xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-06 12:18:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

extend ed alignment

Browse Source
This commit is contained in:
chhylp123
2022-09-13 17:29:27 -04:00
parent ee51a6dddc
commit 5da05f308f
11 changed files with 2348 additions and 111 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Correct.h
+5
View File
@@ -1130,6 +1130,10 @@ void correct_ul_overlap(overlap_region_alloc* overlap_list, const ul_idx_t *uref
kvec_t_u64_warp* v_idx, window_list_alloc* win_ciagr_buf,
int force_repeat, int is_consensus, int* fully_cov, int* abnormal,
double max_ov_diff_ec, long long winLen, void *km);
void ul_lalign(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *uref, char *qstr,
uint64_t ql, UC_Read* qu, UC_Read* tu, Correct_dumy* dumy,
haplotype_evdience_alloc* hap, kvec_t_u64_warp* v_idx,
double e_rate, int64_t wl, uint64_t is_base, void *km);
void lchain_align(overlap_region_alloc* overlap_list, const ul_idx_t *uref,
UC_Read* g_read, Correct_dumy* dumy, UC_Read* overlap_read,
@@ -1267,6 +1271,7 @@ inline void push_cigar_cell(window_list_alloc *res, uint8_t c, uint32_t len)
uint16_t p = c; p <<= 14; p += (uint16_t)len;
kv_push(uint16_t, res->c, p);
}
int64_t get_num_wins(int64_t s, int64_t e, int64_t block_s);
#define FORWARD_KSW 0
#define BACKWARD_KSW 1