mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-15 20:57:57 +08:00
372 lines
9.8 KiB
C++
372 lines
9.8 KiB
C++
#include <stdio.h>
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#include <stdlib.h>
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#include <stdint.h>
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#include "Hash_Table.h"
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void init_Count_Table(Count_Table** table)
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{
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*table = kh_init(COUNT64);
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}
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void init_Pos_Table(Pos_Table** table)
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{
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*table = kh_init(POS64);
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}
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void init_Total_Count_Table(int k, Total_Count_Table* TCB)
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{
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if(k>64)
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{
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fprintf(stdout, "k-mer is too long. The length of k-mer must <= 64.");
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fflush(stdout);
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exit(0);
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}
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int total_bits = k * 2;
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TCB->prefix_bits = PREFIX_BITS;
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TCB->suffix_bits = total_bits - TCB->prefix_bits;
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if (TCB->suffix_bits > MAX_SUFFIX_BITS)
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{
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TCB->suffix_bits = MAX_SUFFIX_BITS;
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TCB->prefix_bits = total_bits - TCB->suffix_bits;
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}
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///TCB->suffix_mode = (1ULL<<TCB->suffix_bits) - 1;
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///这个右移是安全的，因为TCB->suffix_bits不可能是0
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TCB->suffix_mode = ALL >> (64 - TCB->suffix_bits);
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///number of small hash table
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TCB->size = (1ULL<<TCB->prefix_bits);
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TCB->sub_h = (Count_Table**)malloc(sizeof(Count_Table*)*TCB->size);
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TCB->sub_h_lock = (Hash_table_spin_lock*)malloc(sizeof(Hash_table_spin_lock)*TCB->size);
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memset(TCB->sub_h_lock, 0, sizeof(Hash_table_spin_lock)*TCB->size);
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int i = 0;
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for (i = 0; i < TCB->size; i++)
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{
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init_Count_Table(&(TCB->sub_h[i]));
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TCB->sub_h_lock[i].lock = 0;
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}
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TCB->non_unique_k_mer = 0;
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}
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void init_Total_Pos_Table(Total_Pos_Table* TCB, Total_Count_Table* pre_TCB)
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{
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TCB->prefix_bits = pre_TCB->prefix_bits;
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TCB->suffix_bits = pre_TCB->suffix_bits;
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TCB->suffix_mode = pre_TCB->suffix_mode;
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TCB->size = pre_TCB->size;
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TCB->useful_k_mer = 0;
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TCB->total_occ = 0;
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TCB->k_mer_index = NULL;
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TCB->sub_h_lock = (Hash_table_spin_lock*)malloc(sizeof(Hash_table_spin_lock)*TCB->size);
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memset(TCB->sub_h_lock, 0, sizeof(Hash_table_spin_lock)*TCB->size);
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TCB->sub_h = (Pos_Table**)malloc(sizeof(Pos_Table*)*TCB->size);
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TCB->pos = NULL;
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int i = 0;
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for (i = 0; i < TCB->size; i++)
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{
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init_Pos_Table(&(TCB->sub_h[i]));
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TCB->sub_h_lock[i].lock = 0;
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}
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}
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void destory_Total_Count_Table(Total_Count_Table* TCB)
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{
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int i;
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for (i = 0; i < TCB->size; i++)
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{
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kh_destroy(COUNT64, TCB->sub_h[i]);
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}
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free(TCB->sub_h);
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free(TCB->sub_h_lock);
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}
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void destory_Total_Pos_Table(Total_Pos_Table* TCB)
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{
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free(TCB->k_mer_index);
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free(TCB->sub_h_lock);
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free(TCB->pos);
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int i;
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for (i = 0; i < TCB->size; i++)
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{
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kh_destroy(POS64, TCB->sub_h[i]);
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}
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free(TCB->sub_h);
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}
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void write_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name)
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{
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fprintf(stdout, "Writing index to disk ...... \n");
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char* index_name = (char*)malloc(strlen(read_file_name)+5);
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sprintf(index_name, "%s.idx", read_file_name);
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FILE* fp = fopen(index_name, "w");
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fwrite(&TCB->prefix_bits, sizeof(TCB->prefix_bits), 1, fp);
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fwrite(&TCB->suffix_bits, sizeof(TCB->suffix_bits), 1, fp);
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fwrite(&TCB->suffix_mode, sizeof(TCB->suffix_mode), 1, fp);
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fwrite(&TCB->size, sizeof(TCB->size), 1, fp);
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fwrite(&TCB->useful_k_mer, sizeof(TCB->useful_k_mer), 1, fp);
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fwrite(&TCB->total_occ, sizeof(TCB->total_occ), 1, fp);
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fwrite(TCB->k_mer_index, sizeof(uint64_t), TCB->useful_k_mer+1, fp);
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fwrite(TCB->pos, sizeof(k_mer_pos), TCB->total_occ, fp);
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int i;
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for (i = 0; i < TCB->size; i++)
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{
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kh_write(POS64, TCB->sub_h[i], fp);
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}
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free(index_name);
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fclose(fp);
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fprintf(stdout, "Index has been written.\n");
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}
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void load_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name)
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{
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fprintf(stdout, "Loading index to disk ...... \n");
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char* index_name = (char*)malloc(strlen(read_file_name)+5);
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sprintf(index_name, "%s.idx", read_file_name);
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FILE* fp = fopen(index_name, "r");
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fread(&TCB->prefix_bits, sizeof(TCB->prefix_bits), 1, fp);
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fread(&TCB->suffix_bits, sizeof(TCB->suffix_bits), 1, fp);
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fread(&TCB->suffix_mode, sizeof(TCB->suffix_mode), 1, fp);
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fread(&TCB->size, sizeof(TCB->size), 1, fp);
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fread(&TCB->useful_k_mer, sizeof(TCB->useful_k_mer), 1, fp);
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fread(&TCB->total_occ, sizeof(TCB->total_occ), 1, fp);
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if (TCB->useful_k_mer+1)
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{
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TCB->k_mer_index = (uint64_t*)malloc(sizeof(uint64_t)*(TCB->useful_k_mer+1));
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fread(TCB->k_mer_index, sizeof(uint64_t), TCB->useful_k_mer+1, fp);
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}
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else
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{
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TCB->k_mer_index = NULL;
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}
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if (TCB->total_occ)
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{
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TCB->pos = (k_mer_pos*)malloc(sizeof(k_mer_pos)*TCB->total_occ);
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fread(TCB->pos, sizeof(k_mer_pos), TCB->total_occ, fp);
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}
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else
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{
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TCB->pos = NULL;
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}
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TCB->sub_h_lock = (Hash_table_spin_lock*)malloc(sizeof(Hash_table_spin_lock)*TCB->size);
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memset(TCB->sub_h_lock, 0, sizeof(Hash_table_spin_lock)*TCB->size);
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TCB->sub_h = (Pos_Table**)malloc(sizeof(Pos_Table*)*TCB->size);
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int i;
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for (i = 0; i < TCB->size; i++)
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{
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init_Pos_Table(&(TCB->sub_h[i]));
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TCB->sub_h_lock[i].lock = 0;
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kh_load(POS64, TCB->sub_h[i], fp);
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}
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free(index_name);
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fclose(fp);
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fprintf(stdout, "Index has been loaded.\n");
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}
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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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{
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int i;
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Count_Table* h;
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khint_t k;
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uint64_t sub_key;
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uint64_t sub_ID;
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PCB->useful_k_mer = 0;
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PCB->total_occ = 0;
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///init_Total_Pos_Table(PCB, TCB);
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khint_t t; ///这就是个迭代器
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int absent;
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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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///只有符合频率范围要求的k-mer，才会被加入到pos table中
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if (kh_value(h, k)>=k_mer_min_freq && kh_value(h, k)<=k_mer_max_freq)
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{
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sub_ID = i;
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sub_key = kh_key(h, k);
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t = kh_put(POS64, PCB->sub_h[sub_ID], sub_key, &absent);
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if (absent)
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{
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///kh_value(PCB->sub_h[sub_ID], t) = useful_k_mer + total_occ;
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kh_value(PCB->sub_h[sub_ID], t) = PCB->useful_k_mer;
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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(PCB->sub_h[sub_ID], t)++;
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fprintf(stderr, "ERROR\n");
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}
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PCB->useful_k_mer++;
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PCB->total_occ = PCB->total_occ + kh_value(h, k);
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}
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}
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}
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}
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fprintf(stdout, "useful_k_mer: %lld\n",PCB->useful_k_mer);
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fprintf(stdout, "total_occ: %lld\n",PCB->total_occ);
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PCB->k_mer_index = (uint64_t*)malloc(sizeof(uint64_t)*(PCB->useful_k_mer+1));
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PCB->k_mer_index[0] = 0;
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PCB->total_occ = 0;
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PCB->useful_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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if (kh_value(h, k)>=k_mer_min_freq && kh_value(h, k)<=k_mer_max_freq)
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{
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PCB->useful_k_mer++;
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PCB->total_occ = PCB->total_occ + kh_value(h, k);
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PCB->k_mer_index[PCB->useful_k_mer] = PCB->total_occ;
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}
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}
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}
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}
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PCB->pos = (k_mer_pos*)malloc(sizeof(k_mer_pos)*PCB->total_occ);
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memset(PCB->pos, 0, sizeof(k_mer_pos)*PCB->total_occ);
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}
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int cmp_k_mer_pos(const void * a, const void * b)
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{
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if ((*(k_mer_pos*)a).readID != (*(k_mer_pos*)b).readID)
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{
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return (*(k_mer_pos*)a).readID > (*(k_mer_pos*)b).readID ? 1 : -1;
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}
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else
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{
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if ((*(k_mer_pos*)a).offset != (*(k_mer_pos*)b).offset)
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{
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return (*(k_mer_pos*)a).offset > (*(k_mer_pos*)b).offset ? 1 : -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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}
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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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{
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fprintf(stderr, "#%llu: Start debug_mode...\n", thread_ID);
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uint64_t i;
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for (i = thread_ID; i < 4,294,967,296; i = i + thread_num)
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{
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if(i%d != mod_d(0, i, d))
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{
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fprintf(stderr, "ERROR mode, i: %llu\n", i);
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fprintf(stderr, "i mod d: %llu\n", i%d);
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fprintf(stderr, "mod_d(0, i, d): %llu\n", mod_d(0, i, d));
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}
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}
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fprintf(stderr, "#%llu: Finish debug_mode\n", thread_ID);
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}
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/********************************for debug***************************************/
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void test_COUNT64()
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{
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uint64_t sb[7] = {5000000000, 6000000000, 7000000000, 8000000000, 9000000000, 10000000000 ,5000000000};
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Count_Table* h;
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///构建哈希表
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init_Count_Table(&h);
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int i;
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khint_t k; ///这就是个迭代器
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int absent;
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for (i = 0; i < 7; i++)
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{
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///将5作为key插入到哈希表COUNT64中
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///absent为0代表哈希表里面已经有这个key了
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k = kh_put(COUNT64, h, sb[i], &absent);
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///代表插入了一个哈希表中没有的元素
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///则直接插入
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if (absent)
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{
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kh_value(h, k) = i;
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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(h, k) = i;
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}
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}
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for (i = 0; i < 7; i++)
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{
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///查询哈希表，key为k
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k = kh_get(COUNT64, h, sb[i]);
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if (k != kh_end(h))
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{
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fprintf(stderr, "value: %d\n", kh_value(h, k));
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}
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else
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{
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fprintf(stderr, "not found!\n");
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}
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}
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kh_destroy(COUNT64, h);
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} |