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extend ed alignment

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chhylp123
2022-09-13 17:29:27 -04:00
parent ee51a6dddc
commit 5da05f308f
11 changed files with 2348 additions and 111 deletions
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anchor.cpp
+8 -9
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@@ -896,7 +896,7 @@ void lchain_gen(Candidates_list* cl, overlap_region_alloc* ol, uint32_t rid, uin
int64_t max_skip, int64_t max_iter, int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate, int64_t quick_check, uint32_t gen_off)
{
// fprintf(stderr, "+[M::%s]\n", __func__);
uint64_t i, k, l, m, sm, cn = cl->length, srt = 0; overlap_region *r;
uint64_t i, k, l, m, sm, cn = cl->length; overlap_region *r; ///srt = 0
clear_overlap_region_alloc(ol);
clear_fake_cigar(&(tf->f_cigar));
@@ -913,13 +913,11 @@ void lchain_gen(Candidates_list* cl, overlap_region_alloc* ol, uint32_t rid, uin
rl, rdb?Get_READ_LENGTH((*rdb), (*tf).y_id):udb->ug->u.a[(*tf).y_id].len, quick_check);
// assert(sm > 0);
if(ovlp_chain_gen(ol, tf, rl, rdb?Get_READ_LENGTH((*rdb), (*tf).y_id):udb->ug->u.a[(*tf).y_id].len, apend_be, cl->list+m, sm)) {
if(gen_off) {
r = &(ol->list[ol->length-1]);
if(r->y_pos_strand) {
reverse_k_mer_hit(cl->list+m, sm, rl, rdb?Get_READ_LENGTH((*rdb), r->y_id):udb->ug->u.a[r->y_id].len);
}
gen_fake_cigar(&(r->f_cigar), r, apend_be, cl->list+m, sm);
r = &(ol->list[ol->length-1]); r->non_homopolymer_errors = m;
if(r->y_pos_strand) {
reverse_k_mer_hit(cl->list+m, sm, rl, rdb?Get_READ_LENGTH((*rdb), r->y_id):udb->ug->u.a[r->y_id].len);
}
if(gen_off) gen_fake_cigar(&(r->f_cigar), r, apend_be, cl->list+m, sm);
m += sm;
}
}
@@ -933,7 +931,7 @@ void lchain_gen(Candidates_list* cl, overlap_region_alloc* ol, uint32_t rid, uin
if (ol->length > max_n_chain) {
int32_t w, n[4], s[4]; overlap_region t;
n[0] = n[1] = n[2] = n[3] = 0, s[0] = s[1] = s[2] = s[3] = 0;
ks_introsort_or_ss(ol->length, ol->list); srt = 1;
ks_introsort_or_ss(ol->length, ol->list); ///srt = 1;
for (i = 0; i < ol->length; ++i) {
r = &(ol->list[i]);
w = ha_ov_type(r, rl);
@@ -959,7 +957,7 @@ void lchain_gen(Candidates_list* cl, overlap_region_alloc* ol, uint32_t rid, uin
ol->length = k;
}
}
/**
if(!gen_off) {
if(srt) ks_introsort_or_id(ol->length, ol->list);
uint64_t cln = cl->length;
@@ -979,6 +977,7 @@ void lchain_gen(Candidates_list* cl, overlap_region_alloc* ol, uint32_t rid, uin
}
cl->length = m;
}
**/
ks_introsort_or_xs(ol->length, ol->list);
}