xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-15 12:47:57 +08:00
Code Issues Packages Projects Releases Wiki Activity

Accelerate overlap merge

Browse Source
This commit is contained in:
Haoyu Cheng
2019-05-18 11:36:42 -04:00
parent ddd96d8456
commit 63509bcb7f
5 changed files with 221 additions and 6 deletions
Download Patch File Download Diff File Expand all files Collapse all files

53
Hash_Table.cpp
View File

@@ -24,17 +24,60 @@ 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)
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)
{
list->length++;
if (list->length > list->size)
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 - 1].list = n_list;
list->list[list->length - 1].length = n_length;
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++;
}
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)
{
return 1;
}
else if ((*(k_mer_pos_list*)a).length < (*(k_mer_pos_list*)b).length)
{
return -1;
}
else
{
return 0;
}
}
void merge_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list, Candidates_list* candidates)
{
qsort(list->list, list->length, sizeof(k_mer_pos_list), cmp_k_mer_pos_list);
uint64_t i;
for (i = 0; i < list->length; i++)
{
/**
if (i > 0 && (list->list[i].length < list->list[i-1].length || list->list[i].length == 0 || list->list[i-1].length == 0))
{
fprintf(stderr, "ERROR\n");
}
**/
merge_Candidates_list(candidates, list->list[i].list, list->list[i].length,
list->list[i].end_pos, list->list[i].direction);
}
}
void init_Count_Table(Count_Table** table)