xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-19 02:48:34 +08:00
Code Issues Packages Projects Releases Wiki Activity

prefilter

Browse Source
This commit is contained in:
Haoyu Cheng
2019-07-09 15:11:04 -04:00
parent 1892b4d2db
commit 4eddb02dbd
5 changed files with 560 additions and 66 deletions
Download Patch File Download Diff File Expand all files Collapse all files

29
Hash_Table.cpp
View File

@@ -317,6 +317,7 @@ void append_overlap_region_alloc(overlap_region_alloc* list, overlap_region* tmp
list->list[list->length].shared_seed = tmp->shared_seed;
list->list[list->length].align_length = 0;
list->length++;
}
@@ -661,12 +662,8 @@ 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);
}
void destory_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list)
{
free(list->list);
//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)
@@ -674,6 +671,10 @@ 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)
@@ -693,6 +694,9 @@ uint64_t n_end_pos, uint8_t n_direction)
list->length++;
}
int cmp_k_mer_pos_list(const void * a, const void * b)
{
if ((*(k_mer_pos_list*)a).length > (*(k_mer_pos_list*)b).length)
@@ -716,18 +720,7 @@ inline void append_pos_to_Candidates_list(Candidates_list* candidates, ElemType*
candidates->length++;
}
void pre_filter_by_nearby(k_mer_pos* n_list, uint64_t n_length, uint64_t n_end_pos, uint8_t n_direction, UC_Read* g_read)
{
char* x_string = NULL;
char* y_string = NULL;
long long i = 0;
for (i = 0; i < n_length; i++)
{
/* code */
}
}
void test_single_list(Candidates_list* candidates, k_mer_pos* n_list, uint64_t n_lengh, uint64_t end_pos, uint64_t strand)