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https://github.com/chhylp123/hifiasm.git
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218 lines
6.8 KiB
C
218 lines
6.8 KiB
C
#ifndef __HASHTABLE__
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#define __HASHTABLE__
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#include "htab.h"
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#define PREFIX_BITS 16
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#define MAX_SUFFIX_BITS 64
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#define MODE_VALUE 101
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#define WINDOW 375
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#define WINDOW_BOUNDARY 375
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///for one side, the first or last WINDOW_UNCORRECT_SINGLE_SIDE_BOUNDARY bases should not be corrected
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#define WINDOW_UNCORRECT_SINGLE_SIDE_BOUNDARY 25
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#define THRESHOLD 15
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#define OVERLAP_THRESHOLD_FILTER 0.9
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#define OVERLAP_THRESHOLD_FILTER_HPC 0.75
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#define HIGH_HET_OVERLAP_THRESHOLD_FILTER 0.3
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#define HIGH_HET_ERROR_RATE 0.08
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#define THRESHOLD_MAX_SIZE 31
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#define THRESHOLD_UL_MAX 0.2
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#define WINDOW_UL 75
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#define WINDOW_UL_H 200
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// #define WINDOW_UL_H 150
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#define MIN_UL_ALIN_RATE 0.5
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#define MIN_UL_ALIN_LEN (WINDOW_UL*6)
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#define WINDOW_UL_BOUND 48
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#define WINDOW_UL_BOUND_RATE 0.55
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#define GROUP_SIZE 4
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///the max cigar likes 10M10D10M10D10M
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///#define CIGAR_MAX_LENGTH THRESHOLD*2+2
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#define CIGAR_MAX_LENGTH 31*2+4
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typedef struct
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{
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uint32_t offset;
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uint32_t readID:31, rev:1;
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} k_mer_pos;
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typedef struct
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{
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k_mer_pos* list;
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uint64_t length;
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uint64_t size;
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uint8_t direction;
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uint64_t end_pos;
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} k_mer_pos_list;
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typedef struct
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{
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///the begining and end of a window, instead of the whole overlap
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int32_t x_start, x_end;
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int32_t y_start, y_end;
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int16_t extra_begin, extra_end;
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int16_t error, error_threshold;
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uint32_t cidx, clen;
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} window_list;
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typedef struct
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{
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size_t n, m;
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window_list *a;
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kvec_t(uint16_t) c;
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} window_list_alloc;
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typedef struct
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{
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uint64_t* buffer;
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uint32_t length;
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uint32_t size;
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} Fake_Cigar;
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typedef struct
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{
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uint32_t x_id;
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///the begining and end of the whole overlap
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uint32_t x_pos_s;
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uint32_t x_pos_e;
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uint32_t x_pos_strand;
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uint32_t y_id;
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uint32_t y_pos_s;
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uint32_t y_pos_e;
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uint32_t y_pos_strand;
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uint32_t overlapLen;
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int32_t shared_seed;
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uint32_t align_length;
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uint8_t is_match;
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uint8_t without_large_indel;
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int8_t strong;
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uint32_t non_homopolymer_errors;
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// window_list* w_list;
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// uint32_t w_list_size;
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// uint32_t w_list_length;
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Fake_Cigar f_cigar;
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window_list_alloc w_list;
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window_list_alloc boundary_cigars;
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} overlap_region;
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typedef struct
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{
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overlap_region* list;
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uint64_t size;
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uint64_t length;
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int64_t mapped_overlaps_length;
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} overlap_region_alloc;
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typedef struct
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{
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uint32_t readID:31, strand:1;
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uint32_t offset, self_offset, cnt;
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} k_mer_hit;
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typedef struct {
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int32_t *score;
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int64_t *pre;
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int32_t *indels;
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int32_t *self_length;
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int32_t *occ;
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int64_t *tmp; // MUST BE 64-bit integer
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int64_t length;
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int64_t size;
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} Chain_Data;
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typedef struct
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{
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k_mer_hit* list;
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long long length;
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long long size;
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Chain_Data chainDP;
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} Candidates_list;
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void init_Candidates_list(Candidates_list* l);
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void clear_Candidates_list(Candidates_list* l);
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void destory_Candidates_list(Candidates_list* l);
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void destory_Candidates_list_buf(void *km, Candidates_list* l, int is_z);
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void init_overlap_region_alloc(overlap_region_alloc* list);
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void clear_overlap_region_alloc(overlap_region_alloc* list);
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void destory_overlap_region_alloc(overlap_region_alloc* list);
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void append_window_list(overlap_region* region, uint64_t x_start, uint64_t x_end, int y_start, int y_end, int error,
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int extra_begin, int extra_end, int error_threshold, int blockLen, void *km);
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void overlap_region_sort_y_id(overlap_region *a, long long n);
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void calculate_overlap_region_by_chaining(Candidates_list* candidates, overlap_region_alloc* overlap_list, kvec_t_u64_warp* chain_idx,
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uint64_t readID, uint64_t readLength, All_reads* R_INF, const ul_idx_t *uref, double band_width_threshold, int add_beg_end, overlap_region* f_cigar, void *km);
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void init_fake_cigar(Fake_Cigar* x);
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void destory_fake_cigar(Fake_Cigar* x);
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void clear_fake_cigar(Fake_Cigar* x);
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void add_fake_cigar(Fake_Cigar* x, uint32_t gap_site, int32_t gap_shift, void *km);
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void resize_fake_cigar(Fake_Cigar* x, uint64_t size, void *km);
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int get_fake_gap_pos(Fake_Cigar* x, int index);
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int get_fake_gap_shift(Fake_Cigar* x, int index);
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static inline long long y_start_offset(long long x_start, Fake_Cigar* o)
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{
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if(x_start == get_fake_gap_pos(o, o->length - 1))
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{
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return get_fake_gap_shift(o, o->length - 1);
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}
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long long i;
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for (i = 0; i < (long long)o->length; i++)
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{
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if(x_start < get_fake_gap_pos(o, i))
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{
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break;
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}
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}
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if(i == 0 || i == (long long)o->length)
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{
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fprintf(stderr, "ERROR at %s:%d\n", __FILE__, __LINE__);
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exit(0);
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}
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///note here return i - 1
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return get_fake_gap_shift(o, i - 1);
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}
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void resize_Chain_Data(Chain_Data* x, long long size, void *km);
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void init_window_list_alloc(window_list_alloc* x);
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void clear_window_list_alloc(window_list_alloc* x);
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void destory_window_list_alloc(window_list_alloc* x);
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void resize_window_list_alloc(window_list_alloc* x, uint64_t size);
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long long chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* result, double band_width_threshold, int max_skip, int x_readLen, int y_readLen, void *km);
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uint64_t lchain_dp(k_mer_hit* a, int64_t a_n, k_mer_hit* des, Chain_Data* dp, overlap_region* res,
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int64_t max_skip, int64_t max_iter, int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate,
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int64_t xl, int64_t yl, int64_t quick_check);
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int ovlp_chain_gen(overlap_region_alloc* ol, overlap_region* t, int64_t xl, int64_t yl, int64_t apend_be, k_mer_hit* hit, int64_t n_hit);
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void gen_fake_cigar(Fake_Cigar* z, overlap_region *o, int64_t apend_be, k_mer_hit* hit, int64_t n_hit);
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int append_utg_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_region* tmp,
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ma_utg_v *ua, int add_beg_end, void *km);
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#define kv_pushp_cl(type, v, p) do { \
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if ((v).length == (v).size) { \
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(v).size = (v).size? (v).size<<1 : 2; \
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(v).list = (type*)realloc((v).list, sizeof(type) * (v).size); \
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} \
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*(p) = &((v).list[(v).length++]); \
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} while (0)
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#define is_alnw(a) (((a).readID) == ((uint32_t)(0x7fffffff)))
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#define is_pri_aln(a) ((((a).readID) == ((uint32_t)(0x7fffffff)))||((a).cnt >= (a).readID))
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uint64_t lchain_dp_trace(k_mer_hit* a, int64_t a_n, int64_t max_lgap, double sgap_rate, int64_t sgap);
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uint64_t lchain_qdp(k_mer_hit* a, int64_t a_n, k_mer_hit* des, Chain_Data* dp, overlap_region* res,
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int64_t max_skip, int64_t max_iter, int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate,
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int64_t xl, int64_t yl, int64_t quick_check);
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int ovlp_chain_qgen(overlap_region_alloc* ol, overlap_region* t, int64_t xl, int64_t yl, int64_t apend_be, k_mer_hit* hit, int64_t n_hit);
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uint64_t lchain_refine(k_mer_hit* a, int64_t a_n, k_mer_hit* des, Chain_Data* dp,
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int64_t max_skip, int64_t max_iter, int64_t max_dis, int64_t long_gap);
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#endif
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