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clean graph alignment

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chhylp123
2023-02-20 14:50:55 -05:00
parent b55e4396d2
commit 3abd3793fb
6 changed files with 836 additions and 164 deletions
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Correct.h
+2 -2
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@@ -1148,7 +1148,7 @@ void correct_ul_overlap(overlap_region_alloc* overlap_list, const ul_idx_t *uref
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, st_mt_t *stb, void *km);
double e_rate, int64_t wl, kv_ul_ov_t *aln, int64_t sid, uint64_t hpc_k, st_mt_t *stb, idx_emask_t *mm, mask_ul_ov_t *mk, 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,
@@ -1347,7 +1347,7 @@ All_reads *rref, UC_Read* tu, asg64_v* idx, asg64_v *b0, asg64_v *b1, int64_t ql
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);
void convert_ul_ov_t(ul_ov_t *des, overlap_region *src, ma_ug_t *ug);
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);