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This commit is contained in:
Heng Li
2018-09-16 14:49:53 -04:00
parent c63a33904f
commit 2b653ecda3
5 changed files with 113 additions and 3 deletions
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minimap.h
+10
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@@ -58,13 +58,20 @@ typedef struct {
uint32_t len; // length
} mm_idx_seq_t;
typedef struct {
uint64_t x;
int32_t end, idx;
} mm_idx_bed_t;
typedef struct {
int32_t b, w, k, flag;
uint32_t n_seq; // number of reference sequences
int32_t index;
uint32_t n_R;
mm_idx_seq_t *seq; // sequence name, length and offset
uint32_t *S; // 4-bit packed sequence
struct mm_idx_bucket_s *B; // index (hidden)
mm_idx_bed_t *R;
void *km, *h;
} mm_idx_t;
@@ -365,6 +372,9 @@ int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, ui
void mm_mapopt_init(mm_mapopt_t *opt);
mm_idx_t *mm_idx_build(const char *fn, int w, int k, int flag, int n_threads);
int mm_idx_read_bed(mm_idx_t *mi, const char *fn);
int mm_idx_bed_query(const mm_idx_t *mi, uint64_t x);
#ifdef __cplusplus
}
#endif