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removed k_mer_pos_list_alloc

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This commit is contained in:
Heng Li
2020-03-27 11:27:36 -04:00
parent 293f4b6b58
commit 8dbb4140bd
3 changed files with 1 additions and 60 deletions
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Assembly.cpp
+1 -12
View File
@@ -397,8 +397,6 @@ void* Overlap_calculate_heap_merge(void* arg)
init_Graph(&DAGCon);
init_Graph(&POA_Graph);
init_Candidates_list(&l);
k_mer_pos_list_alloc array_list;
init_k_mer_pos_list_alloc(&array_list);
overlap_region_alloc overlap_list;
init_overlap_region_alloc(&overlap_list);
@@ -425,7 +423,7 @@ void* Overlap_calculate_heap_merge(void* arg)
for (i = thr_ID; i < (long long)R_INF.total_reads; i = i + asm_opt.thread_num)
{
///get_new_candidates(i, &g_read, &overlap_list, &array_list, &heap, &l, THRESHOLD_RATE*1.5);
//get_new_candidates(i, &g_read, &overlap_list, &array_list, &heap, &l, THRESHOLD_RATE*1.5);
//get_new_candidates(i, &g_read, &overlap_list, &array_list, &l, 0.02, 1);
ha_get_new_candidates(ab, i, &g_read, &overlap_list, &l, 0.02, 1);
@@ -463,7 +461,6 @@ void* Overlap_calculate_heap_merge(void* arg)
destory_buffer_sub_block(&current_sub_buffer);
destory_Candidates_list(&l);
destory_overlap_region_alloc(&overlap_list);
destory_k_mer_pos_list_alloc(&array_list);
destory_Graph(&POA_Graph);
destory_Graph(&DAGCon);
destory_UC_Read(&g_read);
@@ -513,9 +510,6 @@ void* Output_related_reads(void* arg)
init_Candidates_list(&l);
//init_Candidates_list(&debug_l);
k_mer_pos_list_alloc array_list;
init_k_mer_pos_list_alloc(&array_list);
overlap_region_alloc overlap_list;
init_overlap_region_alloc(&overlap_list);
@@ -577,7 +571,6 @@ void* Output_related_reads(void* arg)
destory_buffer_sub_block(&current_sub_buffer);
destory_Candidates_list(&l);
destory_overlap_region_alloc(&overlap_list);
destory_k_mer_pos_list_alloc(&array_list);
destory_Graph(&POA_Graph);
destory_Graph(&DAGCon);
destory_UC_Read(&g_read);
@@ -1100,9 +1093,6 @@ void* Final_overlap_calculate_heap_merge(void* arg)
Candidates_list l;
init_Candidates_list(&l);
k_mer_pos_list_alloc array_list;
init_k_mer_pos_list_alloc(&array_list);
overlap_region_alloc overlap_list;
init_overlap_region_alloc(&overlap_list);
@@ -1156,7 +1146,6 @@ void* Final_overlap_calculate_heap_merge(void* arg)
destory_Candidates_list(&l);
destory_overlap_region_alloc(&overlap_list);
destory_k_mer_pos_list_alloc(&array_list);
destory_UC_Read(&g_read);
destory_UC_Read(&overlap_read);
destory_Cigar_record_alloc(&cigarline);
Hash_Table.cpp
-35
View File
@@ -687,41 +687,6 @@ void append_window_list(overlap_region* region, uint64_t x_start, uint64_t x_end
region->w_list_length++;
}
void init_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list)
{
list->size = 1000;
list->length = 0;
//list->list = (k_mer_pos_list*)malloc(sizeof(k_mer_pos_list)*list->size);
list->list = (k_mer_pos_list*)calloc(list->size, sizeof(k_mer_pos_list));
}
void clear_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list)
{
list->length = 0;
}
void destory_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list)
{
free(list->list);
}
void append_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list, k_mer_pos* n_list, uint64_t n_length,
uint64_t n_end_pos, uint8_t n_direction)
{
if (list->length + 1 > list->size)
{
list->size = list->size * 2;
list->list = (k_mer_pos_list*)realloc(list->list, sizeof(k_mer_pos_list)*list->size);
}
list->list[list->length].list = n_list;
list->list[list->length].length = n_length;
list->list[list->length].direction = n_direction;
list->list[list->length].end_pos = n_end_pos;
list->length++;
}
void test_single_list(Candidates_list* candidates, k_mer_pos* n_list, uint64_t n_lengh, uint64_t end_pos, uint64_t strand)
{
uint64_t i;
Hash_Table.h
-13
View File
@@ -43,13 +43,6 @@ typedef struct
uint64_t end_pos;
} k_mer_pos_list;
typedef struct
{
k_mer_pos_list* list;
uint64_t size;
uint64_t length;
} k_mer_pos_list_alloc;
typedef struct
{
int C_L[CIGAR_MAX_LENGTH];
@@ -152,12 +145,6 @@ void init_Candidates_list(Candidates_list* l);
void clear_Candidates_list(Candidates_list* l);
void destory_Candidates_list(Candidates_list* l);
void init_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list);
void destory_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list);
void clear_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list);
void append_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list, k_mer_pos* n_list, uint64_t n_length,
uint64_t n_end_pos, uint8_t n_direction);
void init_overlap_region_alloc(overlap_region_alloc* list);
void clear_overlap_region_alloc(overlap_region_alloc* list);
void destory_overlap_region_alloc(overlap_region_alloc* list);