mirror of
https://github.com/chhylp123/hifiasm.git
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117 lines
3.9 KiB
C
117 lines
3.9 KiB
C
#ifndef __HA_HTAB_H__
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#define __HA_HTAB_H__
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#define __STDC_LIMIT_MACROS
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#include <stdint.h>
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#include "Process_Read.h"
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#include "CommandLines.h"
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typedef struct {
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uint64_t x; ///x is the hash key
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///rid is the read id, pos is the end pos of this minimizer, rev is the direction
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///span is the length of this k-mer. For non-HPC k-mer, span may not be equal to k
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uint64_t rid:28, pos:27, rev:1, span:8;
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} ha_mz1_t;
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typedef struct {
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uint64_t rid:28, pos:27, rev:1, span:8; // actually it is not necessary to keep span in the index
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} ha_idxpos_t;
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typedef struct { uint32_t n, m; ha_mz1_t *a; } ha_mz1_v;
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struct ha_pt_s;
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typedef struct ha_pt_s ha_pt_t;
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struct ha_abuf_s;
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typedef struct ha_abuf_s ha_abuf_t;
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extern const unsigned char seq_nt4_table[256];
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extern void *ha_flt_tab;
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extern ha_pt_t *ha_idx;
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extern void *ha_flt_tab_hp;
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extern ha_pt_t *ha_idx_hp;
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extern void *ha_ct_table;
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void *ha_ft_gen(const hifiasm_opt_t *asm_opt, All_reads *rs, int *hom_cov, int is_hp_mode);
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int32_t ha_ft_cnt(const void *hh, uint64_t y);
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void ha_ft_destroy(void *h);
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ha_pt_t *ha_pt_gen(const hifiasm_opt_t *asm_opt, const void *flt_tab, int read_from_store, int is_hp_mode, All_reads *rs, int *hom_cov, int *het_cov);
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void ha_pt_destroy(ha_pt_t *h);
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const ha_idxpos_t *ha_pt_get(const ha_pt_t *h, uint64_t hash, int *n);
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int write_pt_index(void *flt_tab, ha_pt_t *ha_idx, All_reads* r, hifiasm_opt_t* opt, char* file_name);
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int load_pt_index(void **r_flt_tab, ha_pt_t **r_ha_idx, All_reads* r, hifiasm_opt_t* opt, char* file_name);
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int write_ct_index(void *ct_idx, char* file_name);
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int load_ct_index(void **ct_idx, char* file_name);
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int query_ct_index(void* ct_idx, uint64_t hash);
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ha_abuf_t *ha_abuf_init(void);
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void ha_abuf_destroy(ha_abuf_t *ab);
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uint64_t ha_abuf_mem(const ha_abuf_t *ab);
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double yak_cputime(void);
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void yak_reset_realtime(void);
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double yak_realtime(void);
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long yak_peakrss(void);
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double yak_peakrss_in_gb(void);
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double yak_cpu_usage(void);
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void ha_triobin(const hifiasm_opt_t *opt);
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void ha_sketch(const char *str, int len, int w, int k, uint32_t rid, int is_hpc, ha_mz1_v *p, const void *hf, int sample_dist, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* dbg_ct);
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int ha_analyze_count(int n_cnt, int start_cnt, const int64_t *cnt, int *peak_het);
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void debug_adapter(const hifiasm_opt_t *asm_opt, All_reads *rs);
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static inline uint64_t yak_hash64(uint64_t key, uint64_t mask) // invertible integer hash function
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{
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key = (~key + (key << 21)) & mask; // key = (key << 21) - key - 1;
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key = key ^ key >> 24;
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key = ((key + (key << 3)) + (key << 8)) & mask; // key * 265
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key = key ^ key >> 14;
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key = ((key + (key << 2)) + (key << 4)) & mask; // key * 21
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key = key ^ key >> 28;
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key = (key + (key << 31)) & mask;
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return key;
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}
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static inline uint64_t yak_hash64_64(uint64_t key)
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{
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key = ~key + (key << 21);
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key = key ^ key >> 24;
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key = (key + (key << 3)) + (key << 8);
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key = key ^ key >> 14;
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key = (key + (key << 2)) + (key << 4);
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key = key ^ key >> 28;
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key = key + (key << 31);
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return key;
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}
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static inline uint64_t yak_hash_long(uint64_t x[4])
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{
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///compare forward k-mer and reverse complementary strand
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int j = x[1] < x[3]? 0 : 1;
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return yak_hash64_64(x[j<<1|0]) + yak_hash64_64(x[j<<1|1]);
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}
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#define CALLOC(ptr, len) ((ptr) = (__typeof__(ptr))calloc((len), sizeof(*(ptr))))
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#define MALLOC(ptr, len) ((ptr) = (__typeof__(ptr))malloc((len) * sizeof(*(ptr))))
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#define REALLOC(ptr, len) ((ptr) = (__typeof__(ptr))realloc((ptr), (len) * sizeof(*(ptr))))
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#ifndef kroundup32
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#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
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#endif
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#ifndef kroundup64
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#define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, x|=(x)>>32, ++(x))
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#endif
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#ifndef klib_unused
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#if (defined __clang__ && __clang_major__ >= 3) || (defined __GNUC__ && __GNUC__ >= 3)
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#define klib_unused __attribute__ ((__unused__))
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#else
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#define klib_unused
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#endif
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#endif /* klib_unused */
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#endif // __YAK_H__
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