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52 lines
1.6 KiB
C
52 lines
1.6 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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void 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, hc_links* link);
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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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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;
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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;
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uint32_t check_het;
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asg_t *b_g;
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uint32_t *b_g_index;
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ma_ug_t* b_ug;
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uint32_t *b_ug_index;
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kvec_t(chain_w_type) chain_weight;
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} bubble_type;
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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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#endif
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