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Change stupid merge function

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This commit is contained in:
Haoyu Cheng
2019-05-19 05:02:28 -04:00
parent 63509bcb7f
commit e3924b5c08
5 changed files with 696 additions and 1 deletions
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Assembly.cpp
+141 -1
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@@ -575,6 +575,7 @@ void* Overlap_calculate(void* arg)
k_mer_pos_list_alloc array_list;
init_k_mer_pos_list_alloc(&array_list);
for (i = thr_ID; i < R_INF.total_reads; i = i + thread_num)
///for (i = thr_ID; i < R_INF.total_reads/50; i = i + thread_num)
{
@@ -674,6 +675,144 @@ void* Overlap_calculate(void* arg)
}
void* Overlap_calculate_heap_merge(void* arg)
{
int thr_ID = *((int*)arg);
long long i = 0;
int avalible_k = 0;
UC_Read g_read;
init_UC_Read(&g_read);
HPC_seq HPC_read;
Hash_code k_code;
uint64_t code;
uint64_t end_pos;
k_mer_pos* list;
uint64_t list_length;
uint64_t sub_ID;
Candidates_list l;
//Candidates_list debug_l;
init_Candidates_list(&l);
//init_Candidates_list(&debug_l);
k_mer_pos_list_alloc array_list;
init_k_mer_pos_list_alloc(&array_list);
HeapSq heap;
Init_Heap(&heap);
for (i = thr_ID; i < R_INF.total_reads; i = i + thread_num)
{
clear_Heap(&heap);
clear_Candidates_list(&l);
///clear_Candidates_list(&debug_l);
clear_k_mer_pos_list_alloc(&array_list);
recover_UC_Read(&g_read, &R_INF, i);
///forward strand
init_HPC_seq(&HPC_read, g_read.seq, g_read.length);
init_Hash_code(&k_code);
avalible_k = 0;
while ((code = get_HPC_code(&HPC_read, &end_pos)) != 6)
{
if(code < 4)
{
k_mer_append(&k_code,code,k_mer_length);
avalible_k++;
if (avalible_k>=k_mer_length)
{
list_length = locate_Total_Pos_Table(&PCB, &k_code, &list, k_mer_length, &sub_ID);
if (list_length != 0)
{
append_k_mer_pos_list_alloc(&array_list, list, list_length, end_pos, 0);
}
///merge_Candidates_list(&l, list, list_length, end_pos, 0);
//merge_Candidates_list_version(&debug_l, list, list_length, end_pos, 0);
}
}
else
{
avalible_k = 0;
init_Hash_code(&k_code);
}
///HPC_base++;
}
///reverse complement strand
reverse_complement(g_read.seq, g_read.length);
init_HPC_seq(&HPC_read, g_read.seq, g_read.length);
init_Hash_code(&k_code);
avalible_k = 0;
while ((code = get_HPC_code(&HPC_read, &end_pos)) != 6)
{
if(code < 4)
{
k_mer_append(&k_code,code,k_mer_length);
avalible_k++;
if (avalible_k>=k_mer_length)
{
list_length = locate_Total_Pos_Table(&PCB, &k_code, &list, k_mer_length, &sub_ID);
if (list_length != 0)
{
append_k_mer_pos_list_alloc(&array_list, list, list_length, end_pos, 1);
}
///merge_Candidates_list(&l, list, list_length, end_pos, 1);
//merge_Candidates_list_version(&debug_l, list, list_length, end_pos, 1);
}
}
else
{
avalible_k = 0;
init_Hash_code(&k_code);
}
///HPC_base++;
}
///merge_k_mer_pos_list_alloc(&array_list, &l);
merge_k_mer_pos_list_alloc_heap_sort(&array_list, &l, &heap);
/**
if (array_list.length < 3)
{
merge_k_mer_pos_list_alloc(&array_list, &l);
}
else
{
merge_k_mer_pos_list_alloc_heap_sort_advance(&array_list, &l, &heap);
}
**/
///merge_k_mer_pos_list_alloc_heap_sort_advance(&array_list, &l, &heap);
///debug_merge_result(&l, &debug_l);
}
destory_Candidates_list(&l);
//destory_Candidates_list(&debug_l);
destory_Heap(&heap);
destory_k_mer_pos_list_alloc(&array_list);
}
@@ -698,7 +837,8 @@ void Overlap_calculate_multipe_thr()
int *arg = (int*)malloc(sizeof(*arg));
*arg = i;
pthread_create(_r_threads + i, NULL, Overlap_calculate, (void*)arg);
pthread_create(_r_threads + i, NULL, Overlap_calculate_heap_merge, (void*)arg);
//pthread_create(_r_threads + i, NULL, Overlap_calculate, (void*)arg);
}