mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-15 12:47:57 +08:00
261 lines
9.0 KiB
C
261 lines
9.0 KiB
C
#ifndef __HASHTABLE__
|
|
#define __HASHTABLE__
|
|
#include "htab.h"
|
|
|
|
#define PREFIX_BITS 16
|
|
#define MAX_SUFFIX_BITS 64
|
|
#define MODE_VALUE 101
|
|
|
|
#define WINDOW 375
|
|
#define WINDOW_BOUNDARY 375
|
|
#define WINDOW_HC 775
|
|
///ONT high error
|
|
// #define WINDOW_OHC 475
|
|
#define WINDOW_OHC 375
|
|
#define WINDOW_HC_FAST 512
|
|
///for one side, the first or last WINDOW_UNCORRECT_SINGLE_SIDE_BOUNDARY bases should not be corrected
|
|
#define WINDOW_UNCORRECT_SINGLE_SIDE_BOUNDARY 25
|
|
#define THRESHOLD 15
|
|
#define OVERLAP_THRESHOLD_HIFI_FILTER 0.9
|
|
#define OVERLAP_THRESHOLD_NOSI_FILTER 0.7
|
|
#define OVERLAP_THRESHOLD_FILTER_HPC 0.75
|
|
#define HIGH_HET_OVERLAP_THRESHOLD_FILTER 0.3
|
|
#define HIGH_HET_ERROR_RATE 0.08
|
|
#define THRESHOLD_MAX_SIZE 31
|
|
#define THRESHOLD_UL_MAX 0.2
|
|
#define WINDOW_UL 75
|
|
#define WINDOW_UL_H 200
|
|
// #define WINDOW_UL_H 150
|
|
#define MIN_UL_ALIN_RATE 0.5
|
|
#define MIN_UL_ALIN_LEN (WINDOW_UL*6)
|
|
#define WINDOW_UL_BOUND 48
|
|
#define WINDOW_UL_BOUND_RATE 0.55
|
|
|
|
#define GROUP_SIZE 4
|
|
///the max cigar likes 10M10D10M10D10M
|
|
///#define CIGAR_MAX_LENGTH THRESHOLD*2+2
|
|
#define CIGAR_MAX_LENGTH 31*2+4
|
|
|
|
typedef struct
|
|
{
|
|
uint32_t offset;
|
|
uint32_t readID:31, rev:1;
|
|
} k_mer_pos;
|
|
|
|
typedef struct
|
|
{
|
|
k_mer_pos* list;
|
|
uint64_t length;
|
|
uint64_t size;
|
|
uint8_t direction;
|
|
uint64_t end_pos;
|
|
} k_mer_pos_list;
|
|
|
|
typedef struct
|
|
{
|
|
///the begining and end of a window, instead of the whole overlap
|
|
int32_t x_start, x_end;
|
|
int32_t y_start, y_end;
|
|
int16_t extra_begin, extra_end;
|
|
int16_t error, error_threshold;
|
|
uint32_t cidx, clen;
|
|
} window_list;
|
|
|
|
typedef struct
|
|
{
|
|
size_t n, m;
|
|
window_list *a;
|
|
kvec_t(uint16_t) c;
|
|
} window_list_alloc;
|
|
|
|
typedef struct
|
|
{
|
|
uint64_t* buffer;
|
|
uint32_t length;
|
|
uint32_t size;
|
|
} Fake_Cigar;
|
|
|
|
typedef struct
|
|
{
|
|
uint32_t x_id;
|
|
///the begining and end of the whole overlap
|
|
uint32_t x_pos_s;
|
|
uint32_t x_pos_e;
|
|
uint32_t x_pos_strand;
|
|
|
|
uint32_t y_id;
|
|
uint32_t y_pos_s;
|
|
uint32_t y_pos_e;
|
|
uint32_t y_pos_strand;
|
|
|
|
uint32_t overlapLen;
|
|
int32_t shared_seed;
|
|
uint32_t align_length;
|
|
uint8_t is_match;
|
|
uint8_t without_large_indel;
|
|
int8_t strong;
|
|
uint32_t non_homopolymer_errors;
|
|
|
|
// window_list* w_list;
|
|
// uint32_t w_list_size;
|
|
// uint32_t w_list_length;
|
|
Fake_Cigar f_cigar;
|
|
|
|
window_list_alloc w_list;
|
|
window_list_alloc boundary_cigars;
|
|
} overlap_region;
|
|
|
|
typedef struct
|
|
{
|
|
overlap_region* list;
|
|
uint64_t size;
|
|
uint64_t length;
|
|
int64_t mapped_overlaps_length;
|
|
} overlap_region_alloc;
|
|
|
|
typedef struct
|
|
{
|
|
uint32_t readID:31, strand:1;
|
|
uint32_t offset, self_offset, cnt;
|
|
} k_mer_hit;
|
|
|
|
typedef struct {
|
|
int32_t *score;
|
|
int64_t *pre;
|
|
int32_t *indels;
|
|
int32_t *self_length;
|
|
int32_t *occ;
|
|
int64_t *tmp; // MUST BE 64-bit integer
|
|
int64_t length;
|
|
int64_t size;
|
|
} Chain_Data;
|
|
|
|
typedef struct
|
|
{
|
|
k_mer_hit* list;
|
|
long long length;
|
|
long long size;
|
|
Chain_Data chainDP;
|
|
} Candidates_list;
|
|
|
|
void init_Candidates_list(Candidates_list* l);
|
|
void clear_Candidates_list(Candidates_list* l);
|
|
void destory_Candidates_list(Candidates_list* l);
|
|
void destory_Candidates_list_buf(void *km, Candidates_list* l, int is_z);
|
|
|
|
void init_overlap_region_alloc(overlap_region_alloc* list);
|
|
void clear_overlap_region_alloc(overlap_region_alloc* list);
|
|
void destory_overlap_region_alloc(overlap_region_alloc* list);
|
|
void append_window_list(overlap_region* region, uint64_t x_start, uint64_t x_end, int y_start, int y_end, int error,
|
|
int extra_begin, int extra_end, int error_threshold, int blockLen, void *km);
|
|
|
|
void overlap_region_sort_y_id(overlap_region *a, long long n);
|
|
|
|
void calculate_overlap_region_by_chaining(Candidates_list* candidates, overlap_region_alloc* overlap_list, kvec_t_u64_warp* chain_idx,
|
|
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);
|
|
|
|
void init_fake_cigar(Fake_Cigar* x);
|
|
void destory_fake_cigar(Fake_Cigar* x);
|
|
void clear_fake_cigar(Fake_Cigar* x);
|
|
void add_fake_cigar(Fake_Cigar* x, uint32_t gap_site, int32_t gap_shift, void *km);
|
|
void resize_fake_cigar(Fake_Cigar* x, uint64_t size, void *km);
|
|
int get_fake_gap_pos(Fake_Cigar* x, int index);
|
|
int get_fake_gap_shift(Fake_Cigar* x, int index);
|
|
|
|
static inline long long y_start_offset(long long x_start, Fake_Cigar* o)
|
|
{
|
|
if(x_start == get_fake_gap_pos(o, o->length - 1))
|
|
{
|
|
return get_fake_gap_shift(o, o->length - 1);
|
|
}
|
|
|
|
long long i;
|
|
for (i = 0; i < (long long)o->length; i++)
|
|
{
|
|
if(x_start < get_fake_gap_pos(o, i))
|
|
{
|
|
break;
|
|
}
|
|
}
|
|
|
|
if(i == 0 || i == (long long)o->length)
|
|
{
|
|
fprintf(stderr, "ERROR at %s:%d\n", __FILE__, __LINE__);
|
|
exit(0);
|
|
}
|
|
|
|
///note here return i - 1
|
|
return get_fake_gap_shift(o, i - 1);
|
|
}
|
|
|
|
void resize_Chain_Data(Chain_Data* x, long long size, void *km);
|
|
void init_window_list_alloc(window_list_alloc* x);
|
|
void clear_window_list_alloc(window_list_alloc* x);
|
|
void destory_window_list_alloc(window_list_alloc* x);
|
|
void resize_window_list_alloc(window_list_alloc* x, uint64_t size);
|
|
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);
|
|
uint64_t lchain_dp(k_mer_hit* a, int64_t a_n, k_mer_hit* des, Chain_Data* dp, overlap_region* res,
|
|
int64_t max_skip, int64_t max_iter, int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate,
|
|
int64_t xl, int64_t yl, int64_t quick_check);
|
|
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);
|
|
void gen_fake_cigar(Fake_Cigar* z, overlap_region *o, int64_t apend_be, k_mer_hit* hit, int64_t n_hit);
|
|
int append_utg_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_region* tmp,
|
|
ma_utg_v *ua, int add_beg_end, void *km);
|
|
|
|
#define kv_pushp_cl(type, v, p) do { \
|
|
if ((v).length == (v).size) { \
|
|
(v).size = (v).size? (v).size<<1 : 2; \
|
|
(v).list = (type*)realloc((v).list, sizeof(type) * (v).size); \
|
|
} \
|
|
*(p) = &((v).list[(v).length++]); \
|
|
} while (0)
|
|
|
|
#define kv_resize_cl(type, v, s) do { \
|
|
if ((v).size < (s)) { \
|
|
(v).size = (s); \
|
|
kv_roundup32((v).size); \
|
|
(v).list = (type*)realloc((v).list, sizeof(type) * (v).size); \
|
|
} \
|
|
} while (0)
|
|
|
|
#define is_alnw(a) (((a).readID) == ((uint32_t)(0x7fffffff)))
|
|
#define is_pri_aln(a) ((((a).readID) == ((uint32_t)(0x7fffffff)))||((a).cnt >= (a).readID))
|
|
|
|
uint64_t lchain_dp_trace(k_mer_hit* a, int64_t a_n, int64_t max_lgap, double sgap_rate, int64_t sgap);
|
|
uint64_t lchain_qdp(k_mer_hit* a, int64_t a_n, k_mer_hit* des, Chain_Data* dp, overlap_region* res,
|
|
int64_t max_skip, int64_t max_iter, int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate,
|
|
int64_t xl, int64_t yl, int64_t quick_check);
|
|
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);
|
|
uint64_t lchain_refine(k_mer_hit* a, int64_t a_n, k_mer_hit* des, Chain_Data* dp,
|
|
int64_t max_skip, int64_t max_iter, int64_t max_dis, int64_t long_gap);
|
|
uint64_t lchain_qdp_fix(k_mer_hit* a, int64_t a_n, Chain_Data* dp, int64_t max_skip,
|
|
int64_t max_iter, int64_t max_dis, double chn_pen_gap, double chn_pen_skip,
|
|
double bw_rate, int64_t xl, int64_t yl, int64_t quick_check,
|
|
int64_t left_fix, int64_t right_fix);
|
|
uint64_t lchain_simple(k_mer_hit* a, int64_t a_n, k_mer_hit* des, Chain_Data* dp,
|
|
int64_t max_skip, int64_t max_iter);
|
|
uint64_t lchain_qdp_mcopy(Candidates_list *cl, int64_t a_idx, int64_t a_n, int64_t des_idx,
|
|
Chain_Data* dp, overlap_region_alloc* res, int64_t max_skip, int64_t max_iter,
|
|
int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate,
|
|
uint32_t xid, int64_t xl, int64_t yl, int64_t quick_check, uint32_t apend_be,
|
|
int64_t gen_cigar, int64_t enable_mcopy, double mcopy_rate, int64_t mcopy_khit_cutoff,
|
|
int64_t khit_n);
|
|
|
|
uint64_t lchain_qdp_mcopy_fast(Candidates_list *cl, int64_t a_idx, int64_t a_n, int64_t des_idx,
|
|
Chain_Data* dp, overlap_region_alloc* res, int64_t max_skip, int64_t max_iter,
|
|
int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate,
|
|
uint32_t xid, int64_t xl, int64_t yl, int64_t quick_check, uint32_t apend_be,
|
|
int64_t gen_cigar, int64_t enable_mcopy, double mcopy_rate, int64_t mcopy_khit_cutoff,
|
|
int64_t khit_n);
|
|
|
|
#define kv_pushp_ol(type, v, p) do { \
|
|
if ((v).length == (v).size) { \
|
|
(v).list = (type*)realloc((v).list, sizeof(type)*((v).size?((v).size<<1):(2))); \
|
|
memset((v).list+(v).size, 0, sizeof(overlap_region)*(((v).size?((v).size<<1):2)-(v).size));\
|
|
(v).size = (v).size?((v).size<<1):(2); \
|
|
} \
|
|
*(p) = &((v).list[(v).length++]); \
|
|
} while (0)
|
|
|
|
#endif
|