mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-15 12:47:57 +08:00
473 lines
9.8 KiB
C
473 lines
9.8 KiB
C
#ifndef __HASHTABLE__
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#define __HASHTABLE__
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#include "khash.h"
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#include "kmer.h"
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KHASH_MAP_INIT_INT64(COUNT64, int)
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typedef khash_t(COUNT64) Count_Table;
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KHASH_MAP_INIT_INT64(POS64, uint64_t)
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typedef khash_t(POS64) Pos_Table;
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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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typedef struct
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{
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volatile int lock;
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}Hash_table_spin_lock;
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typedef struct
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{
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Count_Table** sub_h;
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Hash_table_spin_lock* sub_h_lock;
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int prefix_bits;
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int suffix_bits;
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int size;
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uint64_t suffix_mode;
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uint64_t non_unique_k_mer;
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} Total_Count_Table;
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typedef struct
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{
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uint64_t offset;
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uint64_t readID;
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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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} k_mer_pos_list;
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typedef struct
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{
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k_mer_pos_list* list;
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uint64_t size;
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uint64_t length;
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} k_mer_pos_list_alloc;
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typedef struct
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{
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uint64_t offset;
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uint64_t readID;
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uint64_t self_offset;
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uint8_t strand;
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} k_mer_hit;
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typedef struct
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{
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k_mer_hit* list;
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k_mer_hit* tmp;
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long long length;
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long long size;
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uint64_t foward_pos;
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uint64_t rc_pos;
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} Candidates_list;
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typedef struct
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{
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Pos_Table** sub_h;
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Hash_table_spin_lock* sub_h_lock;
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int prefix_bits;
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int suffix_bits;
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int size;
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uint64_t suffix_mode;
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k_mer_pos* pos;
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uint64_t useful_k_mer;
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uint64_t total_occ;
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uint64_t* k_mer_index;
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} Total_Pos_Table;
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/********************************for debug***************************************/
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inline void print_64bit(uint64_t x)
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{
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int i;
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for(i = 63; i >= 0; i--)
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{
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if(x & ((1ULL<<i)))
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fprintf(stderr, "1");
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else
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fprintf(stderr, "0");
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}
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fprintf(stderr, "\n");
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}
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inline uint64_t mod_d(uint64_t h_key, uint64_t low_key, uint64_t d)
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{
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uint64_t result = (h_key >> 32) % d;
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result = ((result << 32) + (h_key & (uint64_t)0xffffffff)) % d;
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result = ((result << 32) + (low_key >> 32)) % d;
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result = ((result << 32) + (low_key & (uint64_t)0xffffffff)) % d;
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return result;
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}
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///inline int get_sub_table(uint64_t* get_sub_ID, uint64_t* get_sub_key, Total_Count_Table* TCB, Hash_code* code, int k)
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inline int get_sub_table(uint64_t* get_sub_ID, uint64_t* get_sub_key, uint64_t suffix_mode, int suffix_bits,
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Hash_code* code, int k)
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{
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uint64_t h_key, low_key;
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///k有可能是64，所以可能会有问题
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///low_key = code->x[0] | (code->x[1] << k);
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low_key = code->x[0] | (code->x[1] << SAFE_SHIFT(k));
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//k不可能为0, 所以这个右移不会有问题
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h_key = code->x[1] >> (64 - k);
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if(mod_d(h_key, low_key, MODE_VALUE) > 3)
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{
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return 0;
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}
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///注意suffix_bits最大就是64
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///前一个右移不安全，因为TCB->suffix_bits有可能为64
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///后一个左移安全，因为TCB->suffix_bits不可能为0
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//uint64_t sub_ID = (low_key >> TCB->suffix_bits) | (h_key << (64 - TCB->suffix_bits));
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uint64_t sub_ID = (low_key >> SAFE_SHIFT(suffix_bits)) | (h_key << (64 - suffix_bits));
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uint64_t sub_key = (low_key & suffix_mode);
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*get_sub_ID = sub_ID;
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*get_sub_key = sub_key;
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return 1;
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}
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inline int insert_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int k)
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{
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uint64_t sub_ID, sub_key;
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if(!get_sub_table(&sub_ID, &sub_key, TCB->suffix_mode, TCB->suffix_bits, code, k))
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{
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return 0;
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}
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khint_t t; ///这就是个迭代器
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int absent;
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while (__sync_lock_test_and_set(&TCB->sub_h_lock[sub_ID].lock, 1))
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{
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while (TCB->sub_h_lock[sub_ID].lock);
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}
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t = kh_put(COUNT64, TCB->sub_h[sub_ID], sub_key, &absent);
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if (absent)
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{
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kh_value(TCB->sub_h[sub_ID], t) = 1;
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}
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else ///哈希表中已有的元素
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{
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//kh_value(TCB->sub_h[sub_ID], t) = kh_value(TCB->sub_h[sub_ID], t) + 1;
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kh_value(TCB->sub_h[sub_ID], t)++;
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}
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__sync_lock_release(&TCB->sub_h_lock[sub_ID].lock);
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return 1;
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}
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inline int get_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int k)
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{
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uint64_t sub_ID, sub_key;
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if(!get_sub_table(&sub_ID, &sub_key, TCB->suffix_mode, TCB->suffix_bits, code, k))
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{
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return 0;
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}
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khint_t t; ///这就是个迭代器
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int absent;
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///查询哈希表，key为k
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t = kh_get(COUNT64, TCB->sub_h[sub_ID], sub_key);
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if (t != kh_end(TCB->sub_h[sub_ID]))
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{
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return kh_value(TCB->sub_h[sub_ID], t);
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}
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else
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{
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return 0;
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}
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}
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inline uint64_t get_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, int k, uint64_t* r_sub_ID)
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{
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uint64_t sub_ID, sub_key;
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if(!get_sub_table(&sub_ID, &sub_key, PCB->suffix_mode, PCB->suffix_bits, code, k))
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{
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return (uint64_t)-1;
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}
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khint_t t; ///这就是个迭代器
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int absent;
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///查询哈希表，key为k
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t = kh_get(POS64, PCB->sub_h[sub_ID], sub_key);
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if (t != kh_end(PCB->sub_h[sub_ID]))
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{
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*r_sub_ID = sub_ID;
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return kh_value(PCB->sub_h[sub_ID], t);
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}
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else
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{
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return (uint64_t)-1;
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}
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}
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inline uint64_t count_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, int k)
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{
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uint64_t sub_ID;
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uint64_t ret = get_Total_Pos_Table(PCB, code, k, &sub_ID);
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if(ret != (uint64_t)-1)
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{
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return PCB->k_mer_index[ret + 1] - PCB->k_mer_index[ret];
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}
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else
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{
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return 0;
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}
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}
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inline uint64_t locate_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, k_mer_pos** list, int k, uint64_t* r_sub_ID)
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{
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uint64_t ret = get_Total_Pos_Table(PCB, code, k, r_sub_ID);
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if(ret != (uint64_t)-1)
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{
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*list = PCB->k_mer_index[ret] + PCB->pos;
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return PCB->k_mer_index[ret + 1] - PCB->k_mer_index[ret];
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}
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else
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{
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*list = NULL;
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return 0;
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}
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}
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int cmp_k_mer_pos(const void * a, const void * b);
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//inline uint64_t insert_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, int k, uint64_t readID, uint64_t pos, uint64_t direction)
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inline uint64_t insert_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, int k, uint64_t readID, uint64_t pos)
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{
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k_mer_pos* list;
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int flag = 0;
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uint64_t sub_ID;
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uint64_t occ = locate_Total_Pos_Table(PCB, code, &list, k, &sub_ID);
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if (occ)
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{
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while (__sync_lock_test_and_set(&PCB->sub_h_lock[sub_ID].lock, 1))
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{
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while (PCB->sub_h_lock[sub_ID].lock);
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}
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if (list[0].offset + 1 < occ)
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{
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list[0].offset++;
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list[list[0].offset].readID = readID;
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///list[list[0].offset].readID = readID|direction;
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list[list[0].offset].offset = pos;
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}
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else
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{
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list[0].readID = readID;
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///list[0].readID = readID|direction;
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list[0].offset = pos;
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flag = 1;
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}
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__sync_lock_release(&PCB->sub_h_lock[sub_ID].lock);
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///当所有位置都存好后，不会再有其他线程修改该list
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///所以可以在临界区外排序
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if (flag && occ>1)
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{
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qsort(list, occ, sizeof(k_mer_pos), cmp_k_mer_pos);
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}
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return 1;
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}
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else
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{
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return 0;
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}
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}
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void init_Total_Count_Table(int k, Total_Count_Table* TCB);
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void init_Total_Pos_Table(Total_Pos_Table* TCB, Total_Count_Table* pre_TCB);
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void destory_Total_Count_Table(Total_Count_Table* TCB);
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void init_Count_Table(Count_Table** table);
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void init_Pos_Table(Count_Table** pre_table, Pos_Table** table);
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void destory_Total_Pos_Table(Total_Pos_Table* TCB);
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void write_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name);
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int load_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name);
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void Traverse_Counting_Table(Total_Count_Table* TCB, Total_Pos_Table* PCB, int k_mer_min_freq, int k_mer_max_freq);
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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 merge_Candidates_list(Candidates_list* l, k_mer_pos* n_list, uint64_t n_lengh, uint64_t end_pos, int strand);
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/********************************for debug***************************************/
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inline int verify_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int k)
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{
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uint64_t sub_ID, sub_key;
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if(!get_sub_table(&sub_ID, &sub_key, TCB->suffix_mode, TCB->suffix_bits, code, k))
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{
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return 0;
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}
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khint_t t; ///这就是个迭代器
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int absent;
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///查询哈希表，key为k
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t = kh_get(COUNT64, TCB->sub_h[sub_ID], sub_key);
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if (t != kh_end(TCB->sub_h[sub_ID]))
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{
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kh_value(TCB->sub_h[sub_ID], t)--;
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if (kh_value(TCB->sub_h[sub_ID], t)<0)
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{
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return -1;
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}
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else
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{
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return 1;
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}
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}
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else
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{
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return -1;
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}
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}
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/********************************for debug***************************************/
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inline int Traverse_Total_Count_Table(Total_Count_Table* TCB)
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{
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int i;
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Count_Table* h;
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khint_t k;
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long long non_empty_k_mer = 0;
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for (i = 0; i < TCB->size; i++)
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{
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h = TCB->sub_h[i];
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for (k = kh_begin(h); k != kh_end(h); ++k)
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{
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if (kh_exist(h, k)) // test if a bucket contains data
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{
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non_empty_k_mer++;
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if (kh_value(h, k)!= 0)
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{
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fprintf(stderr, "ERROR when Traversing!\n");
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}
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}
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}
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}
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fprintf(stdout, "non_empty_k_mer: %lld\n", non_empty_k_mer);
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}
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/********************************for debug***************************************/
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void test_COUNT64();
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/********************************for debug***************************************/
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void debug_mode(uint64_t d, uint64_t thread_ID, uint64_t thread_num);
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/********************************for debug***************************************/
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void merge_Candidates_list_version(Candidates_list* l, k_mer_pos* n_list, uint64_t n_lengh, uint64_t end_pos, int strand);
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#endif |