fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-02 22:58:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

start to work on alignment

Browse Source
This commit is contained in:
Heng Li
2017-06-23 13:44:45 -04:00
parent c6d5dea314
commit 44cdd18de0
6 changed files with 65 additions and 10 deletions
Download Patch File Download Diff File Expand all files Collapse all files
minimap.h
+3 -2
View File
@@ -29,7 +29,7 @@ typedef struct {
typedef struct {
char *name; // name of the db sequence
uint64_t offset; // offset in mm_idx_t::seq16
uint64_t offset; // offset in mm_idx_t::S
uint32_t len; // length
} mm_idx_seq_t;
@@ -47,10 +47,10 @@ typedef struct {
int32_t score;
int32_t qs, qe, rs, re;
int32_t parent, subsc;
int32_t as;
} mm_reg1_t;
typedef struct {
int n_frag_mini;
float max_occ_frac;
float mid_occ_frac;
int sdust_thres; // score threshold for SDUST; 0 to disable
@@ -91,6 +91,7 @@ mm_idx_t *mm_idx_gen(struct bseq_file_s *fp, int w, int k, int b, int is_hpc, in
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);
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);