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fix high-coverage issue for ONT

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chhylp123
2024-12-07 20:02:57 -05:00
parent dbdef7ff63
commit 4889f1c6d8
4 changed files with 105 additions and 32 deletions
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Overlaps.cpp
+14 -17
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@@ -1136,7 +1136,7 @@ void set_reverse_overlap(ma_hit_t* dest, ma_hit_t* source)
void normalize_ma_hit_t_single_side_advance(ma_hit_t_alloc* sources, long long num_sources)
void normalize_ma_hit_t_single_side_advance(ma_hit_t_alloc* sources, long long num_sources, uint32_t recuse_el)
{
double startTime = Get_T();
@@ -1160,38 +1160,35 @@ void normalize_ma_hit_t_single_side_advance(ma_hit_t_alloc* sources, long long n
///if(index != -1 && sources[tn].buffer[index].del == 0)
if(index != -1)
{
if(index != -1) {
is_del = 0;
if(sources[i].buffer[j].del || sources[tn].buffer[index].del)
{
if(sources[i].buffer[j].del || sources[tn].buffer[index].del) {
is_del = 1;
}
qLen_0 = Get_qe(sources[i].buffer[j]) - Get_qs(sources[i].buffer[j]);
qLen_1 = Get_qe(sources[tn].buffer[index]) - Get_qs(sources[tn].buffer[index]);
if(qLen_0 == qLen_1)
{
if(qLen_0 == qLen_1) {
///qn must be not equal to tn
///make sources[qn] = sources[tn] if qn > tn
if(qn < tn)
{
if(qn < tn) {
set_reverse_overlap(&(sources[tn].buffer[index]), &(sources[i].buffer[j]));
}
}
else if(qLen_0 > qLen_1)
{
} else if(qLen_0 > qLen_1) {
set_reverse_overlap(&(sources[tn].buffer[index]), &(sources[i].buffer[j]));
}
if(recuse_el && sources[i].buffer[j].el && sources[tn].buffer[index].el) is_del = 0;
sources[i].buffer[j].del = is_del;
sources[tn].buffer[index].del = is_del;
}
else ///means this edge just occurs in one direction
{
} else {///means this edge just occurs in one direction
set_reverse_overlap(&ele, &(sources[i].buffer[j]));
sources[i].buffer[j].del = ele.del = 1;
if(recuse_el && sources[i].buffer[j].el && ele.el) {
sources[i].buffer[j].del = ele.del = 0;
}
add_ma_hit_t_alloc(&(sources[tn]), &ele);
}
}
@@ -38700,9 +38697,9 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
///it's hard to say which function is better
///normalize_ma_hit_t_single_side(sources, n_read);
normalize_ma_hit_t_single_side_advance(sources, n_read);
normalize_ma_hit_t_single_side_advance(sources, n_read, asm_opt.is_ont);
// normalize_ma_hit_t_single_side_advance_mult(sources, n_read, asm_opt.thread_num);
normalize_ma_hit_t_single_side_advance(reverse_sources, n_read);
normalize_ma_hit_t_single_side_advance(reverse_sources, n_read, 0);
// normalize_ma_hit_t_single_side_advance_mult(reverse_sources, n_read, asm_opt.thread_num);
if (ha_opt_triobin(&asm_opt))