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more cutting methods

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This commit is contained in:
Haoyu Cheng
2019-11-20 15:43:44 -05:00
parent e8ff0c1dbc
commit 3425bd020b
6 changed files with 660 additions and 118 deletions
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41
Assembly.cpp
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@@ -1180,6 +1180,7 @@ void push_overlaps(ma_hit_t_alloc* paf, overlap_region_alloc* overlap_list, int
tmp.bl = R_INF.read_length[overlap_list->list[i].y_id];
tmp.ml = overlap_list->list[i].strong;
tmp.no_l_indel = overlap_list->list[i].without_large_indel;
add_ma_hit_t_alloc(paf, &tmp);
}
@@ -1281,7 +1282,7 @@ overlap_region_alloc* overlap_list, UC_Read* x_read, UC_Read* y_read)
tmp.bl = R_INF.read_length[overlap_list->list[i].y_id];
tmp.ml = overlap_list->list[i].strong;
tmp.no_l_indel = overlap_list->list[i].without_large_indel;
@@ -1842,7 +1843,7 @@ void* Overlap_calculate_heap_merge(void* arg)
long long num_correct_base = 0;
long long num_second_correct_base = 0;
long long j;
int fully_cov;
int fully_cov, abnormal;
int thr_ID = *((int*)arg);
uint64_t POA_i;
@@ -1919,7 +1920,7 @@ void* Overlap_calculate_heap_merge(void* arg)
correct_overlap(&overlap_list, &R_INF, &g_read, &correct, &overlap_read, &POA_Graph, &DAGCon,
&matched_overlap_0, &matched_overlap_1, &potiental_matched_overlap_0, &potiental_matched_overlap_1,
&current_cigar, &hap, &second_round, 0, 1, &fully_cov);
&current_cigar, &hap, &second_round, 0, 1, &fully_cov, &abnormal);
num_read_base = num_read_base + g_read.length;
num_correct_base = num_correct_base + correct.corrected_base;
@@ -1933,18 +1934,6 @@ void* Overlap_calculate_heap_merge(void* arg)
R_INF.paf[i].is_fully_corrected = 0;
if(fully_cov)
{
/**
if(current_cigar.length == 1 && second_round.cigar.length == 1)
{
if(Get_Cigar_Type(current_cigar.record[0]) == 0 &&
Get_Cigar_Length(current_cigar.record[0]) == g_read.length &&
Get_Cigar_Type(second_round.cigar.record[0]) == 0 &&
Get_Cigar_Length(second_round.cigar.record[0]) == g_read.length)
{
R_INF.paf[i].is_fully_corrected = 1;
}
}
**/
if(
get_cigar_errors(&current_cigar) == 0
&&
@@ -1953,6 +1942,10 @@ void* Overlap_calculate_heap_merge(void* arg)
R_INF.paf[i].is_fully_corrected = 1;
}
}
R_INF.paf[i].is_abnormal = abnormal;
push_overlaps(&(R_INF.paf[i]), &overlap_list, 1);
@@ -2828,8 +2821,8 @@ void* Final_overlap_calculate_heap_merge(void* arg)
long long matched_overlap_1 = 0;
long long potiental_matched_overlap_0 = 0;
long long potiental_matched_overlap_1 = 0;
long long num_read_base = 0;
long long num_correct_base = 0;
long long num_read_base = 0;
long long num_second_correct_base = 0;
long long j, inner_j;
@@ -2937,6 +2930,7 @@ void* Final_overlap_calculate_heap_merge(void* arg)
overlap_list.list[j].is_match = 1;
overlap_list.list[j].strong = R_INF.paf[i].buffer[inner_j].ml;
overlap_list.list[j].without_large_indel = R_INF.paf[i].buffer[inner_j].no_l_indel;
overlap_list.mapped_overlaps_length++;
if(overlap_list.list[j].strong == 1)
@@ -2951,6 +2945,15 @@ void* Final_overlap_calculate_heap_merge(void* arg)
{
fprintf(stderr, "error\n");
}
if(overlap_list.list[j].without_large_indel == 0)
{
num_second_correct_base++;
}
}
j++;
inner_j++;
@@ -2958,6 +2961,7 @@ void* Final_overlap_calculate_heap_merge(void* arg)
}
///recover missing exact overlaps
reverse_complement(g_read.seq, g_read.length);
for (j = 0; j < overlap_list.length; j++)
{
@@ -2978,6 +2982,7 @@ void* Final_overlap_calculate_heap_merge(void* arg)
{
overlap_list.list[j].is_match = 1;
overlap_list.list[j].strong = 0;
overlap_list.list[j].without_large_indel = 1;
overlap_list.mapped_overlaps_length++;
potiental_matched_overlap_0++;
}
@@ -3024,11 +3029,15 @@ void* Final_overlap_calculate_heap_merge(void* arg)
total_potiental_matched_overlap_0 += potiental_matched_overlap_0;
total_potiental_matched_overlap_1 += potiental_matched_overlap_1;
total_num_correct_base += num_correct_base;
total_second_num_correct_base += num_second_correct_base;
complete_threads++;
if(complete_threads == thread_num)
{
fprintf(stderr, "overlaps with large indels: %llu\n", total_second_num_correct_base);
fprintf(stderr, "weak overlaps: %llu\n", total_matched_overlap_0);
fprintf(stderr, "strong overlaps: %llu\n", total_matched_overlap_1);
fprintf(stderr, "recover weak overlaps: %llu\n", total_potiental_matched_overlap_0);