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r852 -> hybrid correction

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chhylp123
2026-02-11 16:38:27 -05:00
parent ec9a8b222d
commit d6ba102d42
73 changed files with 190525 additions and 180074 deletions
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Assembly.h
+56 -56
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@@ -1,56 +1,56 @@
#ifndef __ASSEMBLY__
#define __ASSEMBLY__
#include "CommandLines.h"
#include "Overlaps.h"
#include "Process_Read.h"
#include "Hash_Table.h"
#include "Correct.h"
#define FORWARD 0
#define REVERSE_COMPLEMENT (0x8000000000000000)
#define Get_Cigar_Type(RECORD) (RECORD&3)
#define Get_Cigar_Length(RECORD) (RECORD>>2)
#define RESEED_DP 4
#define RESEED_PEAK_RATE 0.15
#define RESEED_LEN 2000
#define RESEED_HP_RATE 0.9
typedef struct {
int is_final, save_ov;
// chaining and overlapping related buffers
UC_Read self_read, ovlp_read;
Candidates_list clist;
overlap_region_alloc olist;
overlap_region_alloc olist_hp;
ha_abuf_t *ab;
ha_abufl_t *abl;
// error correction related buffers
int64_t num_read_base, num_correct_base, num_recorrect_base;
Cigar_record cigar1;
Graph POA_Graph;
Graph DAGCon;
Correct_dumy correct;
haplotype_evdience_alloc hap;
Round2_alignment round2;
kvec_t_u32_warp b_buf;
kvec_t_u64_warp r_buf;
kvec_t_u8_warp k_flag;
overlap_region tmp_region;
ma_utg_v *ua;
st_mt_t sp;
bit_extz_t exz;
} ha_ovec_buf_t;
int ha_assemble(void);
int ha_assemble_pair(void);
void ug_idx_build(ma_ug_t *ug, int hap_n);
ha_ovec_buf_t *ha_ovec_init(int is_final, int save_ov, int is_ug);
ha_ovec_buf_t *ha_ovec_buf_init(void *km, int is_final, int save_ov, int is_ug);
void ha_ovec_destroy(ha_ovec_buf_t *b);
int64_t ha_ovec_mem(const ha_ovec_buf_t *b, int64_t *mem_a);
int ha_assemble_ovec(void);
int ha_ec_dbg(void);
#endif
#ifndef __ASSEMBLY__
#define __ASSEMBLY__
#include "CommandLines.h"
#include "Overlaps.h"
#include "Process_Read.h"
#include "Hash_Table.h"
#include "Correct.h"
#define FORWARD 0
#define REVERSE_COMPLEMENT (0x8000000000000000)
#define Get_Cigar_Type(RECORD) (RECORD&3)
#define Get_Cigar_Length(RECORD) (RECORD>>2)
#define RESEED_DP 4
#define RESEED_PEAK_RATE 0.15
#define RESEED_LEN 2000
#define RESEED_HP_RATE 0.9
typedef struct {
int is_final, save_ov;
// chaining and overlapping related buffers
UC_Read self_read, ovlp_read;
Candidates_list clist;
overlap_region_alloc olist;
overlap_region_alloc olist_hp;
ha_abuf_t *ab;
ha_abufl_t *abl;
// error correction related buffers
int64_t num_read_base, num_correct_base, num_recorrect_base;
Cigar_record cigar1;
Graph POA_Graph;
Graph DAGCon;
Correct_dumy correct;
haplotype_evdience_alloc hap;
Round2_alignment round2;
kvec_t_u32_warp b_buf;
kvec_t_u64_warp r_buf;
kvec_t_u8_warp k_flag;
overlap_region tmp_region;
ma_utg_v *ua;
st_mt_t sp;
bit_extz_t exz;
} ha_ovec_buf_t;
int ha_assemble(void);
int ha_assemble_pair(void);
void ug_idx_build(ma_ug_t *ug, int hap_n);
ha_ovec_buf_t *ha_ovec_init(int is_final, int save_ov, int is_ug);
ha_ovec_buf_t *ha_ovec_buf_init(void *km, int is_final, int save_ov, int is_ug);
void ha_ovec_destroy(ha_ovec_buf_t *b);
int64_t ha_ovec_mem(const ha_ovec_buf_t *b, int64_t *mem_a);
int ha_assemble_ovec(void);
int ha_ec_dbg(void);
#endif