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clean contained read; fixed for deep_graph_clean

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chhylp123
2023-03-07 15:28:24 -05:00
parent a0f2f70d91
commit 85c643e85d
9 changed files with 1027 additions and 37 deletions
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gfa_ut.cpp
+103 -30
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@@ -22,7 +22,6 @@ KRADIX_SORT_INIT(srt64, uint64_t, generic_key, 8)
#define ASG_ET_MULTI_NEI 3
#define UL_TRAV_HERATE 0.2
#define UL_TRAV_FT_RATE 0.8
#define is_contain_r(ri, z) (((z)<(ri).len)&&((ri).index[(z)]!=(uint32_t)(-1))&&(!((ri).index[(z)]>>31)))
KDQ_INIT(uint64_t)
@@ -98,6 +97,8 @@ typedef struct{
double min_ovlp_drop_ratio;
double max_ovlp_drop_ratio;
double hom_check_drop_rate;
double min_path_drop_ratio;
double max_path_drop_ratio;
int64_t max_tip, max_tip_hifi;
uint32_t is_trio;
}ulg_opt_t;
@@ -2747,7 +2748,7 @@ double ou_drop_rate, int64_t max_tip, int64_t gap_fuzz, bub_label_t *b_mask_t, i
double step =
(clean_round==1?max_ovlp_drop_ratio:((max_ovlp_drop_ratio-min_ovlp_drop_ratio)/(clean_round-1)));
double drop = min_ovlp_drop_ratio;
int64_t i; asg64_v bu = {0,0,0}, ba = {0,0,0}; uint32_t l_drop = 2000; flex_asg_t *fg = NULL; uint32_t min_diff = (is_ou?2000:0);
int64_t i; asg64_v bu = {0,0,0}, ba = {0,0,0}; uint32_t l_drop = 2000; flex_asg_t *fg = NULL; uint32_t min_diff = 0, step_diff = 2000;
if(is_ou) fg = init_flex_asg_t(sg, uopt->sources, uopt->min_ovlp, uopt->max_hang, asm_opt.max_hang_rate, gap_fuzz);
// if(is_ou) update_sg_uo(sg, src);///do not do it here
// print_debug_gfa(sg, NULL, uopt->coverage_cut, "UL.dirty.debug", uopt->sources, uopt->ruIndex, uopt->max_hang, uopt->min_ovlp, 1, 0, 0);
@@ -2772,6 +2773,10 @@ double ou_drop_rate, int64_t max_tip, int64_t gap_fuzz, bub_label_t *b_mask_t, i
for (i = 0; i < clean_round; i++, drop += step) {
if(drop > max_ovlp_drop_ratio) drop = max_ovlp_drop_ratio;
if(is_ou) {
if(drop <= 0.500001) min_diff = step_diff>>1;
else min_diff = step_diff;
}
// fprintf(stderr, "(0):i->%ld, drop->%f\n", i, drop);
// prt_specfic_sge(sg, 10531, 10519, "--0--");
@@ -2813,14 +2818,20 @@ double ou_drop_rate, int64_t max_tip, int64_t gap_fuzz, bub_label_t *b_mask_t, i
if(is_ou) {
if(ul_refine_alignment(uopt, sg)) update_sg_uo(sg, src);
// debug_out = 1;
if(clean_contain_g(uopt, sg, 1)) update_sg_uo(sg, src);
// exit(1);
}
}
if(is_ou) min_diff = step_diff;
// print_debug_gfa(sg, NULL, uopt->coverage_cut, "UL.dirty4.debug", uopt->sources, uopt->ruIndex, uopt->max_hang, uopt->min_ovlp, 1, 0, 0);
// debug_info_of_specfic_node("m64012_190921_234837/111673711/ccs", sg, rI, "end");
// debug_info_of_specfic_node("m64011_190830_220126/95028102/ccs", sg, rI, "end");
if(is_ou) {
asg_arc_cut_contain(fg, &bu, &ba, rI, ou_drop_rate, 0);
asg_arc_cut_contain(fg, &bu, &ba, rI, -1, 1);
if(clean_contain_g(uopt, sg, 1)) update_sg_uo(sg, src);
}
if(!is_ou) asg_iterative_semi_circ(sg, src, &bu, max_tip, 1);
@@ -7720,6 +7731,7 @@ void ma_integer_ug_print0(const ma_ug_t *ug, ul_resolve_t *uidx, int print_seq,
for (i = 0; i < ug->u.n; ++i) { // the Segment lines in GFA
p = &ug->u.a[i];
if(p->m == 0) continue;
if(ug->g && ug->g->seq[i].del) continue;
sprintf(name, "%s%.6d%c", prefix, i + 1, "lc"[p->circ]);
if(is_seq) {
gen_ul_seq(uidx, i, &t);
@@ -9369,6 +9381,9 @@ uint32_t ulg_arc_cut_supports(ul_resolve_t *uidx, ma_ug_t *ug, int32_t max_ext,
float len_rat, uint32_t is_trio, uint32_t topo_level, uint32_t skip_hom, uint32_t *max_drop_len, uint32_t collapse_check,
asg64_v *in, asg64_v *ib)
{
// fprintf(stderr, "\n[M::%s::] max_ext::%d, max_ext_hifi::%d, len_rat::%f, is_trio::%u, topo_level::%u, skip_hom::%u, collapse_check::%u\n",
// __func__, max_ext, max_ext_hifi, len_rat, is_trio, topo_level, skip_hom, collapse_check);
asg64_v tx = {0,0,0}, tb = {0,0,0}, *b = NULL, *ub = NULL; asg_t *g = ug->g;
uint32_t v, w, i, k, kv, nv, kw, nw, cnt = 0, n_vtx = g->n_seq<<1, to_del, collapse;
asg_arc_t *av, *aw, *ve, *we; uint64_t w_q, w_t, pb;
@@ -9398,7 +9413,8 @@ asg64_v *in, asg64_v *ib)
kt_for(uidx->str_b.n_thread, worker_update_ul_arc_supports, uidx, b->n);///all ul + ug
uidx->uovl.iug_tra = NULL;
// fprintf(stderr, "#[M::%s::] Done\n", __func__);
// fprintf(stderr, "#[M::%s::] collapse_check::%u, len_rat::%f\n", __func__, collapse_check, len_rat);
radix_sort_srt64(b->a, b->a + b->n);
for (k = 0; k < b->n; k++) {
if(g->arc[(uint32_t)b->a[k]].del) continue;
@@ -9434,7 +9450,7 @@ asg64_v *in, asg64_v *ib)
}
}
// if((v>>1) == 409 && (w>>1) == 407) {
// if(((v>>1) == 6788 && (w>>1) == 17213) || ((w>>1) == 6788 && (v>>1) == 17213)) {
// fprintf(stderr, "#[M::%s::] v>>1::%u, v&1::%u, kv::%u, w>>1::%u, w&1::%u, kw::%u, collapse::%u\n",
// __func__, v>>1, v&1, kv, w>>1, w&1, kw, collapse);
// }
@@ -9448,6 +9464,10 @@ asg64_v *in, asg64_v *ib)
// fprintf(stderr, "+[M::%s::] v>>1::%u, v&1::%u, kv::%u, w>>1::%u, w&1::%u, kw::%u, w_q::%lu, w_t::%lu\n",
// __func__, v>>1, v&1, kv, w>>1, w&1, kw, w_q, w_t);
// }
// if(((v>>1) == 6788 && (w>>1) == 17213) || ((w>>1) == 6788 && (v>>1) == 17213)) {
// fprintf(stderr, "+[M::%s::] v>>1::%u, v&1::%u, w_q::%lu, w>>1::%u, w&1::%u, w_t::%lu\n",
// __func__, v>>1, v&1, w_q, w>>1, w&1, w_t);
// }
if(w_q == (uint64_t)-1) continue;
if(w_q > w_t*len_rat) continue;
}
@@ -9460,13 +9480,21 @@ asg64_v *in, asg64_v *ib)
// fprintf(stderr, "-[M::%s::] v>>1::%u, v&1::%u, kv::%u, w>>1::%u, w&1::%u, kw::%u, w_q::%lu, w_t::%lu\n",
// __func__, v>>1, v&1, kv, w>>1, w&1, kw, w_q, w_t);
// }
// if(((v>>1) == 6788 && (w>>1) == 17213) || ((w>>1) == 6788 && (v>>1) == 17213)) {
// fprintf(stderr, "-[M::%s::] v>>1::%u, v&1::%u, w_q::%lu, w>>1::%u, w&1::%u, w_t::%lu\n",
// __func__, v>>1, v&1, w_q, w>>1, w&1, w_t);
// }
if(w_q == (uint64_t)-1) continue;
if(w_q > w_t*len_rat) continue;
}
}
to_del = check_ulg_to_del(uidx, ug, v, w, kv, kw, max_ext, max_ext_hifi, topo_level, collapse, b, ub);
// if(((v>>1) == 6788 && (w>>1) == 17213) || ((w>>1) == 6788 && (v>>1) == 17213)) {
// fprintf(stderr, "#[M::%s::] v>>1::%u, v&1::%u, kv::%u, w>>1::%u, w&1::%u, kw::%u, to_del::%u\n",
// __func__, v>>1, v&1, kv, w>>1, w&1, kw, to_del);
// }
if (to_del) {
ve->del = we->del = 1, ++cnt;
}
@@ -15779,14 +15807,18 @@ void u2g_clean(ul_resolve_t *uidx, ulg_opt_t *ulopt, uint32_t keep_raw_utg, uint
{
ul2ul_idx_t *idx = &(uidx->uovl); asg64_v bu = {0,0,0}, uu = {0,0,0}; int64_t max_tip_hifi0 = ulopt->max_tip_hifi;
ma_ug_t *iug = idx->i_ug; int64_t i, mm_tip = ulopt->max_tip; uint64_t cnt = 1, topo_level, ss = 0;
double step = (ulopt->clean_round==1?ulopt->max_ovlp_drop_ratio:
((ulopt->max_ovlp_drop_ratio-ulopt->min_ovlp_drop_ratio)/(ulopt->clean_round-1)));
double drop = ulopt->min_ovlp_drop_ratio; CALLOC(iug->g->seq_vis, iug->g->n_seq*2);
double step = (ulopt->clean_round==1?ulopt->max_path_drop_ratio:
((ulopt->max_path_drop_ratio-ulopt->min_path_drop_ratio)/(ulopt->clean_round-1)));
double drop = ulopt->min_path_drop_ratio; CALLOC(iug->g->seq_vis, iug->g->n_seq*2);
// char sb[1000];
// output_integer_graph(uidx, iug, "ig_h0", 0);
for (ss = 0; ss < 2; ss++) {
for (i = 0, drop = ulopt->min_ovlp_drop_ratio; i < ulopt->clean_round; i++, drop += step) {
if(drop > ulopt->max_ovlp_drop_ratio) drop = ulopt->max_ovlp_drop_ratio;
for (i = 0, drop = ulopt->min_path_drop_ratio; i < ulopt->clean_round; i++, drop += step) {
if(drop > ulopt->max_path_drop_ratio) drop = ulopt->max_path_drop_ratio;
// fprintf(stderr, "\n[M::%s::] Starting round-%ld, drop::%f\n", __func__, i, drop);
cnt = 1; topo_level = 2; mm_tip = ulopt->max_tip;
while (cnt) {
@@ -15812,16 +15844,23 @@ void u2g_clean(ul_resolve_t *uidx, ulg_opt_t *ulopt, uint32_t keep_raw_utg, uint
cnt += ulg_arc_cut_tips(uidx, iug, mm_tip, ulopt->max_tip_hifi, 0, &bu, &uu);
}
// fprintf(stderr, "[M::%s::] Done round-%ld, drop::%f\n", __func__, i, drop);
// sprintf(sb, "ig_ss_%lu_i_%ld", ss, i);
// output_integer_graph(uidx, iug, sb, 0);
}
ulg_pop_bubble(uidx, iug, NULL, ((int64_t)0x7fffffff), ulopt->max_tip_hifi, 1, &bu, &uu);
while(ulg_arc_cut_z(uidx, iug, ((int64_t)0x7fffffff), ulopt->max_tip_hifi, 1.5, 0.15, 100, 0.8, ulopt->is_trio, 1, NULL, &bu, &uu));
// sprintf(sb, "ig_ss_%lu_i_%ld", ss, i);
// output_integer_graph(uidx, iug, sb, 0);
ulopt->max_tip_hifi <<= 1;
}
ulopt->max_tip_hifi = max_tip_hifi0;
// output_integer_graph(uidx, iug, "ig_h1", 0);
u2g_threading(uidx, ulopt, 3, is_bridg, &bu, &uu);
@@ -16132,7 +16171,12 @@ void renew_u2g_bg(ul_resolve_t *uidx)
bg->bg = asg_init();
bg->bg->n_seq = 0; bg->bg->m_seq = raw->g->n_seq; MALLOC(bg->bg->seq, bg->bg->m_seq);
for (k = 0; k < raw->g->n_seq; k++) {
raw_id = k; if(IF_HOM(raw_id, *bub)) continue;
raw_id = k;
if(IF_HOM(raw_id, *bub)) {///updated-line
// asg_seq_set(bg->bg, k, raw->g->seq[k].len, 1);
// bg->bg->seq[k].c = 0;
continue;
}
raw_a = idx->cc.iug_b + idx->cc.iug_idx[raw_id];
raw_n = idx->cc.iug_idx[raw_id+1] - idx->cc.iug_idx[raw_id];
for (z = 0, buf.n = 0; z < raw_n; z++) {
@@ -16369,8 +16413,10 @@ void gen_cul_g_t(ul_resolve_t *uidx)
}
}
void init_ulg_opt_t(ulg_opt_t *z, ug_opt_t *uopt, int64_t clean_round, double min_ovlp_drop_ratio,
double max_ovlp_drop_ratio, double hom_check_drop_rate, int64_t max_tip, int64_t max_tip_hifi, bub_label_t *b_mask_t, uint32_t is_trio)
void init_ulg_opt_t(ulg_opt_t *z, ug_opt_t *uopt, int64_t clean_round,
double min_path_drop_ratio, double max_path_drop_ratio,
double min_ovlp_drop_ratio, double max_ovlp_drop_ratio, double hom_check_drop_rate,
int64_t max_tip, int64_t max_tip_hifi, bub_label_t *b_mask_t, uint32_t is_trio)
{
z->tipsLen = uopt->tipsLen;
z->tip_drop_ratio = uopt->tip_drop_ratio;
@@ -16381,6 +16427,8 @@ double max_ovlp_drop_ratio, double hom_check_drop_rate, int64_t max_tip, int64_t
z->b_mask_t = b_mask_t;
z->clean_round = clean_round;
z->min_path_drop_ratio = min_path_drop_ratio;
z->max_path_drop_ratio = max_path_drop_ratio;
z->min_ovlp_drop_ratio = min_ovlp_drop_ratio;
z->max_ovlp_drop_ratio = max_ovlp_drop_ratio;
z->hom_check_drop_rate = hom_check_drop_rate;
@@ -17070,7 +17118,7 @@ ul_renew_t *ropt, const char *bin_file, uint64_t free_uld, uint64_t is_bridg, ui
if(deep_clean) {
// print_debug_gfa(sg, NULL, uopt->coverage_cut, "bclean", uopt->sources, uopt->ruIndex, uopt->max_hang, uopt->min_ovlp, 0, 0, 0);
deep_graph_clean(uopt, sg, 1, is_trio, asm_opt.max_short_tip, asm_opt.min_drop_rate,
MIN(asm_opt.max_drop_rate, 0.7), 0.75, 1, asm_opt.clean_round, 20);
MIN(asm_opt.max_drop_rate, 0.7), 0.75, 1, asm_opt.clean_round, 10/**20**/);
// print_debug_gfa(sg, NULL, uopt->coverage_cut, "aclean", uopt->sources, uopt->ruIndex, uopt->max_hang, uopt->min_ovlp, 0, 0, 0);
}
@@ -17103,11 +17151,11 @@ ul_renew_t *ropt, const char *bin_file, uint64_t free_uld, uint64_t is_bridg, ui
// exit(1);
// if(free_uld) {
print_raw_uls_seq(uidx, asm_opt.output_file_name);
// print_raw_uls_aln(uidx, asm_opt.output_file_name);
print_raw_uls_aln(uidx, asm_opt.output_file_name);
// }
ul_re_correct(uidx, 3);
init_ulg_opt_t(&uu, uopt, clean_round, min_ovlp_drop_ratio, max_ovlp_drop_ratio, 0.55, max_tip, max_ul_tip, b_mask_t, is_trio);
init_ulg_opt_t(&uu, uopt, clean_round, 0.2, 0.6, min_ovlp_drop_ratio, max_ovlp_drop_ratio, 0.55, max_tip, max_ul_tip, b_mask_t, is_trio);
// print_debug_gfa(sg, init_ug, uopt->coverage_cut, "UL.debug0", uopt->sources, uopt->ruIndex, uopt->max_hang, uopt->min_ovlp, 0, 0, 1);
/**ul2ul_idx_t *u2o = **/gen_ul2ul(uidx, uopt, &uu, 0, is_bridg);
// print_ul_alignment(init_ug, &UL_INF, 47072, "after-3");
@@ -17118,9 +17166,9 @@ ul_renew_t *ropt, const char *bin_file, uint64_t free_uld, uint64_t is_bridg, ui
// free(r_het); destory_bubbles(bub); free(bub);
// if(free_uld) {
// uidx->uovl.hybrid_ug = gen_hybrid_ug(uidx, uidx->uovl.h_usg);
uidx->uovl.hybrid_ug = gen_hybrid_ug(uidx, uidx->uovl.h_usg);
// // print_debug_gfa(sg, uidx->uovl.hybrid_ug, uopt->coverage_cut, "hybrid_ug", uopt->sources, uopt->ruIndex, uopt->max_hang, uopt->min_ovlp, 0, 0, 1);
// print_debug_gfa(sg, uidx->uovl.hybrid_ug, uopt->coverage_cut, "hybrid_ug", uopt->sources, uopt->ruIndex, uopt->max_hang, uopt->min_ovlp, 0, 0, 0);
print_debug_gfa(sg, uidx->uovl.hybrid_ug, uopt->coverage_cut, "hybrid_ug", uopt->sources, uopt->ruIndex, uopt->max_hang, uopt->min_ovlp, 0, 0, 0);
// // print_debug_gfa(sg, init_ug, uopt->coverage_cut, bin_file, uopt->sources, uopt->ruIndex, uopt->max_hang, uopt->min_ovlp, 0, 0, 0);
// }
// if(is_trio) gen_ul_trio_graph(uopt, uidx, o_file);
@@ -17304,12 +17352,9 @@ uint32_t usg_topocut_aux_unambi1(asg_t *g, uint32_t v)
int usg_topocut_aux_del(ma_ug_t *ug, uint32_t v, int max_ext, asg64_v *b)
{
int32_t n_ext;
for (n_ext = 1; n_ext < max_ext && v != (uint32_t)-1; ++n_ext) {
if (usg_topocut_aux_unambi1(ug->g, v^1) == (uint32_t)-1) {
--n_ext;
break;
}
kv_push(uint64_t, *b, v);
for (n_ext = 0; n_ext < max_ext && v != (uint32_t)-1; ) {
if (usg_topocut_aux_unambi1(ug->g, v^1) == (uint32_t)-1) break;
if(b) kv_push(uint64_t, *b, v); n_ext += ug->u.a[v>>1].n;
v = usg_topocut_aux_unambi1(ug->g, v);
}
return n_ext;
@@ -17335,10 +17380,28 @@ inline void asg_arc_del_by_ug(asg_t *sg, ma_ug_t *ug, uint32_t uv, uint32_t uw,
av[i].del = del;
}
void cal_bub_best_by_len(ug_clean_t *sl, asg64_v *in, uint32_t max_ext, uint32_t is_trio, uint32_t is_ou, double len_rat, double ou_rat, uint32_t min_ou)
uint32_t cal_utg_occ(ma_ug_t *ug, uint32_t begNode)
{
uint32_t v = begNode, w, kv, occ = 0; ma_utg_t *u;
while (1) {
kv = get_real_length(ug->g, v, NULL);
u = &(ug->u.a[v>>1]); occ += u->n;
if(kv!=1) break;
///kv must be 1 here
kv = get_real_length(ug->g, v, &w);
if(get_real_length(ug->g, w^1, NULL)!=1) break;
v = w;
if(v == begNode) break;
}
return occ;
}
void cal_bub_best_by_len(ug_clean_t *sl, asg64_v *in, uint32_t max_ext, uint32_t is_trio, uint32_t is_ou, double len_rat, double ou_rat, uint32_t min_ou,
uint32_t min_node)
{
// fprintf(stderr, "[M::%s]\tStart\n", __func__);
ma_ug_t *ug = sl->ug; asg_t *g = sl->ug->g; uint32_t ol_max, ou_max;
ma_ug_t *ug = sl->ug; asg_t *g = sl->ug->g; uint32_t ol_max, ou_max, lnid;
uint32_t v, w, n_vtx = (g->n_seq<<1), nv, nw, i, k, z, kv, kw, bb, to_del, bn, tip;
asg64_v tx = {0,0,0}, *b = NULL; asg_arc_t *av, *aw, *ve, *we; ma_utg_t *u;
uint32_t trioF = (uint32_t)-1, ntrioF = (uint32_t)-1, mm_ol, mm_ou, cnt = 0, del_v, del_w;
@@ -17391,7 +17454,7 @@ void cal_bub_best_by_len(ug_clean_t *sl, asg64_v *in, uint32_t max_ext, uint32_t
}
}
///mm_ol and mm_ou are used to make edge with long indel more easy to be cutted
mm_ol = MIN(ve->ol, we->ol); mm_ou = MIN(ve->ou, we->ou);
mm_ol = MIN(ve->ol, we->ol); mm_ou = MIN(ve->ou, we->ou); lnid = 0;
for (i = kv = ol_max = ou_max = 0; i < nv; ++i) {
if(av[i].del) continue;
@@ -17399,6 +17462,9 @@ void cal_bub_best_by_len(ug_clean_t *sl, asg64_v *in, uint32_t max_ext, uint32_t
if(is_trio && get_ug_tip_trio_infor(ug, av[i].v) == ntrioF) continue;
if(ol_max < av[i].ol) ol_max = av[i].ol;
if(ou_max < av[i].ou) ou_max = av[i].ou;
if((!lnid) && ((is_best_arc((*sl), v, av[i].v)))) {
if((cal_utg_occ(ug, v^1) >= min_node) || (cal_utg_occ(ug, av[i].v) >= min_node)) lnid = 1;
}
}
if (kv < 1) continue;
if (kv >= 2) {
@@ -17413,6 +17479,9 @@ void cal_bub_best_by_len(ug_clean_t *sl, asg64_v *in, uint32_t max_ext, uint32_t
if(is_trio && get_ug_tip_trio_infor(ug, aw[i].v) == ntrioF) continue;
if(ol_max < aw[i].ol) ol_max = aw[i].ol;
if(ou_max < aw[i].ou) ou_max = aw[i].ou;
if((!lnid) && ((is_best_arc((*sl), w, aw[i].v)))) {
if((cal_utg_occ(ug, w^1) >= min_node) || (cal_utg_occ(ug, aw[i].v) >= min_node)) lnid = 1;
}
}
if (kw < 1) continue;
if (kw >= 2) {
@@ -17421,22 +17490,26 @@ void cal_bub_best_by_len(ug_clean_t *sl, asg64_v *in, uint32_t max_ext, uint32_t
}
if (kv <= 1 && kw <= 1) continue;
if(!lnid) continue;
to_del = 0; del_v = del_w = (uint32_t)-1; tip = 0;
if (kv > 1 && kw > 1) {
to_del = 1;
} else if (kw == 1) {
tip = asg_topocut_aux(g, w^1, max_ext);
// tip = asg_topocut_aux(g, w^1, max_ext);
tip = usg_topocut_aux_del(ug, w^1, max_ext, NULL);
if (tip < max_ext) {
to_del = 1; del_w = w^1;
}
} else if (kv == 1) {
tip = asg_topocut_aux(g, v^1, max_ext);
// tip = asg_topocut_aux(g, v^1, max_ext);
tip = usg_topocut_aux_del(ug, v^1, max_ext, NULL);
if (tip < max_ext) {
to_del = 1; del_v = v^1;
}
}
if (to_del) {
bn = b->n;
if(del_v != ((uint32_t)-1)) usg_topocut_aux_del(ug, del_v, max_ext, b);
@@ -17630,7 +17703,7 @@ double min_ovlp_drop_ratio, double max_ovlp_drop_ratio, double ou_rat, int64_t m
if(sl->len_rat > max_ovlp_drop_ratio) sl->len_rat = max_ovlp_drop_ratio;
update_ug_clean_t(sl);
kt_for(asm_opt.thread_num, cal_bub_best, sl, sl->ug->g->n_seq);
cal_bub_best_by_len(sl, &b, max_ext, is_trio, sl->is_ou, sl->len_rat, sl->ou_rat, min_ou);
cal_bub_best_by_len(sl, &b, max_ext, is_trio, sl->is_ou, sl->len_rat, sl->ou_rat, min_ou, long_tip);
}
// if(is_ou) {