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ont simplex support

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chhylp123
2024-11-27 13:27:13 -05:00
parent 80fa5ed436
commit 676385cf8e
10 changed files with 896 additions and 88 deletions
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ecovlp.h
+2 -48
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@@ -7,58 +7,12 @@
#include "Process_Read.h"
#include "kdq.h"
KDQ_INIT(uint32_t)
typedef struct {
uint32_t v:31, f:1;
uint32_t sc;
} cns_arc;
typedef struct {size_t n, m, nou; cns_arc *a; } cns_arc_v;
typedef struct {
// uint16_t c:2, t:2, f:1, sc:3;
uint32_t c:2, f:1, sc:29;
cns_arc_v arc;
}cns_t;
typedef struct {
size_t n, m;
cns_t *a;
uint32_t si, ei, off, bn, bb0, bb1, cns_g_wl;
kdq_t(uint32_t) *q;
}cns_gfa;
typedef struct {
// chaining and overlapping related buffers
UC_Read self_read, ovlp_read;
Candidates_list clist;
overlap_region_alloc olist;
ha_abuf_t *ab;
// int64_t num_read_base, num_correct_base, num_recorrect_base;
uint64_t cnt[6], rr;
haplotype_evdience_alloc hap;
bit_extz_t exz;
kv_ul_ov_t pidx;
asg64_v v64;
asg32_v v32;
asg16_v v16;
asg8_v v8q, v8t;
kvec_t_u8_warp k_flag;
st_mt_t sp;
cns_gfa cns;
} ec_ovec_buf_t0;
typedef struct {
ec_ovec_buf_t0 *a;
uint32_t n, rev;
} ec_ovec_buf_t;
ec_ovec_buf_t* gen_ec_ovec_buf_t(uint32_t n);
void destroy_ec_ovec_buf_t(ec_ovec_buf_t *p);
void prt_chain(overlap_region_alloc *o);
void cal_ec_r(uint64_t n_thre, uint64_t round, uint64_t n_round, uint64_t n_a, uint64_t is_sv, uint64_t *tot_b, uint64_t *tot_e);
void sl_ec_r(uint64_t n_thre, uint64_t n_a);
void cal_ov_r(uint64_t n_thre, uint64_t n_a, uint64_t new_idx);
void handle_chemical_r(uint64_t n_thre, uint64_t n_a);
void handle_chemical_arc(uint64_t n_thre, uint64_t n_a);
#endif