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replaced khash with khashl

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This commit is contained in:
Heng Li
2020-03-23 10:21:46 -04:00
parent cfb0a5c8ec
commit 3a27d104c6
4 changed files with 40 additions and 710 deletions
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37
Hash_Table.cpp
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@@ -1016,12 +1016,12 @@ void merge_k_mer_pos_list_alloc_heap_sort(k_mer_pos_list_alloc* list, Candidates
void init_Count_Table(Count_Table** table)
{
*table = kh_init(COUNT64);
*table = ha_ct_init();
}
void init_Pos_Table(Pos_Table** table)
{
*table = kh_init(POS64);
*table = ha_pt_init();
}
void init_Total_Count_Table(int k, Total_Count_Table* TCB)
@@ -1091,7 +1091,7 @@ void destory_Total_Count_Table(Total_Count_Table* TCB)
int i;
for (i = 0; i < TCB->size; i++)
{
kh_destroy(COUNT64, TCB->sub_h[i]);
ha_ct_destroy(TCB->sub_h[i]);
}
free(TCB->sub_h);
free(TCB->sub_h_lock);
@@ -1107,12 +1107,12 @@ void destory_Total_Pos_Table(Total_Pos_Table* TCB)
int i;
for (i = 0; i < TCB->size; i++)
{
kh_destroy(POS64, TCB->sub_h[i]);
ha_pt_destroy(TCB->sub_h[i]);
}
free(TCB->sub_h);
}
/*
void write_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name)
{
fprintf(stderr, "Writing index to disk... \n");
@@ -1212,6 +1212,7 @@ int load_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name)
return 1;
}
*/
typedef struct
{
@@ -1268,7 +1269,7 @@ void get_peak_debug(Total_Count_Table* TCB, long long* min, long long* max)
for (i = 0; i < TCB->size; i++)
{
h = TCB->sub_h[i];
for (k = kh_begin(h); k != kh_end(h); ++k)
for (k = 0; k != kh_end(h); ++k)
{
if (kh_exist(h, k)) // test if a bucket contains data
{
@@ -1308,7 +1309,7 @@ void get_peak_debug(Total_Count_Table* TCB, long long* min, long long* max)
///get_Total_Count_Table(&TCB, &k_code, k_mer_length);
c_count = kh_value(h, k);
c_count = kh_val(h, k);
if(get_Total_Count_Table(TCB, &code, asm_opt.k_mer_length) != c_count)
{
@@ -1436,7 +1437,7 @@ void get_peak(Total_Count_Table* TCB, long long* min, long long* max, long long*
for (i = 0; i < TCB->size; i++)
{
h = TCB->sub_h[i];
for (k = kh_begin(h); k != kh_end(h); ++k)
for (k = 0; k != kh_end(h); ++k)
{
if (kh_exist(h, k)) // test if a bucket contains data
{
@@ -1548,7 +1549,7 @@ void Traverse_Counting_Table(Total_Count_Table* TCB, Total_Pos_Table* PCB, int k
for (i = 0; i < TCB->size; i++)
{
h = TCB->sub_h[i];
for (k = kh_begin(h); k != kh_end(h); ++k)
for (k = 0; k != kh_end(h); ++k)
{
if (kh_exist(h, k)) // test if a bucket contains data
{
@@ -1558,22 +1559,22 @@ void Traverse_Counting_Table(Total_Count_Table* TCB, Total_Pos_Table* PCB, int k
if (count>=k_mer_min_freq && count<=k_mer_max_freq)
{
t = kh_put(POS64, PCB->sub_h[sub_ID], sub_key, &absent);
t = ha_pt_put(PCB->sub_h[sub_ID], sub_key, &absent);
if (absent)
{
///kh_value(PCB->sub_h[sub_ID], t) = useful_k_mer + total_occ;
kh_value(PCB->sub_h[sub_ID], t) = PCB->useful_k_mer;
///kh_val(PCB->sub_h[sub_ID], t) = useful_k_mer + total_occ;
kh_val(PCB->sub_h[sub_ID], t) = PCB->useful_k_mer;
}
else
{
///kh_value(PCB->sub_h[sub_ID], t)++;
///kh_val(PCB->sub_h[sub_ID], t)++;
fprintf(stderr, "ERROR\n");
}
PCB->useful_k_mer++;
PCB->total_occ = PCB->total_occ + kh_value(h, k);
PCB->total_occ = PCB->total_occ + kh_val(h, k);
}
}
}
@@ -1593,7 +1594,7 @@ void Traverse_Counting_Table(Total_Count_Table* TCB, Total_Pos_Table* PCB, int k
for (i = 0; i < TCB->size; i++)
{
h = TCB->sub_h[i];
for (k = kh_begin(h); k != kh_end(h); ++k)
for (k = 0; k != kh_end(h); ++k)
{
if (kh_exist(h, k)) // test if a bucket contains data
{
@@ -1601,11 +1602,11 @@ void Traverse_Counting_Table(Total_Count_Table* TCB, Total_Pos_Table* PCB, int k
sub_key = kh_key(h, k);
get_total_freq(TCB, sub_ID, sub_key, &count);
///if (kh_value(h, k)>=k_mer_min_freq && kh_value(h, k)<=k_mer_max_freq)
///if (kh_val(h, k)>=k_mer_min_freq && kh_val(h, k)<=k_mer_max_freq)
if (count>=k_mer_min_freq && count<=k_mer_max_freq)
{
PCB->useful_k_mer++;
PCB->total_occ = PCB->total_occ + kh_value(h, k);
PCB->total_occ = PCB->total_occ + kh_val(h, k);
PCB->k_mer_index[PCB->useful_k_mer] = PCB->total_occ;
}
}
@@ -1849,4 +1850,4 @@ void resize_window_list_alloc(window_list_alloc* x, long long size)
x->length = 0;
}
}