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Merge overlap

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This commit is contained in:
Haoyu Cheng
2019-05-18 01:03:24 -04:00
parent 87a6091ffe
commit ddd96d8456
11 changed files with 619 additions and 21 deletions
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Assembly.cpp
+159 -15
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@@ -33,6 +33,8 @@ void* Perform_Counting(void* arg)
uint64_t code;
uint64_t end_pos;
Hash_code k_code;
int avalible_k = 0;
@@ -54,7 +56,7 @@ void* Perform_Counting(void* arg)
avalible_k = 0;
while ((code = get_HPC_code(&HPC_read)) != 6)
while ((code = get_HPC_code(&HPC_read, &end_pos)) != 6)
{
if(code < 4)
{
@@ -90,7 +92,7 @@ void* Perform_Counting(void* arg)
avalible_k = 0;
while ((code = get_HPC_code(&HPC_read)) != 6)
while ((code = get_HPC_code(&HPC_read, &end_pos)) != 6)
{
if(code < 4)
{
@@ -148,8 +150,9 @@ void* Build_hash_table(void* arg)
int file_flag = 1;
uint64_t code;
uint64_t end_pos;
long long HPC_base;
///long long HPC_base;
Hash_code k_code;
@@ -171,9 +174,9 @@ void* Build_hash_table(void* arg)
avalible_k = 0;
HPC_base = 0;
///HPC_base = 0;
while ((code = get_HPC_code(&HPC_read)) != 6)
while ((code = get_HPC_code(&HPC_read, &end_pos)) != 6)
{
if(code < 4)
{
@@ -189,7 +192,7 @@ void* Build_hash_table(void* arg)
///所以如果当前k-mer在PCB表中存在，则他的位置一定要加入到候选位置中去
///insert_Total_Pos_Table(&PCB, &k_code, k_mer_length, curr_sub_block.read[i].ID, HPC_base - k_mer_length + 1, FORWARD);
insert_Total_Pos_Table(&PCB, &k_code, k_mer_length,
curr_sub_block.read[i].ID, HPC_base - k_mer_length + 1);
curr_sub_block.read[i].ID, end_pos);
}
}
@@ -199,7 +202,7 @@ void* Build_hash_table(void* arg)
init_Hash_code(&k_code);
}
HPC_base++;
///HPC_base++;
}
@@ -222,7 +225,7 @@ void* Build_hash_table(void* arg)
HPC_base = 0;
while ((code = get_HPC_code(&HPC_read)) != 6)
while ((code = get_HPC_code(&HPC_read, &end_pos)) != 6)
{
if(code < 4)
{
@@ -411,6 +414,145 @@ void Build_hash_table_multiple_thr()
}
void* Overlap_calculate(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;
k_mer_pos_list* merge_list;
init_Candidates_list(&l);
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)
{
/**
if (i % 1000 == 0)
{
fprintf(stderr, "i: %llu\n", i);
}
**/
clear_Candidates_list(&l);
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);
merge_Candidates_list(&l, list, list_length, end_pos, 0);
//merge_Candidates_list_version(&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);
merge_Candidates_list(&l, list, list_length, end_pos, 1);
//merge_Candidates_list_version(&l, list, list_length, end_pos, 1);
}
}
else
{
avalible_k = 0;
init_Hash_code(&k_code);
}
///HPC_base++;
}
}
destory_Candidates_list(&l);
}
void Overlap_calculate_multipe_thr()
{
double start_time = Get_T();
fprintf(stdout, "Begin Overlap Calculate ...... \n");
pthread_t *_r_threads;
_r_threads = (pthread_t *)malloc(sizeof(pthread_t)*thread_num);
int i = 0;
for (i = 0; i < thread_num; i++)
{
int *arg = (int*)malloc(sizeof(*arg));
*arg = i;
pthread_create(_r_threads + i, NULL, Overlap_calculate, (void*)arg);
}
for (i = 0; i<thread_num; i++)
pthread_join(_r_threads[i], NULL);
free(_r_threads);
fprintf(stdout, "Finish Overlap Calculate.\n");
fprintf(stdout, "%-30s%18.2f\n\n", "Calculate Overlap time:", Get_T() - start_time);
}
int load_pre_cauculated_index()
{
if(load_Total_Pos_Table(&PCB, read_file_name) && load_All_reads(&R_INF, read_file_name))
@@ -437,6 +579,7 @@ void Verify_Counting()
HPC_seq HPC_read;
uint64_t code;
uint64_t end_pos;
Hash_code k_code;
int avalible_k = 0;
@@ -450,7 +593,7 @@ void Verify_Counting()
avalible_k = 0;
while ((code = get_HPC_code(&HPC_read)) != 6)
while ((code = get_HPC_code(&HPC_read, &end_pos)) != 6)
{
if(code < 4)
{
@@ -502,10 +645,11 @@ void verify_Position_hash_table()
long long read_number = 0;
long long HPC_base;
///long long HPC_base;
HPC_seq HPC_read;
uint64_t code;
uint64_t end_pos;
Hash_code k_code;
int avalible_k = 0;
k_mer_pos* list;
@@ -554,9 +698,9 @@ void verify_Position_hash_table()
init_Hash_code(&k_code);
avalible_k = 0;
HPC_base = 0;
///HPC_base = 0;
while ((code = get_HPC_code(&HPC_read)) != 6)
while ((code = get_HPC_code(&HPC_read, &end_pos)) != 6)
{
@@ -601,7 +745,7 @@ void verify_Position_hash_table()
{
for(j=0; j<count2; j++)
{
if(list[j].readID == read_number && list[j].offset == HPC_base - k_mer_length + 1)
if(list[j].readID == read_number && list[j].offset == end_pos)
{
break;
}
@@ -610,7 +754,7 @@ void verify_Position_hash_table()
if(j == count2)
{
fprintf(stderr, "locate error, read_number: %llu, pos: %llu\n",
read_number, HPC_base - k_mer_length + 1);
read_number, end_pos);
for(j=0; j<count2; j++)
{
@@ -637,7 +781,7 @@ void verify_Position_hash_table()
init_Hash_code(&k_code);
}
HPC_base++;
///HPC_base++;
}