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backup for minimizer

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chhylp123
2022-09-28 11:16:09 -04:00
parent 236bc7b9ee
commit 20a7dac82a
7 changed files with 812 additions and 80 deletions
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Correct.h
+5 -2
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@@ -19,6 +19,8 @@
#define DELETION 3
#define ERROR_RATE 1.25
#define UL_TOPN 50
#define SGAP 16
#define MAX_LGAP(ql) ((((ql)*0.33)>2000)?((ql)*0.33):2000)
#define WINDOW_MAX_SIZE (WINDOW + (int)(1.0 / HA_MIN_OV_DIFF) + 3) // TODO: why 1/max_ov_diff?
@@ -1135,7 +1137,7 @@ 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, 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,
double e_rate, int64_t wl, kv_ul_ov_t *aln, int64_t sid, void *km);
double e_rate, int64_t wl, kv_ul_ov_t *aln, int64_t sid, uint64_t hpc_k, 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,
@@ -1325,7 +1327,8 @@ void inline resize_UC_Read(UC_Read *z, int64_t s)
}
void update_sketch_trace(overlap_region_alloc* ol, const ul_idx_t *uref, const ug_opt_t *uopt,
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);
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);
#define copy_asg_arr(des, src) ((des).a = (src).a, (des).n = (src).n, (des).m = (src).m)