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2019_9_5

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This commit is contained in:
Haoyu Cheng
2019-09-05 11:47:54 -04:00
parent d5327fe9ee
commit b57923d050
6 changed files with 876 additions and 137 deletions
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Assembly.cpp
+79 -13
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@@ -1158,6 +1158,8 @@ char* new_read, int new_length, int correct_base)
}
inline void push_cigar(Compressed_Cigar_record* records, long long ID, Cigar_record* input)
{
@@ -1304,13 +1306,20 @@ void* Overlap_calculate_heap_merge(void* arg)
haplotype_evdience_alloc hap;
InitHaplotypeEvdience(&hap);
Round2_alignment second_round;
init_Round2_alignment(&second_round);
for (i = thr_ID; i < R_INF.total_reads; i = i + thread_num)
{
clear_Cigar_record(&current_cigar);
clear_Round2_alignment(&second_round);
clear_Heap(&heap);
clear_Candidates_list(&l);
///clear_Candidates_list(&debug_l);
@@ -1445,14 +1454,19 @@ void* Overlap_calculate_heap_merge(void* arg)
///clear_Graph(&POA_Graph);
correct_overlap(&overlap_list, &R_INF, &g_read, &correct, &overlap_read, &POA_Graph,
&matched_overlap_0, &matched_overlap_1, &potiental_matched_overlap_0, &potiental_matched_overlap_1,
&current_cigar, &hap);
correct_overlap(&overlap_list, &R_INF, &g_read, &correct, &overlap_read, &POA_Graph,
&matched_overlap_0, &matched_overlap_1, &potiental_matched_overlap_0, &potiental_matched_overlap_1,
&current_cigar, &hap, &second_round);
num_read_base = num_read_base + g_read.length;
num_correct_base = num_correct_base + correct.corrected_base;
push_cigar(R_INF.cigars, i, &current_cigar);
push_cigar(R_INF.second_round_cigar, i, &(second_round.cigar));
/**
fprintf(stderr, "current_cigar.new_read_length: %d, second_round.cigar.new_read_length: %d\n",
current_cigar.new_read_length, second_round.cigar.new_read_length);
**/
/**
if(memcmp("m54334_180926_225337/39780640/ccs", Get_NAME(R_INF, i), Get_NAME_LENGTH(R_INF, i)) == 0)
@@ -1589,6 +1603,8 @@ void* Overlap_calculate_heap_merge(void* arg)
destoryHaplotypeEvdience(&hap);
destory_Round2_alignment(&second_round);
pthread_mutex_lock(&statistics);
total_matched_overlap_0 += matched_overlap_0;
@@ -1614,6 +1630,8 @@ void* Overlap_calculate_heap_merge(void* arg)
}
void* Save_corrected_reads(void* arg)
{
int thr_ID = *((int*)arg);
@@ -1621,20 +1639,31 @@ void* Save_corrected_reads(void* arg)
UC_Read g_read;
init_UC_Read(&g_read);
int new_read_size = 10000;
char* new_read = (char*)malloc(new_read_size);
int first_round_read_size = 10000;
char* first_round_read = (char*)malloc(first_round_read_size);
int second_round_read_size = 10000;
char* second_round_read = (char*)malloc(second_round_read_size);
Cigar_record cigar;
int new_read_length;
int first_round_read_length;
int second_round_read_length;
uint64_t N_occ;
char* new_read;
int new_read_length;
for (i = thr_ID; i < R_INF.total_reads; i = i + thread_num)
{
recover_UC_Read(&g_read, &R_INF, i);
if(R_INF.cigars[i].new_length>new_read_size)
/********************************1 round******************************/
if(R_INF.cigars[i].new_length > first_round_read_size)
{
new_read_size = R_INF.cigars[i].new_length;
new_read = (char*)realloc(new_read, new_read_size);
first_round_read_size = R_INF.cigars[i].new_length;
first_round_read = (char*)realloc(first_round_read, first_round_read_size);
}
cigar.length = R_INF.cigars[i].length;
@@ -1642,7 +1671,43 @@ void* Save_corrected_reads(void* arg)
cigar.record = R_INF.cigars[i].record;
cigar.lost_base = R_INF.cigars[i].lost_base;
get_corrected_read_from_cigar(&cigar, g_read.seq, g_read.length, new_read, &new_read_length);
get_corrected_read_from_cigar(&cigar, g_read.seq, g_read.length, first_round_read, &first_round_read_length);
/**
if(first_round_read_length != R_INF.cigars[i].new_length)
{
fprintf(stderr, "error\n");
}
**/
/********************************1 round******************************/
/********************************2 round******************************/
if(R_INF.second_round_cigar[i].new_length > second_round_read_size)
{
second_round_read_size = R_INF.second_round_cigar[i].new_length;
second_round_read = (char*)realloc(second_round_read, second_round_read_size);
}
cigar.length = R_INF.second_round_cigar[i].length;
cigar.lost_base_length = R_INF.second_round_cigar[i].lost_base_length;
cigar.record = R_INF.second_round_cigar[i].record;
cigar.lost_base = R_INF.second_round_cigar[i].lost_base;
get_corrected_read_from_cigar(&cigar, first_round_read, first_round_read_length,
second_round_read, &second_round_read_length);
/**
if(second_round_read_length != R_INF.second_round_cigar[i].new_length)
{
fprintf(stderr, "error\n");
}
**/
/********************************2 round******************************/
///new_read = first_round_read;
///new_read_length = first_round_read_length;
new_read = second_round_read;
new_read_length = second_round_read_length;
///need modification
reverse_complement(new_read, new_read_length);
@@ -1674,7 +1739,8 @@ void* Save_corrected_reads(void* arg)
}
destory_UC_Read(&g_read);
free(new_read);
free(first_round_read);
free(second_round_read);
free(arg);
}