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r188: renamed bseq* to mm_bseq*

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to avoid naming collisions between minimap2 and bwa/fermi-lite/etc
This commit is contained in:
Heng Li
2017-07-19 09:26:46 -04:00
parent b9b0b6f49c
commit 71c988f6ab
10 changed files with 65 additions and 57 deletions
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minimap.h
+6 -6
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@@ -15,6 +15,10 @@
#define MM_IDX_MAGIC "MMI\2"
#ifdef __cplusplus
extern "C" {
#endif
typedef struct {
uint64_t x, y;
} mm128_t;
@@ -100,22 +104,18 @@ extern double mm_realtime0;
struct mm_tbuf_s;
typedef struct mm_tbuf_s mm_tbuf_t;
struct bseq_file_s;
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)
#ifdef __cplusplus
extern "C" {
#endif
// 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);
// 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 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);
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);
uint32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f);
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);