xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-10-08 05:08:13 +08:00
Code Issues Packages Projects Releases Wiki Activity

uodate gchain

Browse Source
This commit is contained in:
chhylp123
2022-10-07 15:14:08 -04:00
parent 8a4d6a5f24
commit f92cef38f2
5 changed files with 1085 additions and 247 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Correct.h
+8 -2
View File
@@ -1134,10 +1134,10 @@ 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,
void ul_lalign(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *uref, const ug_opt_t *uopt, char *qstr,
uint64_t ql, UC_Read* qu, UC_Read* tu, Correct_dumy* dumy, bit_extz_t *exz,
haplotype_evdience_alloc* hap, kvec_t_u64_warp* v_idx, overlap_region *aux_o,
double e_rate, int64_t wl, kv_ul_ov_t *aln, int64_t sid, uint64_t hpc_k, void *km);
double e_rate, int64_t wl, kv_ul_ov_t *aln, int64_t sid, uint64_t hpc_k, st_mt_t *stb, void *km);
void ul_lalign_old_ed(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,
@@ -1330,6 +1330,12 @@ void update_sketch_trace(overlap_region_alloc* ol, const ul_idx_t *uref, const u
All_reads *rref, UC_Read* tu, asg64_v* idx, asg64_v *b0, asg64_v *b1, int64_t ql, int64_t wl,
kv_ul_ov_t *aln, uint64_t rid, int64_t max_lgap, double sgap_rate);
int64_t infer_rovlp(ul_ov_t *li, ul_ov_t *lj, uc_block_t *bi, uc_block_t *bj, All_reads *ridx, ma_ug_t *ug);
void convert_ul_ov_t(ul_ov_t *des, overlap_region *src, const ul_idx_t *uref);
uint64_t check_connect_ug(const ul_idx_t *uref, uint32_t v, uint32_t w, int64_t bw, double diff_ec_ul, int64_t dq);
uint64_t check_connect_rg(const ul_idx_t *uref, const ug_opt_t *uopt, uint32_t uv, uint32_t uw, int64_t bw, double diff_ec_ul, int64_t dq);
uint32_t govlp_check(const ul_idx_t *uref, const ug_opt_t *uopt, int64_t bw, double diff_ec_ul, ul_ov_t *li, ul_ov_t *lj);
#define copy_asg_arr(des, src) ((des).a = (src).a, (des).n = (src).n, (des).m = (src).m)
#define is_ualn_win(a) (((a).error==INT16_MAX)&&((a).clen==0)&&((a).extra_end<0))
#define is_exact_aln(a) (((a).error<INT16_MAX)&&((a).clen>0))