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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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Correct.cpp
+48 -2
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@@ -8987,6 +8987,7 @@ inline void insert_snp_vv(haplotype_evdience_alloc* h, haplotype_evdience* a, ui
h->snp_stat.a[p->id].score = -1;
}
int insert_snp_ee(haplotype_evdience_alloc* h, haplotype_evdience* a, uint64_t a_n, haplotype_evdience* u_a, UC_Read* g_read, void *km)
{
uint64_t i, m, occ_0, occ_1[5], occ_2, diff;
@@ -9003,6 +9004,7 @@ int insert_snp_ee(haplotype_evdience_alloc* h, haplotype_evdience* a, uint64_t a
// occ_2++;
// diff++;
// }
occ_2 += a[i].cov;
}
/**
@@ -9011,7 +9013,49 @@ int insert_snp_ee(haplotype_evdience_alloc* h, haplotype_evdience* a, uint64_t a
3. if occ_1 = 1, there are only one difference. It must be a sequencing error.
(for repeat, it maybe a snp at repeat. but ...)
**/
SnpStats *p = NULL;
uint32_t is_homopolymer = (uint32_t)-1;
if(occ_0 == 0 || diff <= 1) return 0;
for (i = m = 0; i < 4; i++) {
if(occ_1[i] >= 2){
if(!km) kv_pushp(SnpStats, h->snp_stat, &p);
else kv_pushp_km(km, SnpStats, h->snp_stat, &p);
p->id = h->snp_stat.n-1;
p->occ_0 = 1 + occ_0;
p->occ_1 = occ_1[i];
p->occ_2 = occ_2 - p->occ_0 - p->occ_1;
p->overlap_num = 0;
p->site = a[0].site;
p->score = -1;
p->overlap_num = occ_2;
if(is_homopolymer == (uint32_t)-1) {
is_homopolymer = if_is_homopolymer_strict(p->site, g_read->seq, g_read->length);
}
p->is_homopolymer = is_homopolymer;
occ_1[i] = p->id;
m++;
} else {
occ_1[i] = (uint64_t)-1;
}
}
if(m == 0) return 0;
for (i = m = 0; i < a_n; i++) {
if(a[i].type == 0) {
a[i].overlapSite = h->snp_stat.n-1;
} else if(occ_1[seq_nt6_table[(uint8_t)(a[i].misBase)]]!=(uint64_t)-1){
a[i].cov = a[i].overlapSite;///note: only renew cov here!!!
a[i].overlapSite = occ_1[seq_nt6_table[(uint8_t)(a[i].misBase)]];
} else {
continue;
}
u_a[m++] = a[i];
}
/**
// if(c_snp && ovlp) {
// ;
// }
for (i = m = 0; i < 4; i++) {
if(occ_1[i] >= 2) {
insert_snp_vv(h, a, a_n, s_H[i], g_read, km);
@@ -9027,6 +9071,7 @@ int insert_snp_ee(haplotype_evdience_alloc* h, haplotype_evdience* a, uint64_t a
if(occ_1[seq_nt6_table[(uint8_t)(a[i].misBase)]] >= 2) u_a[m++] = a[i];
}
}
**/
return m;
}
@@ -9441,7 +9486,8 @@ void correct_ul_overlap(overlap_region_alloc* overlap_list, const ul_idx_t *uref
UC_Read* g_read, Correct_dumy* dumy, UC_Read* overlap_read,
Graph* g, Graph* DAGCon, Cigar_record* current_cigar,
haplotype_evdience_alloc* hap, Round2_alignment* second_round,
int force_repeat, int is_consensus, int* fully_cov, int* abnormal, double max_ov_diff_ec, void *km)
int force_repeat, int is_consensus, int* fully_cov, int* abnormal,
double max_ov_diff_ec, long long winLen, void *km)
{
clear_Correct_dumy(dumy, overlap_list, km);
@@ -9450,7 +9496,7 @@ void correct_ul_overlap(overlap_region_alloc* overlap_list, const ul_idx_t *uref
Window_Pool w_inf;
init_Window_Pool(&w_inf, g_read->length, /**WINDOW_UL**//**WINDOW_UL_H**/MIN((((double)THRESHOLD_MAX_SIZE)/max_ov_diff_ec),WINDOW), (int)(1.0/max_ov_diff_ec));
init_Window_Pool(&w_inf, g_read->length, /**WINDOW_UL**//**WINDOW_UL_H**/winLen, (int)(1.0/max_ov_diff_ec));
int flag = 0;
while(get_Window(&w_inf, &window_start, &window_end) && flag != -2)