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r852 -> hybrid correction

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chhylp123
2026-02-11 16:38:27 -05:00
parent ec9a8b222d
commit d6ba102d42
73 changed files with 190525 additions and 180074 deletions
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horder.h
+79 -79
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@@ -1,79 +1,79 @@
#ifndef __HORDER__
#define __HORDER__
#define __STDC_LIMIT_MACROS
#include <stdint.h>
#include "hic.h"
#include "rcut.h"
#define get_hit_srev(x, k) ((x).a.a[(k)].s>>63)
#define get_hit_slen(x, k) ((x).a.a[(k)].len>>32)
#define get_hit_suid(x, k) (((x).a.a[(k)].s<<1)>>(64 - (x).uID_bits))
#define get_hit_spos(x, k) ((x).a.a[(k)].s & (x).pos_mode)
#define get_hit_spos_e(x, k) (get_hit_srev((x),(k))?\
((get_hit_spos((x),(k))+1>=get_hit_slen((x),(k)))?\
(get_hit_spos((x),(k))+1-get_hit_slen((x),(k))):0)\
:(get_hit_spos((x),(k))+get_hit_slen((x),(k))-1))
#define get_hit_erev(x, k) ((x).a.a[(k)].e>>63)
#define get_hit_elen(x, k) ((uint32_t)((x).a.a[(k)].len))
#define get_hit_euid(x, k) (((x).a.a[(k)].e<<1)>>(64 - (x).uID_bits))
#define get_hit_epos(x, k) ((x).a.a[(k)].e & (x).pos_mode)
#define get_hit_epos_e(x, k) (get_hit_erev((x),(k))?\
((get_hit_epos((x),(k))+1>=get_hit_elen((x),(k)))?\
(get_hit_epos((x),(k))+1-get_hit_elen((x),(k))):0)\
:(get_hit_epos((x),(k))+get_hit_elen((x),(k))-1))
typedef struct {
uint32_t v;
uint32_t u;
uint32_t occ:31, del:1;
double w, nw;
} osg_arc_t;
typedef struct {
double mw[2], ez[2];
uint8_t del;
} osg_seq_t;
typedef struct {
uint32_t m_arc, n_arc:31, is_srt:1;
osg_arc_t *arc;
uint32_t m_seq, n_seq:31, is_symm:1;
osg_seq_t *seq;
uint64_t *idx;
} osg_t;
typedef struct {
osg_t *g;
}scg_t;
typedef struct {
kvec_t(uint64_t) avoid;
// kvec_t(uint64_t) occ;
// kvec_t(uint8_t) hf;
kvec_pe_hit r_hits, u_hits;
ma_ug_t *ug;
asg_t *r_g;
scg_t sg;
}horder_t;
horder_t *init_horder_t(kvec_pe_hit *i_hits, uint64_t i_hits_uid_bits, uint64_t i_hits_pos_mode,
asg_t *i_rg, ma_ug_t* i_ug, bubble_type* bub, kv_u_trans_t *ref, ug_opt_t *opt, uint32_t round);
void destory_horder_t(horder_t **h);
void horder_clean_sg_by_utg(asg_t *sg, ma_ug_t *ug);
kvec_pe_hit *get_r_hits_for_trio(kvec_pe_hit *u_hits, asg_t* r_g, ma_ug_t* ug, bubble_type* bub, uint64_t uID_bits, uint64_t pos_mode);
void update_switch_unitig(ma_ug_t *ug, asg_t *rg, kvec_pe_hit *hits, kv_u_trans_t *k_trans, uint64_t cutoff_s, uint64_t cutoff_e,
uint64_t min_ulen, double boundaryRate);
kvec_pe_hit *get_r_hits_order(kvec_pe_hit *uhits, uint64_t hits_uid_bits, uint64_t hits_pos_mode,
asg_t *rg, ma_ug_t* ug, bubble_type* bub);
void ha_aware_order(kvec_pe_hit *r_hits, asg_t *rg, ma_ug_t *ug_fa, ma_ug_t *ug_mo, kv_u_trans_t *ref,
ug_opt_t *opt, uint32_t round);
spg_t *horder_utg(kvec_pe_hit *i_hits, uint64_t i_hits_uid_bits, uint64_t i_hits_pos_mode,
asg_t *i_rg, ma_ug_t* i_ug, bubble_type* bub, ug_opt_t *opt);
void layout_mc_clus_t(const mc_match_t *ma, uint32_t *a, uint32_t an, scg_t *sg, uint32_t *buf, uint64_t *idx, ma_ug_t* ug,
double min_cut, double max_cut, uint64_t cut_round);
void osg_destroy(osg_t *g);
#endif
#ifndef __HORDER__
#define __HORDER__
#define __STDC_LIMIT_MACROS
#include <stdint.h>
#include "hic.h"
#include "rcut.h"
#define get_hit_srev(x, k) ((x).a.a[(k)].s>>63)
#define get_hit_slen(x, k) ((x).a.a[(k)].len>>32)
#define get_hit_suid(x, k) (((x).a.a[(k)].s<<1)>>(64 - (x).uID_bits))
#define get_hit_spos(x, k) ((x).a.a[(k)].s & (x).pos_mode)
#define get_hit_spos_e(x, k) (get_hit_srev((x),(k))?\
((get_hit_spos((x),(k))+1>=get_hit_slen((x),(k)))?\
(get_hit_spos((x),(k))+1-get_hit_slen((x),(k))):0)\
:(get_hit_spos((x),(k))+get_hit_slen((x),(k))-1))
#define get_hit_erev(x, k) ((x).a.a[(k)].e>>63)
#define get_hit_elen(x, k) ((uint32_t)((x).a.a[(k)].len))
#define get_hit_euid(x, k) (((x).a.a[(k)].e<<1)>>(64 - (x).uID_bits))
#define get_hit_epos(x, k) ((x).a.a[(k)].e & (x).pos_mode)
#define get_hit_epos_e(x, k) (get_hit_erev((x),(k))?\
((get_hit_epos((x),(k))+1>=get_hit_elen((x),(k)))?\
(get_hit_epos((x),(k))+1-get_hit_elen((x),(k))):0)\
:(get_hit_epos((x),(k))+get_hit_elen((x),(k))-1))
typedef struct {
uint32_t v;
uint32_t u;
uint32_t occ:31, del:1;
double w, nw;
} osg_arc_t;
typedef struct {
double mw[2], ez[2];
uint8_t del;
} osg_seq_t;
typedef struct {
uint32_t m_arc, n_arc:31, is_srt:1;
osg_arc_t *arc;
uint32_t m_seq, n_seq:31, is_symm:1;
osg_seq_t *seq;
uint64_t *idx;
} osg_t;
typedef struct {
osg_t *g;
}scg_t;
typedef struct {
kvec_t(uint64_t) avoid;
// kvec_t(uint64_t) occ;
// kvec_t(uint8_t) hf;
kvec_pe_hit r_hits, u_hits;
ma_ug_t *ug;
asg_t *r_g;
scg_t sg;
}horder_t;
horder_t *init_horder_t(kvec_pe_hit *i_hits, uint64_t i_hits_uid_bits, uint64_t i_hits_pos_mode,
asg_t *i_rg, ma_ug_t* i_ug, bubble_type* bub, kv_u_trans_t *ref, ug_opt_t *opt, uint32_t round);
void destory_horder_t(horder_t **h);
void horder_clean_sg_by_utg(asg_t *sg, ma_ug_t *ug);
kvec_pe_hit *get_r_hits_for_trio(kvec_pe_hit *u_hits, asg_t* r_g, ma_ug_t* ug, bubble_type* bub, uint64_t uID_bits, uint64_t pos_mode);
void update_switch_unitig(ma_ug_t *ug, asg_t *rg, kvec_pe_hit *hits, kv_u_trans_t *k_trans, uint64_t cutoff_s, uint64_t cutoff_e,
uint64_t min_ulen, double boundaryRate);
kvec_pe_hit *get_r_hits_order(kvec_pe_hit *uhits, uint64_t hits_uid_bits, uint64_t hits_pos_mode,
asg_t *rg, ma_ug_t* ug, bubble_type* bub);
void ha_aware_order(kvec_pe_hit *r_hits, asg_t *rg, ma_ug_t *ug_fa, ma_ug_t *ug_mo, kv_u_trans_t *ref,
ug_opt_t *opt, uint32_t round);
spg_t *horder_utg(kvec_pe_hit *i_hits, uint64_t i_hits_uid_bits, uint64_t i_hits_pos_mode,
asg_t *i_rg, ma_ug_t* i_ug, bubble_type* bub, ug_opt_t *opt);
void layout_mc_clus_t(const mc_match_t *ma, uint32_t *a, uint32_t an, scg_t *sg, uint32_t *buf, uint64_t *idx, ma_ug_t* ug,
double min_cut, double max_cut, uint64_t cut_round);
void osg_destroy(osg_t *g);
#endif