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improve speed

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This commit is contained in:
Haoyu Cheng
2019-08-26 02:22:20 -04:00
parent 6802d873cf
commit 3c0c201cdf
12 changed files with 249 additions and 39 deletions
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10
Hash_Table.cpp
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@@ -4,6 +4,7 @@
#include "Hash_Table.h"
#include "Process_Read.h"
#include "Correct.h"
#include "CommandLines.h"
#include <pthread.h>
pthread_mutex_t output_mutex;
@@ -1304,6 +1305,8 @@ void write_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name)
char* index_name = (char*)malloc(strlen(read_file_name)+5);
sprintf(index_name, "%s.idx", read_file_name);
FILE* fp = fopen(index_name, "w");
fwrite(&k_mer_min_freq, sizeof(k_mer_min_freq), 1, fp);
fwrite(&k_mer_max_freq, sizeof(k_mer_max_freq), 1, fp);
fwrite(&TCB->prefix_bits, sizeof(TCB->prefix_bits), 1, fp);
fwrite(&TCB->suffix_bits, sizeof(TCB->suffix_bits), 1, fp);
fwrite(&TCB->suffix_mode, sizeof(TCB->suffix_mode), 1, fp);
@@ -1337,7 +1340,9 @@ int load_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name)
return 0;
}
fread(&k_mer_min_freq, sizeof(k_mer_min_freq), 1, fp);
fread(&k_mer_max_freq, sizeof(k_mer_max_freq), 1, fp);
fread(&TCB->prefix_bits, sizeof(TCB->prefix_bits), 1, fp);
fread(&TCB->suffix_bits, sizeof(TCB->suffix_bits), 1, fp);
fread(&TCB->suffix_mode, sizeof(TCB->suffix_mode), 1, fp);
@@ -1403,6 +1408,9 @@ void Traverse_Counting_Table(Total_Count_Table* TCB, Total_Pos_Table* PCB, int k
khint_t t; ///这就是个迭代器
int absent;
/********************************************
hash_table(key) ----> PCB->k_mer_index ------> PCB->pos
********************************************/
for (i = 0; i < TCB->size; i++)
{
h = TCB->sub_h[i];