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improve speed

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This commit is contained in:
Haoyu Cheng
2019-08-26 02:22:20 -04:00
parent 6802d873cf
commit 3c0c201cdf
12 changed files with 249 additions and 39 deletions
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86
Assembly.cpp
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@@ -217,14 +217,17 @@ void* Build_hash_table(void* arg)
///HPC_base++;
}
///load read
compress_base(Get_READ(R_INF, curr_sub_block.read[i].ID),
curr_sub_block.read[i].seq.s, curr_sub_block.read[i].seq.l,
&R_INF.N_site[curr_sub_block.read[i].ID], HPC_read.N_occ);
memcpy(R_INF.name+R_INF.name_index[curr_sub_block.read[i].ID],
curr_sub_block.read[i].name.s, curr_sub_block.read[i].name.l);
/**
///reverse complement strand
@@ -342,6 +345,7 @@ void Counting_multiple_thr()
fprintf(stdout, "%-30s%18.2f\n\n", "Counting time:", Get_T() - start_time);
free(is_insert);
}
@@ -421,8 +425,10 @@ void Build_hash_table_multiple_thr()
///destory_All_reads(&R_INF);
///load_All_reads(&R_INF, read_file_name);
}
destory_Total_Count_Table(&TCB);
free(is_insert);
}
@@ -717,6 +723,69 @@ Output_buffer_sub_block* current_sub_buffer)
}
int get_required_read(const char *required_name, long long RID, All_reads* R_INF)
{
int required_name_length = strlen(required_name);
char* debug_name = Get_NAME((*R_INF), RID);
int debug_name_length = Get_NAME_LENGTH((*R_INF), RID);
int i;
if (required_name_length == debug_name_length)
{
for (i = 0; i < debug_name_length; i++)
{
if (required_name[i] != debug_name[i])
{
break;
}
}
if (i == debug_name_length)
{
fprintf(stderr, "required_name: %s\n", required_name);
return 1;
///fprintf(stderr, "read_length: %d\n", R_INF->g_read->length);
/**
int aviable_overlap_name = 0;
for (i = 0; i < overlap_list->length; i++)
{
long long Len_x = overlap_list->list[i].x_pos_e - overlap_list->list[i].x_pos_s + 1;
if (Len_x * OVERLAP_THRESHOLD <= overlap_list->list[i].align_length)
{
fprintf(stderr, "a_i: %d\n", aviable_overlap_name);
fprintf(stderr, "x_pos_s: %d, x_pos_e: %d\n",
overlap_list->list[i].x_pos_s, overlap_list->list[i].x_pos_e);
aviable_overlap_name++;
debug_name = Get_NAME((*R_INF), overlap_list->list[i].y_id);
debug_name_length = Get_NAME_LENGTH((*R_INF), overlap_list->list[i].y_id);
int j = 0;
for (j = 0; j < debug_name_length; j++)
{
fprintf(stderr, "%c", debug_name[j]);
}
fprintf(stderr, "\n");
}
}
**/
}
}
return 0;
}
void* Overlap_calculate_heap_merge(void* arg)
{
@@ -781,10 +850,16 @@ void* Overlap_calculate_heap_merge(void* arg)
init_buffer_sub_block(&current_sub_buffer);
for (i = thr_ID; i < R_INF.total_reads; i = i + thread_num)
{
/**
if(!get_required_read("m54238_180916_191625\/43253934\/ccs", i, &R_INF))
{
continue;
}
**/
clear_Heap(&heap);
clear_Candidates_list(&l);
@@ -1069,6 +1144,9 @@ void* Overlap_calculate_heap_merge(void* arg)
void Overlap_calculate_multipe_thr()
{
fprintf(stderr, "k_mer_min_freq: %lld, CORRECT_THRESHOLD: %f\n", k_mer_min_freq, CORRECT_THRESHOLD);
double start_time = Get_T();
init_output_buffer(thread_num);