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S/L index&reads

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This commit is contained in:
Haoyu Cheng
2019-05-16 21:14:50 -04:00
parent 3c5799aa1b
commit 17553e0a42
14 changed files with 297 additions and 5 deletions
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101
Hash_Table.cpp
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@@ -88,6 +88,105 @@ void destory_Total_Count_Table(Total_Count_Table* TCB)
}
void destory_Total_Pos_Table(Total_Pos_Table* TCB)
{
free(TCB->k_mer_index);
free(TCB->sub_h_lock);
free(TCB->pos);
int i;
for (i = 0; i < TCB->size; i++)
{
kh_destroy(POS64, TCB->sub_h[i]);
}
free(TCB->sub_h);
}
void write_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name)
{
fprintf(stdout, "Writing index to disk ...... \n");
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(&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);
fwrite(&TCB->size, sizeof(TCB->size), 1, fp);
fwrite(&TCB->useful_k_mer, sizeof(TCB->useful_k_mer), 1, fp);
fwrite(&TCB->total_occ, sizeof(TCB->total_occ), 1, fp);
fwrite(TCB->k_mer_index, sizeof(uint64_t), TCB->useful_k_mer+1, fp);
fwrite(TCB->pos, sizeof(k_mer_pos), TCB->total_occ, fp);
int i;
for (i = 0; i < TCB->size; i++)
{
kh_write(POS64, TCB->sub_h[i], fp);
}
free(index_name);
fclose(fp);
fprintf(stdout, "Index has been written.\n");
}
void load_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name)
{
fprintf(stdout, "Loading index to disk ...... \n");
char* index_name = (char*)malloc(strlen(read_file_name)+5);
sprintf(index_name, "%s.idx", read_file_name);
FILE* fp = fopen(index_name, "r");
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);
fread(&TCB->size, sizeof(TCB->size), 1, fp);
fread(&TCB->useful_k_mer, sizeof(TCB->useful_k_mer), 1, fp);
fread(&TCB->total_occ, sizeof(TCB->total_occ), 1, fp);
if (TCB->useful_k_mer+1)
{
TCB->k_mer_index = (uint64_t*)malloc(sizeof(uint64_t)*(TCB->useful_k_mer+1));
fread(TCB->k_mer_index, sizeof(uint64_t), TCB->useful_k_mer+1, fp);
}
else
{
TCB->k_mer_index = NULL;
}
if (TCB->total_occ)
{
TCB->pos = (k_mer_pos*)malloc(sizeof(k_mer_pos)*TCB->total_occ);
fread(TCB->pos, sizeof(k_mer_pos), TCB->total_occ, fp);
}
else
{
TCB->pos = NULL;
}
TCB->sub_h_lock = (Hash_table_spin_lock*)malloc(sizeof(Hash_table_spin_lock)*TCB->size);
memset(TCB->sub_h_lock, 0, sizeof(Hash_table_spin_lock)*TCB->size);
TCB->sub_h = (Pos_Table**)malloc(sizeof(Pos_Table*)*TCB->size);
int i;
for (i = 0; i < TCB->size; i++)
{
init_Pos_Table(&(TCB->sub_h[i]));
TCB->sub_h_lock[i].lock = 0;
kh_load(POS64, TCB->sub_h[i], fp);
}
free(index_name);
fclose(fp);
fprintf(stdout, "Index has been loaded.\n");
}
void Traverse_Counting_Table(Total_Count_Table* TCB, Total_Pos_Table* PCB, int k_mer_min_freq, int k_mer_max_freq)
{
int i;
@@ -98,7 +197,7 @@ void Traverse_Counting_Table(Total_Count_Table* TCB, Total_Pos_Table* PCB, int k
PCB->useful_k_mer = 0;
PCB->total_occ = 0;
init_Total_Pos_Table(PCB, TCB);
///init_Total_Pos_Table(PCB, TCB);
khint_t t; ///这就是个迭代器
int absent;