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chhylp123
2022-10-19 13:23:25 -04:00
parent 3d65bef9de
commit df3e0eeaa3
7 changed files with 3371 additions and 116 deletions
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35
Hash_Table.cpp
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@@ -1933,6 +1933,32 @@ int64_t filter_non_ovlp_chains(overlap_region *a, int64_t a_n, int64_t *n_v)
return n_mchain;
}
int64_t filter_non_ovlp_xchains(overlap_region *a, int64_t a_n, int64_t *n_v)
{
int64_t k, i, n_mchain, omx, opx, ovx, os, oe; overlap_region *m, *p, t;
for (k = n_mchain = (*n_v) = 0; k < a_n; k++) {
m = &(a[k]);
omx = m->x_pos_e + 1 - m->x_pos_s;
for (i = 0; i < n_mchain; i++) {
p = &(a[i]);
opx = p->x_pos_e + 1 - p->x_pos_s;
os = ((m->x_pos_s>=p->x_pos_s)? m->x_pos_s:p->x_pos_s);
oe = ((m->x_pos_e<=p->x_pos_e)? m->x_pos_e:p->x_pos_e) + 1;
ovx = oe>os?oe-os:0;
if((ovx > omx*0.1) || (ovx > opx*0.1)) break;
}
if(i < n_mchain) continue;
if (n_mchain != k) {
t = a[k]; a[k] = a[n_mchain]; a[n_mchain] = t;
}
(*n_v) += a[n_mchain].align_length;
n_mchain++;
}
return n_mchain;
}
uint64_t lchain_qdp_mcopy(Candidates_list *cl, int64_t a_idx, int64_t a_n, int64_t des_idx,
Chain_Data* dp, overlap_region_alloc* res, int64_t max_skip, int64_t max_iter,
int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate,
@@ -2040,7 +2066,7 @@ uint64_t lchain_qdp_mcopy(Candidates_list *cl, int64_t a_idx, int64_t a_n, int64
}
ks_introsort_or_sss(n_u, res->list + n_u0);
res->length = n_u0 + filter_non_ovlp_chains(res->list + n_u0, n_u, &n_v);
res->length = n_u0 + filter_non_ovlp_xchains(res->list + n_u0, n_u, &n_v);
n_u = res->length;
kv_resize_cl(k_mer_hit, (*cl), (n_v+cl->length));
@@ -2291,12 +2317,9 @@ uint64_t lchain_refine(k_mer_hit* a, int64_t a_n, k_mer_hit* des, Chain_Data* dp
sc = f[j] - dd;
if (sc > max_f) {
max_f = sc, max_j = j;
if (n_skip > 0) --n_skip;
} else if (t[j] == (int32_t)i) {
if (++n_skip > max_skip)
break;
}
}
if (p[j] >= 0) t[p[j]] = i;
///[st, i-2]
for (--j; (j >= st) && (a[i].self_offset <= (max_dis + a[j].self_offset)); --j) {
dq = (int64_t)(a[i].self_offset) - (int64_t)(a[j].self_offset);