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backup for minimizer

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chhylp123
2022-09-28 11:16:09 -04:00
parent 236bc7b9ee
commit 20a7dac82a
7 changed files with 812 additions and 80 deletions
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78
Hash_Table.cpp
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@@ -1622,4 +1622,82 @@ uint64_t lchain_dp(k_mer_hit* a, int64_t a_n, k_mer_hit* des, Chain_Data* dp, ov
res->overlapLen = get_chainLen(res->x_pos_s, res->x_pos_e, xl, res->y_pos_s, res->y_pos_e, yl);
for (i = 0; i < cL; i++) des[i] = a[t[cL-i-1]];
return cL;
}
inline int64_t hit_long_gap(k_mer_hit *a, k_mer_hit *b, int64_t max_lgap, double small_bw_rate, int64_t min_small_bw)
{
int64_t dq, dr, dd, dm;
dq = b->self_offset-a->self_offset;
dr = b->offset-a->offset;
dd = dq>=dr? ((dq)-(dr)): ((dr)-(dq));
if(max_lgap>=0) {
if(dd <= max_lgap) return 1;
return 0;
} else {
dm = dq>=dr?dr:dq;
if((dd > (dm*small_bw_rate)) && (dd > min_small_bw)) return 0;
return 1;
}
}
int64_t filter_bad_seed_dp(k_mer_hit *sk, k_mer_hit *ek, k_mer_hit* a, int64_t a_n, int64_t max_lgap, double small_bw_rate, int64_t min_small_bw)
{
int64_t k = 0; k_mer_hit *z; double bw_r; int64_t bw, mmgap, occ = 0;
bw_r = small_bw_rate; bw = min_small_bw; mmgap = max_lgap;
if(sk) {
for (k = 0; k < a_n; k++) {
z = &(a[k]);
if(z->cnt < z->readID) continue;
mmgap = max_lgap;
if(z->cnt <= 1) mmgap = -1;
if((sk && (!hit_long_gap(sk, z, mmgap, bw_r, bw))) ||
(ek && (!hit_long_gap(z, ek, mmgap, bw_r, bw)))) {
z->offset = z->self_offset = (uint32_t)-1; occ++;
} else {
break;
}
}
}
if(ek && k < a_n) {
for (k = a_n-1; k >= 0; k--) {
z = &(a[k]);
if(z->cnt < z->readID) continue;
mmgap = max_lgap;
if(z->cnt <= 1) mmgap = -1;
if((sk && (!hit_long_gap(sk, z, mmgap, bw_r, bw))) ||
(ek && (!hit_long_gap(z, ek, mmgap, bw_r, bw)))) {
z->offset = z->self_offset = (uint32_t)-1; occ++;
} else {
break;
}
}
}
return occ;
}
uint64_t lchain_dp_trace(k_mer_hit* a, int64_t a_n, int64_t max_lgap, double sgap_rate, int64_t sgap)
{
if(a_n <= 0) return 0;
int64_t i, st, occ = 0;
for (i = 1, st = 0; i <= a_n; ++i) {
if((i == a_n) || (is_alnw(a[i]))) {///[st, i)
if(i > st) {
occ += filter_bad_seed_dp((st>0)?&(a[st-1]):NULL, (i<a_n)?&(a[i]):NULL, a, a_n, max_lgap, sgap_rate, sgap);
}
st = i+1;
}
}
if(occ) {
for (i = occ = 0; i < a_n; ++i) {
if(a[i].self_offset == ((uint32_t)-1)) continue;
a[occ++] = a[i];
}
a_n = occ;
}
return a_n;
}