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https://github.com/chhylp123/hifiasm.git
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ul_refine_alignment
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chhylp123
-140
@@ -1535,146 +1535,6 @@ inline int32_t comput_sc_ff(const k_mer_hit *ai, const k_mer_hit *aj, double bw_
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}
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return sc;
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}
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///for backuo
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uint64_t lchain_dp_fciagr(k_mer_hit* a, int64_t a_n, k_mer_hit* des, Chain_Data* dp, overlap_region* res,
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int64_t max_skip, int64_t max_iter, int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate,
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int64_t xl, int64_t yl, int64_t quick_check)
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{
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int64_t *p, *t, max_f, n_skip, st, max_j, end_j, sc, msc, msc_i, bw, max_ii, ovl, movl;
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int32_t *f, max, tmp; int64_t i, j, ret, dq, dr, dd, pdd, cL = 0;
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resize_Chain_Data(dp, a_n, NULL);
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t = dp->tmp; f = dp->score; p = dp->pre;
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bw = ((xl < yl)?xl:yl); bw *= bw_rate;
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msc = msc_i = -1; movl = INT32_MAX;
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if(quick_check) {
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ret = lchain_check(a, a_n, dp, bw_rate);
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if (ret > 0) {
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a_n = ret; msc_i = a_n-1; msc = f[msc_i];
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goto skip_ldp;
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}
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}
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memset(t, 0, (a_n*sizeof((*t))));
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for (i = st = 0, max_ii = -1; i < a_n; ++i) {
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max_f = a[i].cnt&(0xffu);
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n_skip = 0; max_j = end_j = -1;
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if ((i-st) > max_iter) st = i-max_iter;
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for (j = i - 1; j >= st; --j) {
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sc = comput_sc_ch(&a[i], &a[j], bw_rate, chn_pen_gap, chn_pen_skip, xl, yl);
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if (sc == INT32_MIN) continue;
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sc += f[j];
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if (sc > max_f) {
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max_f = sc, max_j = j;
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if (n_skip > 0) --n_skip;
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} else if (t[j] == (int32_t)i) {
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if (++n_skip > max_skip)
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break;
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}
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if (p[j] >= 0) t[p[j]] = i;
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}
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end_j = j;
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if (max_ii < 0 || ((int64_t)a[i].offset) - ((int64_t)a[max_ii].offset) > max_dis) {
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max = INT32_MIN; max_ii = -1;
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for (j = i - 1; (j >= st) && ((((int64_t)a[i].offset)-((int64_t)a[j].offset))<=max_dis); --j) {
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if (max < f[j]) {
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max = f[j], max_ii = j;
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}
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}
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}
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if (max_ii >= 0 && max_ii < end_j) {///just have a try with a[i]<->a[max_ii]
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tmp = comput_sc_ch(&a[i], &a[max_ii], bw_rate, chn_pen_gap, chn_pen_skip, xl, yl);
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if (tmp != INT32_MIN && max_f < tmp + f[max_ii])
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max_f = tmp + f[max_ii], max_j = max_ii;
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}
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f[i] = max_f; p[i] = max_j;
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if ((max_ii < 0) || (((((int64_t)a[i].offset)-((int64_t)a[max_ii].offset))<=max_dis) && (f[max_ii]<f[i]))) {
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max_ii = i;
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}
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if(f[i] >= msc) {
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ovl = get_chainLen(a[i].self_offset, a[i].self_offset, xl, a[i].offset, a[i].offset, yl);
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if(f[i] > msc || ovl < movl) {
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msc = f[i]; msc_i = i; movl = ovl;
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}
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}
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}
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skip_ldp:
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clear_fake_cigar(&(res->f_cigar));
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///a[] has been sorted by offset
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i = msc_i;
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res->x_pos_e = a[i].self_offset;
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res->y_pos_e = a[i].offset;
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res->shared_seed = msc;
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// res->overlapLen = movl;
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dq = res->x_pos_e - a[i].self_offset;
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dr = res->y_pos_e - a[i].offset;
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dd = dr - dq; pdd = dd;
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///record first site
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///the length of f_cigar should be at least 1
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///record the offset of reference
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add_fake_cigar(&(res->f_cigar), a[i].self_offset, dd, NULL);
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cL = 0;
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if(res->x_pos_strand == 1) {
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while (i >= 0) {
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dq = res->x_pos_e - a[i].self_offset;
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dr = res->y_pos_e - a[i].offset;
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dd = dr - dq;
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if(dd != pdd) {
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pdd = dd;
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///record this site
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add_fake_cigar(&(res->f_cigar), a[i].self_offset, pdd, NULL);
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}
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t[cL++] = i;
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res->x_pos_s = a[i].self_offset;
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res->y_pos_s = a[i].offset;
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msc_i = i; i = p[i];
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}
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}
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else {
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while (i >= 0) {
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dq = res->x_pos_e - a[i].self_offset;
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dr = res->y_pos_e - a[i].offset;
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dd = dr - dq;
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if(dd == pdd) {
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res->f_cigar.length--;
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add_fake_cigar(&(res->f_cigar), a[i].self_offset, pdd, NULL);
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} else {
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pdd = dd;
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add_fake_cigar(&(res->f_cigar), a[i].self_offset, pdd, NULL);
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}
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t[cL++] = i;
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res->x_pos_s = a[i].self_offset;
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res->y_pos_s = a[i].offset;
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msc_i = i; i = p[i];
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}
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}
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res->overlapLen = get_chainLen(res->x_pos_s, res->x_pos_e, xl, res->y_pos_s, res->y_pos_e, yl);
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for (i = 0; i < cL; i++) des[i] = a[t[cL-i-1]];
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if(res->x_pos_strand) {
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int64_t hcl = cL>>1; k_mer_hit kp;
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for (i = 0; i < hcl; i++) {
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j = cL-i-1; kp = des[i]; des[i] = des[j]; des[j] = kp;
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des[i].self_offset = xl-des[i].self_offset-1;
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des[i].offset = yl-des[i].offset-1;
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des[j].self_offset = xl-des[j].self_offset-1;
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des[j].offset = yl-des[j].offset-1;
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}
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if(cL&1) {
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des[i].self_offset = xl-des[i].self_offset-1;
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des[i].offset = yl-des[i].offset-1;
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}
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}
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return cL;
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}
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uint64_t lchain_dp(k_mer_hit* a, int64_t a_n, k_mer_hit* des, Chain_Data* dp, overlap_region* res,
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int64_t max_skip, int64_t max_iter, int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate,
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