removed k_mer_pos_list_alloc

Assembly.cpp

@@ -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

@@ -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

@@ -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);