From 8dbb4140bd60b07ee53782385bc02a31f888d328 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Fri, 27 Mar 2020 11:27:36 -0400 Subject: [PATCH] removed k_mer_pos_list_alloc --- Assembly.cpp | 13 +------------ Hash_Table.cpp | 35 ----------------------------------- Hash_Table.h | 13 ------------- 3 files changed, 1 insertion(+), 60 deletions(-) diff --git a/Assembly.cpp b/Assembly.cpp index 39e4d63..9e90b40 100644 --- a/Assembly.cpp +++ b/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(¤t_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(¤t_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); diff --git a/Hash_Table.cpp b/Hash_Table.cpp index a589a02..397d2fd 100644 --- a/Hash_Table.cpp +++ b/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; diff --git a/Hash_Table.h b/Hash_Table.h index 279fecf..8e570ee 100644 --- a/Hash_Table.h +++ b/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);