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

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

79
Assembly.cpp
View File

@@ -13,7 +13,10 @@ Total_Count_Table TCB;
Total_Pos_Table PCB;
All_reads R_INF;
pthread_mutex_t statistics;
long long total_matched_overlap_0 = 0;
long long total_matched_overlap_1 = 0;
long long complete_threads = 0;
void* Perform_Counting(void* arg)
@@ -679,6 +682,14 @@ void* Overlap_calculate(void* arg)
void* Overlap_calculate_heap_merge(void* arg)
{
/************需要注释掉**********/
// long long debug_overlap = 0;
// long long filtered_debug_overlap = 0;
/************需要注释掉**********/
long long matched_overlap_0 = 0;
long long matched_overlap_1 = 0;
long long j;
int thr_ID = *((int*)arg);
uint64_t POA_i;
@@ -721,6 +732,7 @@ void* Overlap_calculate_heap_merge(void* arg)
for (i = thr_ID; i < R_INF.total_reads; i = i + thread_num)
{
clear_Heap(&heap);
clear_Candidates_list(&l);
@@ -749,10 +761,14 @@ void* Overlap_calculate_heap_merge(void* arg)
if (list_length != 0)
{
append_k_mer_pos_list_alloc(&array_list, list, list_length, end_pos, 0);
/************需要注释掉**********/
// debug_overlap = debug_overlap + list_length;
/************需要注释掉**********/
///append_k_mer_pos_list_alloc(&array_list, list, list_length, end_pos, 0);
append_k_mer_pos_list_alloc_prefilter(&array_list, list, list_length, end_pos, 0, &g_read, &R_INF, &correct);
}
///merge_Candidates_list(&l, list, list_length, end_pos, 0);
//merge_Candidates_list_version(&debug_l, list, list_length, end_pos, 0);
///merge_Candidates_list_version(&debug_l, list, list_length, end_pos, 0);
}
}
else
@@ -805,7 +821,11 @@ void* Overlap_calculate_heap_merge(void* arg)
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);
/************需要注释掉**********/
// debug_overlap = debug_overlap + list_length;
/************需要注释掉**********/
///append_k_mer_pos_list_alloc(&array_list, list, list_length, end_pos, 1);
append_k_mer_pos_list_alloc_prefilter(&array_list, list, list_length, end_pos, 1, &g_read, &R_INF, &correct);
}
///merge_Candidates_list(&l, list, list_length, end_pos, 1);
//merge_Candidates_list_version(&debug_l, list, list_length, end_pos, 1);
@@ -820,6 +840,16 @@ void* Overlap_calculate_heap_merge(void* arg)
///HPC_base++;
}
/************需要注释掉**********/
// for (int ijk = 0; ijk < array_list.length; ijk++)
// {
// filtered_debug_overlap = filtered_debug_overlap + array_list.list[ijk].length;
// }
/************需要注释掉**********/
///merge_k_mer_pos_list_alloc(&array_list, &l);
merge_k_mer_pos_list_alloc_heap_sort(&array_list, &l, &heap);
/**
@@ -840,6 +870,22 @@ void* Overlap_calculate_heap_merge(void* arg)
correct_overlap(&overlap_list, &R_INF, &g_read, &correct);
for (j = 0; j < overlap_list.length; j++)
{
long long Len_x = overlap_list.list[j].x_pos_e - overlap_list.list[j].x_pos_s + 1;
if (Len_x * 0.6 <= overlap_list.list[j].align_length)
{
if (overlap_list.list[j].y_pos_strand == 0)
{
matched_overlap_0++;
}
else
{
matched_overlap_1++;
}
}
}
/**
POA_i = 0;
@@ -918,6 +964,16 @@ void* Overlap_calculate_heap_merge(void* arg)
}
/************需要注释掉**********/
// fprintf(stderr, "debug_overlap: %llu\n", debug_overlap);
// fprintf(stderr, "filtered_debug_overlap: %llu\n", filtered_debug_overlap);
/************需要注释掉**********/
/**
fprintf(stderr, "candidate_overlap_reads: %llu\n", candidate_overlap_reads);
fprintf(stderr, "total_shared_seed: %llu\n", total_shared_seed);
@@ -927,12 +983,25 @@ void* Overlap_calculate_heap_merge(void* arg)
//destory_Candidates_list(&debug_l);
destory_Heap(&heap);
destory_k_mer_pos_list_alloc(&array_list);
///destory_k_mer_pos_list_alloc(&array_list);
destory_k_mer_pos_list_alloc_prefilter(&array_list);
destory_Graph(&POA_Graph);
destory_UC_Read(&g_read);
destory_Correct_dumy(&correct);
pthread_mutex_lock(&statistics);
total_matched_overlap_0 += matched_overlap_0;
total_matched_overlap_1 += matched_overlap_1;
complete_threads++;
if(complete_threads == thread_num)
{
fprintf(stderr, "total_matched_overlap_0: %llu\n", total_matched_overlap_0);
fprintf(stderr, "total_matched_overlap_1: %llu\n", total_matched_overlap_1);
}
pthread_mutex_unlock(&statistics);
}