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80 lines
2.8 KiB
C
80 lines
2.8 KiB
C
#ifndef __HORDER__
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#define __HORDER__
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#define __STDC_LIMIT_MACROS
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#include <stdint.h>
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#include "hic.h"
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#include "rcut.h"
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#define get_hit_srev(x, k) ((x).a.a[(k)].s>>63)
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#define get_hit_slen(x, k) ((x).a.a[(k)].len>>32)
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#define get_hit_suid(x, k) (((x).a.a[(k)].s<<1)>>(64 - (x).uID_bits))
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#define get_hit_spos(x, k) ((x).a.a[(k)].s & (x).pos_mode)
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#define get_hit_spos_e(x, k) (get_hit_srev((x),(k))?\
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((get_hit_spos((x),(k))+1>=get_hit_slen((x),(k)))?\
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(get_hit_spos((x),(k))+1-get_hit_slen((x),(k))):0)\
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:(get_hit_spos((x),(k))+get_hit_slen((x),(k))-1))
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#define get_hit_erev(x, k) ((x).a.a[(k)].e>>63)
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#define get_hit_elen(x, k) ((uint32_t)((x).a.a[(k)].len))
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#define get_hit_euid(x, k) (((x).a.a[(k)].e<<1)>>(64 - (x).uID_bits))
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#define get_hit_epos(x, k) ((x).a.a[(k)].e & (x).pos_mode)
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#define get_hit_epos_e(x, k) (get_hit_erev((x),(k))?\
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((get_hit_epos((x),(k))+1>=get_hit_elen((x),(k)))?\
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(get_hit_epos((x),(k))+1-get_hit_elen((x),(k))):0)\
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:(get_hit_epos((x),(k))+get_hit_elen((x),(k))-1))
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typedef struct {
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uint32_t v;
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uint32_t u;
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uint32_t occ:31, del:1;
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double w, nw;
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} osg_arc_t;
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typedef struct {
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double mw[2], ez[2];
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uint8_t del;
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} osg_seq_t;
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typedef struct {
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uint32_t m_arc, n_arc:31, is_srt:1;
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osg_arc_t *arc;
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uint32_t m_seq, n_seq:31, is_symm:1;
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osg_seq_t *seq;
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uint64_t *idx;
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} osg_t;
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typedef struct {
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osg_t *g;
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}scg_t;
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typedef struct {
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kvec_t(uint64_t) avoid;
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// kvec_t(uint64_t) occ;
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// kvec_t(uint8_t) hf;
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kvec_pe_hit r_hits, u_hits;
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ma_ug_t *ug;
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asg_t *r_g;
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scg_t sg;
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}horder_t;
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horder_t *init_horder_t(kvec_pe_hit *i_hits, uint64_t i_hits_uid_bits, uint64_t i_hits_pos_mode,
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asg_t *i_rg, ma_ug_t* i_ug, bubble_type* bub, kv_u_trans_t *ref, ug_opt_t *opt, uint32_t round);
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void destory_horder_t(horder_t **h);
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void horder_clean_sg_by_utg(asg_t *sg, ma_ug_t *ug);
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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);
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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,
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uint64_t min_ulen, double boundaryRate);
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kvec_pe_hit *get_r_hits_order(kvec_pe_hit *uhits, uint64_t hits_uid_bits, uint64_t hits_pos_mode,
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asg_t *rg, ma_ug_t* ug, bubble_type* bub);
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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,
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ug_opt_t *opt, uint32_t round);
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spg_t *horder_utg(kvec_pe_hit *i_hits, uint64_t i_hits_uid_bits, uint64_t i_hits_pos_mode,
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asg_t *i_rg, ma_ug_t* i_ug, bubble_type* bub, ug_opt_t *opt);
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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,
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double min_cut, double max_cut, uint64_t cut_round);
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void osg_destroy(osg_t *g);
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#endif
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