mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-27 17:18:12 +08:00
new ec model
This commit is contained in:
chhylp123
+246
@@ -1986,6 +1986,252 @@ uint64_t lchain_qdp_mcopy(Candidates_list *cl, int64_t a_idx, int64_t a_n, int64
|
||||
return cL;
|
||||
}
|
||||
|
||||
void quick_ck_lchain(k_mer_hit* a, int64_t a_n, int64_t xl, int64_t yl, double chn_pen_gap, double chn_pen_skip, double bw_rate,
|
||||
int64_t *p, int64_t *t, int32_t *f, int32_t *ii, int64_t *plus, int64_t *msc, int64_t *msc_i, int64_t *movl, int64_t *si, int64_t *ei)
|
||||
{
|
||||
if(a_n <= 0) return;
|
||||
int64_t l, k, is_srt = 1, z; k_mer_hit *ai, *aj;
|
||||
int64_t dq, dr, dd, dg, q_span, sc, csc, ddt;
|
||||
int64_t plus0, msc0, msc_i0, movl0; double lin_pen, a_pen;
|
||||
|
||||
*plus = 0; *msc = *msc_i = INT32_MIN; *movl = INT32_MAX; *si = 0; *ei = a_n;
|
||||
|
||||
for (k = 1, l = 0; k <= a_n; k++) {
|
||||
if(k == a_n || a[k].strand != a[l].strand) {
|
||||
t[k-1] = 0; ii[k-1] = 0;
|
||||
if(is_srt) {
|
||||
plus0 = 0; msc0 = msc_i0 = INT32_MIN; movl0 = INT32_MAX; ddt = 0;
|
||||
|
||||
|
||||
p[l] = -1; f[l] = a[l].cnt&(0xffu);
|
||||
if(f[l] >= msc0) {msc0 = f[l]; msc_i0 = l;}///difference
|
||||
if(f[l] < plus0) plus0 = f[l];
|
||||
|
||||
|
||||
for (z = l + 1; z < k; z++) {
|
||||
///roughly same to comput_sc_ch(&a[z], &a[z-1])
|
||||
ai = &a[z]; aj = &a[z-1];
|
||||
dq = (int64_t)(ai->self_offset) - (int64_t)(aj->self_offset);
|
||||
if(dq <= 0) break;
|
||||
dr = (int64_t)(ai->offset) - (int64_t)(aj->offset);
|
||||
if(dr <= 0) break;
|
||||
dd = dr > dq? dr - dq : dq - dr;//gap
|
||||
if((dd > 16) && (dd > cal_bw(&(a[z]), &(a[z-1]), bw_rate, xl, yl))) break;
|
||||
dg = dr < dq? dr : dq;//len
|
||||
q_span = ai->cnt&(0xffu);
|
||||
sc = q_span < dg? q_span : dg;
|
||||
sc = normal_w(sc, ((int32_t)(ai->cnt>>8)));
|
||||
if (dd || (dg > q_span && dg > 0)) {
|
||||
lin_pen = (chn_pen_gap*(double)dd);
|
||||
a_pen = ((double)(sc))*((((double)dd)/((double)dg))/bw_rate);
|
||||
if(lin_pen > a_pen) lin_pen = a_pen;
|
||||
lin_pen += (chn_pen_skip*(double)dg);
|
||||
sc -= (int32_t)lin_pen;
|
||||
}
|
||||
|
||||
sc += f[z-1]; csc = a[z].cnt&(0xffu); if(sc < csc) break;
|
||||
p[z] = z - 1; f[z] = sc; ddt += dd;
|
||||
|
||||
if(f[z] >= msc0) {msc0 = f[z]; msc_i0 = z;}///difference
|
||||
if(f[z] < plus0) plus0 = f[z];
|
||||
}
|
||||
|
||||
if((z >= k) && (msc_i0 == (k - 1))) {
|
||||
if((k - l >= 2) && (ddt > 16) && (ddt > cal_bw(&(a[k-1]), &(a[l]), bw_rate, xl, yl))) msc_i0 = INT32_MIN;
|
||||
if(msc_i0 == (k - 1)) {
|
||||
if(msc0 >= (*msc)) {
|
||||
movl0 = get_chainLen(a[msc_i0].self_offset, a[msc_i0].self_offset, xl, a[msc_i0].offset, a[msc_i0].offset, yl);
|
||||
if(msc0 > (*msc) || movl0 < (*movl)) {
|
||||
*msc = msc0; *msc_i = msc_i0; *movl = movl0;
|
||||
}
|
||||
}
|
||||
if(plus0 < (*plus)) *plus = plus0;
|
||||
if((*ei) > k) {
|
||||
(*si) = k;
|
||||
} else {
|
||||
(*ei) = l;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
l = k; is_srt = 1;
|
||||
} else {
|
||||
if((a[k].self_offset <= a[k-1].self_offset) || (a[k].offset <= a[k-1].offset)) is_srt = 0;
|
||||
t[k-1] = 0; ii[k-1] = 0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
uint64_t lchain_qdp_mcopy_fast(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,
|
||||
uint32_t xid, int64_t xl, int64_t yl, int64_t quick_check, uint32_t apend_be,
|
||||
int64_t gen_cigar, int64_t enable_mcopy, double mcopy_rate, int64_t mcopy_khit_cutoff,
|
||||
int64_t khit_n)
|
||||
{
|
||||
if(a_n <= 0) return 0;
|
||||
int64_t *p, *t, max_f, n_skip, st, max_j, end_j, sc, msc, msc_i, max_ii, ovl, movl, plus = 0, min_sc, ch_n, si, ei;
|
||||
int32_t *f, max, tmp, *ii; int64_t i, k, j, cL = 0; k_mer_hit* a; k_mer_hit* des; k_mer_hit *swap; overlap_region *z;
|
||||
resize_Chain_Data(dp, a_n, NULL); ch_n = 1; // int64_t bw; bw = ((xl < yl)?xl:yl); bw *= bw_rate;
|
||||
t = dp->tmp; f = dp->score; p = dp->pre; ii = dp->occ;
|
||||
|
||||
a = cl->list + a_idx; des = cl->list + des_idx;
|
||||
// if(a_n && a[0].readID == 0) {
|
||||
// fprintf(stderr, "---[M::%s::utg%.6dl::%c]\n",
|
||||
// __func__, (int32_t)a[0].readID+1, "+-"[a[0].strand]);
|
||||
// }
|
||||
if(quick_check) {
|
||||
quick_ck_lchain(a, a_n, xl, yl, chn_pen_gap, chn_pen_skip, bw_rate, p, t, f, ii, &plus, &msc, &msc_i, &movl, &si, &ei);
|
||||
} else {
|
||||
msc = msc_i = INT32_MIN; movl = INT32_MAX; plus = 0; si = 0; ei = a_n;
|
||||
memset(t, 0, (a_n*sizeof((*t))));
|
||||
}
|
||||
|
||||
for (i = st = si, max_ii = -1; i < ei; ++i) {
|
||||
max_f = a[i].cnt&(0xffu);
|
||||
n_skip = 0; max_j = end_j = -1;
|
||||
if ((i-st) > max_iter) st = i-max_iter;
|
||||
while (a[i].strand != a[st].strand) ++st;
|
||||
|
||||
for (j = i - 1; j >= st; --j) {
|
||||
sc = comput_sc_ch(&a[i], &a[j], bw_rate, chn_pen_gap, chn_pen_skip, xl, yl);
|
||||
if (sc == INT32_MIN) continue;
|
||||
sc += f[j];
|
||||
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;
|
||||
}
|
||||
end_j = j;
|
||||
|
||||
if ((max_ii<0) || (a[i].self_offset>a[max_ii].self_offset+max_dis) || (a[i].strand!=a[max_ii].strand)) {
|
||||
max = INT32_MIN; max_ii = -1;
|
||||
for (j=i-1; (j>=st) && (a[i].self_offset<=max_dis+a[j].self_offset)&&(a[i].strand==a[j].strand); --j) {
|
||||
if (max < f[j]) {
|
||||
max = f[j], max_ii = j;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if ((max_ii >= 0) && (max_ii < end_j) && (a[i].strand == a[max_ii].strand)) {///just have a try with a[i]<->a[max_ii]
|
||||
tmp = comput_sc_ch(&a[i], &a[max_ii], bw_rate, chn_pen_gap, chn_pen_skip, xl, yl);
|
||||
if (tmp != INT32_MIN && max_f < tmp + f[max_ii])
|
||||
max_f = tmp + f[max_ii], max_j = max_ii;
|
||||
}
|
||||
f[i] = max_f; p[i] = max_j;
|
||||
if ((max_ii < 0) || ((a[i].self_offset<=max_dis+a[max_ii].self_offset)&&(a[i].strand==a[max_ii].strand)&&(f[max_ii]<f[i]))) {
|
||||
max_ii = i;
|
||||
}
|
||||
if(f[i] >= msc) {
|
||||
ovl = get_chainLen(a[i].self_offset, a[i].self_offset, xl, a[i].offset, a[i].offset, yl);
|
||||
if(f[i] > msc || ovl < movl) {
|
||||
msc = f[i]; msc_i = i; movl = ovl;
|
||||
}
|
||||
}
|
||||
if(f[i] < plus) plus = f[i];
|
||||
ii[i] = 0;///for mcopy, not here
|
||||
// if(a_n && a[0].readID == 0) {
|
||||
// fprintf(stderr, "i::%ld[M::%s::utg%.6dl::%c] x::%u, y::%u, st::%ld, max_ii::%ld, f[i]::%d, p[i]::%ld, msc_i::%ld, msc::%ld, movl::%ld\n",
|
||||
// i, __func__, (int32_t)a[i].readID+1, "+-"[a[i].strand],
|
||||
// a[i].self_offset, a[i].offset, st, max_ii, f[i], p[i], msc_i, msc, movl);
|
||||
// }
|
||||
}
|
||||
|
||||
for (i = msc_i, cL = 0; i >= 0; i = p[i]) { ii[i] = 1; t[cL++] = i;}///label the best chain
|
||||
if((movl < xl) && enable_mcopy/**(movl < yl)**/) {
|
||||
if(cL >= mcopy_khit_cutoff) {///if there are too few k-mers, disable mcopy
|
||||
msc -= plus; min_sc = msc*mcopy_rate/**0.2**/; ii[msc_i] = 0;
|
||||
for (i = ch_n = 0; i < a_n; ++i) {///make all f[] positive
|
||||
f[i] -= plus; if(i >= ch_n) t[i] = 0;
|
||||
if((!(ii[i])) && (f[i] >= min_sc)) {
|
||||
t[ch_n] = ((uint64_t)f[i])<<32; t[ch_n] += (i<<1); ch_n++;
|
||||
}
|
||||
}
|
||||
if(ch_n > 1) {
|
||||
int64_t n_v, n_v0, ni, n_u, n_u0 = res->length;
|
||||
radix_sort_hc64i(t, t + ch_n);
|
||||
for (k = ch_n-1, n_v = n_u = 0; k >= 0; --k) {
|
||||
n_v0 = n_v;
|
||||
for (i = ((uint32_t)t[k])>>1; i >= 0 && (t[i]&1) == 0; ) {
|
||||
ii[n_v++] = i; t[i] |= 1; i = p[i];
|
||||
}
|
||||
if(n_v0 == n_v) continue;
|
||||
sc = (i<0?(t[k]>>32):((t[k]>>32)-f[i]));
|
||||
if(sc >= min_sc) {
|
||||
kv_pushp_ol(overlap_region, (*res), &z);
|
||||
push_ovlp_chain_qgen(z, xid, xl, yl, sc+plus, &(a[ii[n_v-1]]), &(a[ii[n_v0]]));
|
||||
///mcopy_khit_cutoff <= 1: disable the mcopy_khit_cutoff filtering, for the realignment
|
||||
if((mcopy_khit_cutoff <= 1) || ((z->x_pos_e+1-z->x_pos_s) <= (movl<<2))) {
|
||||
z->align_length = n_v-n_v0; z->x_id = n_v0;
|
||||
n_u++;
|
||||
} else {///non-best is too long
|
||||
res->length--; n_v = n_v0;
|
||||
}
|
||||
} else {
|
||||
n_v = n_v0;
|
||||
}
|
||||
}
|
||||
|
||||
if(n_u > 1) ks_introsort_or_sss(n_u, res->list + n_u0);
|
||||
res->length = n_u0 + filter_non_ovlp_xchains(res->list + n_u0, n_u, &n_v);
|
||||
n_u = res->length;
|
||||
if(n_u > n_u0 + 1) {
|
||||
kv_resize_cl(k_mer_hit, (*cl), (n_v+cl->length));
|
||||
a = cl->list + a_idx; des = cl->list + des_idx; swap = cl->list + cl->length;
|
||||
for (k = n_u0, i = n_v0 = n_v = 0; k < n_u; k++) {
|
||||
z = &(res->list[k]);
|
||||
z->non_homopolymer_errors = des_idx + i;
|
||||
n_v0 = z->x_id; ni = z->align_length;
|
||||
for (j = 0; j < ni; j++, i++) {
|
||||
///k0 + (ni - j - 1)
|
||||
swap[i] = a[ii[n_v0 + (ni- j - 1)]];
|
||||
swap[i].readID = k;
|
||||
}
|
||||
z->x_id = xid;
|
||||
if(gen_cigar) gen_fake_cigar(&(z->f_cigar), z, apend_be, swap+i-ni, ni);
|
||||
if(!khit_n) z->align_length = 0;
|
||||
}
|
||||
memcpy(des, swap, i*sizeof((*swap))); //assert(i == ch_n);
|
||||
|
||||
// fprintf(stderr, "[M::%s::msc->%ld] msc_k_hits::%u, cL::%ld, min_sc::%ld, best_sc::%ld, n_u0_sc::%d, mcopy_rate::%f, # chains::%ld\n",
|
||||
// __func__, msc, res->list[n_u0].align_length, cL, min_sc, msc+plus, res->list[n_u0].shared_seed,
|
||||
// mcopy_rate, n_u-n_u0);
|
||||
} else if(n_u == n_u0 + 1) {
|
||||
z = &(res->list[n_u0]); k = n_u0; i = 0;
|
||||
z->non_homopolymer_errors = des_idx + i;
|
||||
n_v0 = z->x_id; ni = z->align_length;
|
||||
for (j = 0; j < ni; j++, i++) {
|
||||
///k0 + (ni - j - 1)
|
||||
des[i] = a[ii[n_v0 + (ni- j - 1)]];
|
||||
des[i].readID = k;
|
||||
}
|
||||
z->x_id = xid;
|
||||
if(gen_cigar) gen_fake_cigar(&(z->f_cigar), z, apend_be, des+i-ni, ni);
|
||||
if(!khit_n) z->align_length = 0;
|
||||
}
|
||||
return i;
|
||||
} else {
|
||||
msc += plus; i = msc_i; cL = 0;
|
||||
while (i >= 0) {t[cL++] = i; i = p[i];}
|
||||
}
|
||||
}
|
||||
}
|
||||
///a[] has been sorted by self_offset
|
||||
// i = msc_i; cL = 0;
|
||||
// while (i >= 0) {t[cL++] = i; i = p[i];}
|
||||
kv_pushp_ol(overlap_region, (*res), &z);
|
||||
push_ovlp_chain_qgen(z, xid, xl, yl, msc, &(a[t[cL-1]]), &(a[t[0]]));
|
||||
for (i = 0; i < cL; i++) {des[i] = a[t[cL-i-1]]; des[i].readID = res->length-1;}
|
||||
z->non_homopolymer_errors = des_idx;
|
||||
if(gen_cigar) gen_fake_cigar(&(z->f_cigar), z, apend_be, des, cL);
|
||||
if(khit_n) z->align_length = cL;
|
||||
return cL;
|
||||
}
|
||||
|
||||
|
||||
#define rev_khit(an, xl, yl) do { \
|
||||
|
||||
Reference in New Issue
Block a user