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https://github.com/chhylp123/hifiasm.git
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79 lines
2.6 KiB
C
79 lines
2.6 KiB
C
#ifndef __HIC__
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#define __HIC__
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#include <stdint.h>
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#include "Overlaps.h"
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#define kdq_clear(q) ((q)->count = (q)->front = 0)
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#define kv_malloc(v, s) ((v).n = 0, (v).m = (s), MALLOC((v).a, (s)))
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#define RC_0 0
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#define RC_1 1
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#define RC_2 2
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hc_edge* get_hc_edge(hc_links* link, uint64_t src, uint64_t dest, uint64_t dir);
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hc_edge* push_hc_edge(hc_linkeage* x, uint64_t uID, double weight, int dir, uint64_t* d);
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void hic_analysis(ma_ug_t *ug, asg_t* read_g, trans_chain* t_ch);
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void hic_benchmark(ma_ug_t *ug, asg_t* read_g);
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typedef struct {
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double w;
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uint32_t id, occ;
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///uint32_t *bid, bid_n;
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ma_utg_t *u;
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uint64_t l_d, r_d;
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}chain_hic_w_type;
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typedef struct {
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size_t n, m;
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chain_hic_w_type* a;
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uint32_t max_bub_id;
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uint32_t *chain_idx, u_n;
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}chain_hic_warp;
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typedef struct {
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long long g_occ, b_occ;
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uint64_t id;
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uint8_t del;
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}chain_w_type;
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typedef struct {
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uint32_t* index, round_id, n_round;
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ma_ug_t* ug;
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kvec_t(uint32_t) list;
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kvec_t(uint32_t) num;
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kvec_t(uint64_t) pathLen;
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kvec_t(uint64_t) b_s_idx;
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uint64_t s_bub, f_bub, b_bub, b_end_bub, tangle_bub, cross_bub, mess_bub;
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uint32_t check_het;
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asg_t *b_g;
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ma_ug_t* b_ug;
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kvec_t(chain_w_type) chain_weight;
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chain_hic_warp c_w;
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} bubble_type;
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typedef struct {
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int8_t *s;
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uint64_t xs;
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} ps_t;
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#define P_het(B) ((B).num.n)
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#define M_het(B) ((B).num.n + 1)
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// #define IF_BUB(ID, B) ((B).index[(ID)] < (B).num.n)
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// #define IF_HET(ID, B) ((B).index[(ID)] == (B).num.n)
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// #define IF_HOM(ID, B) ((B).index[(ID)] > (B).num.n)
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#define IF_BUB(ID, B) ((B).index[(ID)] < (B).f_bub+1)
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#define IF_HET(ID, B) ((B).index[(ID)] == (B).f_bub+1)
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#define IF_HOM(ID, B) ((B).index[(ID)] > (B).f_bub+1)
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#define Get_bub_num(RECORD) ((RECORD).num.n-1)
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void get_bubbles(bubble_type* bub, uint64_t id, uint32_t* beg, uint32_t* sink, uint32_t** a, uint32_t* n, uint64_t* pathBase);
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int load_hc_links(hc_links* link, const char *fn);
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void write_hc_links(hc_links* link, const char *fn);
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void destory_bubbles(bubble_type* bub);
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void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *r_het_flag, kv_u_trans_t *ref);
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void resolve_bubble_chain_tangle(ma_ug_t* ug, bubble_type* bub);
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uint32_t connect_bub_occ(bubble_type* bub, uint32_t root_id, uint32_t check_het);
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void get_bub_id(bubble_type* bub, uint32_t root, uint64_t* id0, uint64_t* id1, uint32_t check_het);
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void update_bubble_chain(ma_ug_t* ug, bubble_type* bub, uint32_t is_middle, uint32_t is_end);
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void set_b_utg_weight_flag(bubble_type* bub, buf_t* b, uint32_t v, uint8_t* vis_flag, uint32_t flag, uint32_t* occ);
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void debug_gfa_space(ma_ug_t* ug, hap_cov_t *cov);
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#endif
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