fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-07 02:38:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

r718: retrieve sequence from the index

Browse Source
This commit is contained in:
Heng Li
2018-02-23 10:18:26 -05:00
parent 29ed675ee5
commit 24a4808826
9 changed files with 115 additions and 20 deletions
Download Patch File Download Diff File Expand all files Collapse all files
minimap.h
+6 -1
View File
@@ -59,7 +59,7 @@ typedef struct {
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)
void *km;
void *km, *h;
} mm_idx_t;
// minimap2 alignment
@@ -297,6 +297,11 @@ int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int
int mm_map_file_frag(const mm_idx_t *idx, int n_segs, const char **fn, const mm_mapopt_t *opt, int n_threads);
// query sequence name and sequence in the minimap2 index
int mm_idx_index_name(mm_idx_t *mi);
int mm_idx_name2id(const mm_idx_t *mi, const char *name);
int mm_idx_getseq(const mm_idx_t *mi, uint32_t rid, uint32_t st, uint32_t en, uint8_t *seq);
// deprecated APIs for backward compatibility
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);