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index can be compiled; not tested yet

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This commit is contained in:
Heng Li
2017-04-07 15:30:30 -04:00
parent 0f160151c7
commit b3bc4911ba
10 changed files with 1383 additions and 12 deletions
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minimap.h
+19 -10
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@@ -4,7 +4,6 @@
#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
@@ -30,13 +29,18 @@ typedef struct {
} 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 to one concatenated string
char *name; // name of the db sequence
uint64_t offset; // offset in mm_idx_t::seq16
uint32_t len; // length
} mm_idx_seq_t;
typedef struct {
int32_t b, w, k;
uint64_t sum_len; // sum of lengths
uint32_t n_seq; // number of reference sequences
mm_idx_seq_t *seq; // sequence name, length and offset
uint32_t *S; // 4-bit packed sequence
mm_idx_bucket_t *B; // index
} mm_idx_t;
typedef struct {
@@ -62,6 +66,11 @@ extern double mm_realtime0;
struct mm_tbuf_s;
typedef struct mm_tbuf_s mm_tbuf_t;
struct bseq_file_s;
#define mm_seq4_set(s, i, c) ((s)[(i)>>8] |= (uint32_t)(c) << (((i)&7)<<2))
#define mm_seq4_get(s, i) ((s)[(i)>>8] >> (((i)&7)<<2) & 0xf)
#ifdef __cplusplus
extern "C" {
#endif
@@ -72,11 +81,11 @@ void mm_sketch(void *km, const char *str, int len, int w, int k, uint32_t rid, i
// 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);
mm_idx_t *mm_idx_gen(struct 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_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);
mm_idx_t *mm_idx_build(const char *fn, int w, int k, int is_hpc, int n_threads);
// minimizer index I/O
void mm_idx_dump(FILE *fp, const mm_idx_t *mi);