> (((i)&7)<<2) & 0xf)
// compute minimizers
void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, int is_hpc, mm128_v *p);
void mm_idxopt_init(mm_idxopt_t *opt);
void mm_mapopt_init(mm_mapopt_t *opt);
int mm_preset(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo);
void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi);
mm_idx_reader_t *mm_idx_reader_open(const char *fn, const mm_idxopt_t *opt);
int mm_idx_reader_is_idx(const mm_idx_reader_t *r);
mm_idx_t *mm_idx_reader_read(mm_idx_reader_t *r, int n_threads);
void mm_idx_reader_close(mm_idx_reader_t *r);
void mm_idx_destroy(mm_idx_t *mi);
// minimizer indexing
mm_idx_t *mm_idx_init(int w, int k, int b, int is_hpc);
void mm_idx_destroy(mm_idx_t *mi);
mm_idx_t *mm_idx_gen(struct mm_bseq_file_s *fp, int w, int k, int b, int is_hpc, int mini_batch_size, int n_threads, uint64_t batch_size, int keep_name);
void mm_idx_stat(const mm_idx_t *idx);
const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n);
int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq);
mm_idx_t *mm_idx_build(const char *fn, int w, int k, int is_hpc, int n_threads);
int mm_idx_is_idx(const char *fn);
// 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);
void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi);
mm_tbuf_t *mm_tbuf_init(void);
void mm_tbuf_destroy(mm_tbuf_t *b);
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);
int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int n_threads);
// obsolete APIs (for backward compatibility)
mm_idx_t *mm_idx_build(const char *fn, int w, int k, int is_hpc, int n_threads);
#ifdef __cplusplus
}