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intergration correctio

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chhylp123
2022-03-01 20:25:53 -05:00
parent 0ce5a7ba5b
commit 9c6a3607d1
8 changed files with 1263 additions and 77 deletions
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Overlaps.cpp
+53 -19
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@@ -853,7 +853,7 @@ inline void set_reverse_overlap(ma_hit_t* dest, ma_hit_t* source)
dest->ml = source->ml;
dest->no_l_indel = source->no_l_indel;
/****************************may have bugs********************************/
dest->bl = Get_qe(*dest) - Get_qs(*dest);
dest->bl = source->bl/**Get_qe(*dest) - Get_qs(*dest)**/;
}
@@ -875,7 +875,7 @@ void normalize_ma_hit_t_single_side_advance(ma_hit_t_alloc* sources, long long n
qn = Get_qn(sources[i].buffer[j]);
tn = Get_tn(sources[i].buffer[j]);
sources[i].buffer[j].bl = Get_qe(sources[i].buffer[j]) - Get_qs(sources[i].buffer[j]);
// sources[i].buffer[j].bl = Get_qe(sources[i].buffer[j]) - Get_qs(sources[i].buffer[j]);
///if(sources[i].buffer[j].del) continue;
@@ -993,15 +993,15 @@ void normalize_ma_hit_t_single_side_aggressive(ma_hit_t_alloc* sources, long lon
qn = Get_qn(sources[i].buffer[j]);
tn = Get_tn(sources[i].buffer[j]);
sources[i].buffer[j].bl = Get_qe(sources[i].buffer[j]) - Get_qs(sources[i].buffer[j]);
// sources[i].buffer[j].bl = Get_qe(sources[i].buffer[j]) - Get_qs(sources[i].buffer[j]);
index = get_specific_overlap(&(sources[tn]), tn, qn);
if(index != -1)
{
sources[tn].buffer[index].bl = Get_qe(sources[tn].buffer[index])
- Get_qs(sources[tn].buffer[index]);
// sources[tn].buffer[index].bl = Get_qe(sources[tn].buffer[index])
// - Get_qs(sources[tn].buffer[index]);
if(Get_qs(sources[i].buffer[j]) == Get_ts(sources[tn].buffer[index])
&&
@@ -1124,15 +1124,15 @@ void normalize_ma_hit_t_single_side(ma_hit_t_alloc* sources, long long num_sourc
qn = Get_qn(sources[i].buffer[j]);
tn = Get_tn(sources[i].buffer[j]);
sources[i].buffer[j].bl = Get_qe(sources[i].buffer[j]) - Get_qs(sources[i].buffer[j]);
// sources[i].buffer[j].bl = Get_qe(sources[i].buffer[j]) - Get_qs(sources[i].buffer[j]);
index = get_specific_overlap(&(sources[tn]), tn, qn);
if(index != -1)
{
sources[tn].buffer[index].bl = Get_qe(sources[tn].buffer[index])
- Get_qs(sources[tn].buffer[index]);
// sources[tn].buffer[index].bl = Get_qe(sources[tn].buffer[index])
// - Get_qs(sources[tn].buffer[index]);
if(Get_qs(sources[i].buffer[j]) == Get_ts(sources[tn].buffer[index])
&&
@@ -9902,9 +9902,9 @@ void clean_weak_ma_hit_t(ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_source
||
!check_weak_ma_hit_reverse(&(reverse_sources[qn]), sources, tn)**/)
{
sources[i].buffer[j].bl = 0;
sources[i].buffer[j].bl |= ((uint32_t)0x40000000);
index = get_specific_overlap(&(sources[tn]), tn, qn);
sources[tn].buffer[index].bl = 0;
sources[tn].buffer[index].bl |= ((uint32_t)0x40000000);
}
}
}
@@ -9919,13 +9919,14 @@ void clean_weak_ma_hit_t(ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_source
{
if(sources[i].buffer[j].del) continue;
if(sources[i].buffer[j].bl != 0)
if(sources[i].buffer[j].bl&((uint32_t)0x40000000))
{
sources[i].buffer[j].del = 0;
sources[i].buffer[j].del = 1;
sources[i].buffer[j].bl -= ((uint32_t)0x40000000);
}
else
{
sources[i].buffer[j].del = 1;
sources[i].buffer[j].del = 0;
}
}
}
@@ -31100,16 +31101,41 @@ char *get_outfile_name(char* output_file_name)
return buf;
}
void create_ul_info(ma_hit_t_alloc* sources, int max_hang, int min_ovlp, long long gap_fuzz)
asg_t *build_init_sg(ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, int64_t n_read,
int64_t min_dp, uint64_t* readLen, int64_t mini_overlap_length, int64_t max_hang_length,
ma_sub_t *coverage_cut, R_to_U* ruIndex)
{
asg_t *sg = NULL;
clean_weak_ma_hit_t(sources, reverse_sources, n_read);
///ma_hit_sub is just use to init coverage_cut,
///it seems we do not need ma_hit_cut & ma_hit_flt
ma_hit_sub(min_dp, sources, n_read, readLen, mini_overlap_length, &coverage_cut);
detect_chimeric_reads(sources, n_read, readLen, coverage_cut, asm_opt.max_ov_diff_final * 2.0);
ma_hit_cut(sources, n_read, readLen, mini_overlap_length, &coverage_cut);
///print_binned_reads(sources, n_read, coverage_cut);
ma_hit_flt(sources, n_read, coverage_cut, max_hang_length, mini_overlap_length);
///fix_binned_reads(sources, n_read, coverage_cut);
///just need to deal with trio here
ma_hit_contained_advance(sources, n_read, coverage_cut, ruIndex, max_hang_length, mini_overlap_length);
sg = ma_sg_gen(sources, n_read, coverage_cut, max_hang_length, mini_overlap_length);
return sg;
}
void create_ul_info(ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, int64_t max_hang, int64_t min_ovlp, int64_t gap_fuzz,
int64_t min_dp, uint64_t* readLen, ma_sub_t *coverage_cut, R_to_U* ruIndex)
{
ug_opt_t opt; memset(&opt, 0, sizeof(opt));
opt.sources = sources;
opt.reverse_sources = reverse_sources;
opt.max_hang = max_hang;
opt.min_ovlp = min_ovlp;
opt.gap_fuzz = gap_fuzz;
opt.min_dp = min_dp;
opt.readLen = readLen;
opt.coverage_cut = coverage_cut;
opt.ruIndex = ruIndex;
ul_load(&opt);
exit(1);
}
void clean_graph(
@@ -31145,10 +31171,18 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
{
memset(R_INF.trio_flag, AMBIGU, R_INF.total_reads*sizeof(uint8_t));
}
if(asm_opt.ar) create_ul_info(sources, max_hang_length, mini_overlap_length, gap_fuzz);
if(asm_opt.ar) {
create_ul_info(sources, reverse_sources, max_hang_length, mini_overlap_length, gap_fuzz,
min_dp, readLen, coverage_cut, ruIndex);
exit(1);
} else {
// sg = build_init_sg(sources, reverse_sources, n_read, min_dp, readLen, mini_overlap_length, max_hang_length,
// coverage_cut, ruIndex);
clean_weak_ma_hit_t(sources, reverse_sources, n_read);
}
///print_binned_reads(sources, n_read, coverage_cut);
clean_weak_ma_hit_t(sources, reverse_sources, n_read);
///ma_hit_sub is just use to init coverage_cut,
///it seems we do not need ma_hit_cut & ma_hit_flt
ma_hit_sub(min_dp, sources, n_read, readLen, mini_overlap_length, &coverage_cut);