xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-30 07:48:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

backup for minimizer

Browse Source
This commit is contained in:
chhylp123
2022-09-28 11:16:09 -04:00
parent 236bc7b9ee
commit 20a7dac82a
7 changed files with 812 additions and 80 deletions
Download Patch File Download Diff File Expand all files Collapse all files
anchor.cpp
+31 -4
View File
@@ -891,6 +891,32 @@ void inline reverse_k_mer_hit(k_mer_hit *a, uint64_t a_n, uint64_t xl, uint64_t
}
}
void inline reset_k_mer_hit(k_mer_hit *a, uint64_t a_n, uint64_t xl, uint64_t yl, uint64_t rev, uint64_t *nid)
{
uint64_t z, han = a_n>>1; k_mer_hit *ai, *aj, ka;
if(rev) {
for (z = 0; z < han; z++) {
ai = &(a[z]); aj = &(a[a_n-z-1]);
ka = (*ai); (*ai) = (*aj); (*aj) = ka;
ai->self_offset = xl-ai->self_offset-1;
ai->offset = yl-ai->offset-1;
aj->self_offset = xl-aj->self_offset-1;
aj->offset = yl-aj->offset-1;
if(nid) ai->readID = aj->readID = (*nid);
}
if(a_n&1) {
a[z].self_offset = xl-a[z].self_offset-1;
a[z].offset = yl-a[z].offset-1;
if(nid) a[z].readID = (*nid);
}
} else if(nid) {
for (z = 0; z < a_n; z++) a[z].readID = (*nid);
}
}
void lchain_gen(Candidates_list* cl, overlap_region_alloc* ol, uint32_t rid, uint64_t rl, All_reads* rdb,
const ul_idx_t *udb, uint32_t apend_be, overlap_region* tf, uint64_t max_n_chain,
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)
@@ -913,10 +939,11 @@ 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)) {
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);
}
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);
// }
reset_k_mer_hit(cl->list+m, sm, rl, rdb?Get_READ_LENGTH((*rdb), r->y_id):udb->ug->u.a[r->y_id].len, r->y_pos_strand, &(ol->length));
if(gen_off) gen_fake_cigar(&(r->f_cigar), r, apend_be, cl->list+m, sm);
m += sm;
}