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avoid misassemblies; better polyploidy graph

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chhylp123
2023-03-22 12:23:53 -04:00
parent d4773a497f
commit 86b7dd424a
12 changed files with 1931 additions and 79 deletions
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Overlaps.h
+23
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@@ -1211,4 +1211,27 @@ int asg_arc_del_trans_ul(asg_t *g, int fuzz);
#define JUNK_COV 5
#define DISCARD_RATE 0.8
typedef struct {
uint32_t n, m, a;
} mmhap_status_t;
typedef struct {
kvec_t(mmhap_status_t) h;
kvec_t(uint32_t) a;
} mmhap_t;
typedef struct { // global data structure for kt_pipeline()
ma_ug_t *ug;
asg_t *rg;
uint64_t *idx;
asg64_v cov;
uint64_t hom_min, hom_max, hom_cov, het_cov;
} ug_rid_cov_t;
ug_rid_cov_t* gen_ug_rid_cov_t(ma_ug_t *ug, asg_t *rg, ma_hit_t_alloc *src);
void destory_ug_rid_cov_t(ug_rid_cov_t *p);
uint32_t append_cov_line_ug_rid_cov_t(uint64_t uid, uint64_t *qcc, u_trans_t *p, ug_rid_cov_t *idx, uint64_t hom_cut, double cut_rate);
uint64_t infer_mmhap_copy(ma_ug_t *ug, asg_t *sg, ma_hit_t_alloc *src, uint8_t *ff, uint64_t uid, uint64_t het_cov, uint64_t n_hap);
uint64_t trans_sec_cut0(kv_u_trans_t *ta, asg64_v *srt, uint32_t id, double sec_rate, uint64_t bd, ma_ug_t *ug);
#endif