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avoid misassemblies; better polyploidy graph

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chhylp123
2023-03-22 12:23:53 -04:00
parent d4773a497f
commit 86b7dd424a
12 changed files with 1931 additions and 79 deletions
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gfa_ut.cpp
+27 -14
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@@ -1262,7 +1262,7 @@ uint32_t minLen, asg64_v *t)
}
void asg_arc_cut_length(asg_t *g, asg64_v *in, int32_t max_ext, float len_rat, float ou_rat, uint32_t is_ou, uint32_t is_trio,
uint32_t is_topo, uint32_t min_diff, ma_hit_t_alloc *rev, R_to_U* rI, uint32_t *max_drop_len)
uint32_t is_topo, uint32_t min_diff, uint32_t min_ou, ma_hit_t_alloc *rev, R_to_U* rI, uint32_t *max_drop_len)
{
asg64_v tx = {0,0,0}, *b = NULL;
uint32_t i, k, v, w, n_vtx = g->n_seq<<1, nv, nw, kv, kw, trioF = (uint32_t)-1, ntrioF = (uint32_t)-1, ol_max, ou_max, to_del, cnt = 0, mm_ol, mm_ou;
@@ -1341,7 +1341,7 @@ uint32_t is_topo, uint32_t min_diff, ma_hit_t_alloc *rev, R_to_U* rI, uint32_t *
if (kv < 1) continue;
if (kv >= 2) {
if (mm_ol > ol_max*len_rat) continue;
if (is_ou && mm_ou > ou_max*ou_rat) continue;
if (is_ou && mm_ou > ou_max*ou_rat && mm_ou > min_ou) continue;
if ((mm_ol + min_diff) > ol_max) continue;
}
@@ -1356,7 +1356,7 @@ uint32_t is_topo, uint32_t min_diff, ma_hit_t_alloc *rev, R_to_U* rI, uint32_t *
if (kw < 1) continue;
if (kw >= 2) {
if (mm_ol > ol_max*len_rat) continue;
if (is_ou && mm_ou > ou_max*ou_rat) continue;
if (is_ou && mm_ou > ou_max*ou_rat && mm_ou > min_ou) continue;
if ((mm_ol + min_diff) > ol_max) continue;
}
@@ -2798,7 +2798,7 @@ double ou_drop_rate, int64_t max_tip, int64_t gap_fuzz, bub_label_t *b_mask_t, i
// prt_specfic_sge(sg, 10531, 10519, "--2--");
asg_arc_identify_simple_bubbles_multi(sg, b_mask_t, 1);
asg_arc_cut_length(sg, &bu, max_tip, drop, ou_drop_rate, is_ou, is_trio, 1, min_diff, NULL, NULL, NULL);
asg_arc_cut_length(sg, &bu, max_tip, drop, ou_drop_rate, is_ou, is_trio, 1, min_diff, 1, NULL, NULL, NULL);
asg_arc_cut_tips(sg, max_tip, &bu, is_ou, is_ou?rI:NULL);
// prt_specfic_sge(sg, 10531, 10519, "--3--");
@@ -2851,13 +2851,18 @@ double ou_drop_rate, int64_t max_tip, int64_t gap_fuzz, bub_label_t *b_mask_t, i
if(!is_ou) {
///asg_arc_del_triangular_directly might be unnecessary
asg_arc_identify_simple_bubbles_multi(sg, b_mask_t, 0);
asg_arc_cut_length(sg, &bu, max_tip, HARD_ORTHOLOGY_DROP/**min_ovlp_drop_ratio**/, ou_drop_rate, is_ou, 0/**is_trio**/, is_ou?1:0, min_diff, rev, rI, NULL);
asg_arc_cut_length(sg, &bu, max_tip, HARD_ORTHOLOGY_DROP/**min_ovlp_drop_ratio**/, ou_drop_rate, is_ou, 0/**is_trio**/, is_ou?1:0, min_diff, 1, rev, rI, NULL);
asg_arc_cut_tips(sg, max_tip, &bu, is_ou, is_ou?rI:NULL);
// print_debug_gfa(sg, NULL, uopt->coverage_cut, "UL.dirty7.debug", uopt->sources, uopt->ruIndex, uopt->max_hang, uopt->min_ovlp, 1, 0, 0);
asg_arc_identify_simple_bubbles_multi(sg, b_mask_t, 0);
asg_arc_cut_length(sg, &bu, max_tip, min_ovlp_drop_ratio, ou_drop_rate, is_ou, 0/**is_trio**/, is_ou?1:0, min_diff, rev, rI, &l_drop);
asg_arc_cut_length(sg, &bu, max_tip, min_ovlp_drop_ratio, ou_drop_rate, is_ou, 0/**is_trio**/, is_ou?1:0, min_diff, 1, rev, rI, &l_drop);
asg_arc_cut_tips(sg, max_tip, &bu, is_ou, is_ou?rI:NULL);
} else {
min_diff = step_diff; l_drop = 6000;
asg_arc_identify_simple_bubbles_multi(sg, b_mask_t, 0);
asg_arc_cut_length(sg, &bu, max_tip, 0.3, 0.9, is_ou, is_trio, 1, min_diff, 8, NULL, NULL, &l_drop);
asg_arc_cut_tips(sg, max_tip, &bu, is_ou, is_ou?rI:NULL);
}
@@ -11923,16 +11928,18 @@ uint32_t ava_pass_unique_bridge(uint64_t *idx, uint64_t *integer_seq, uint64_t s
return 1;
}
uint32_t ava_pass_unique_bridge_tips(usg_t *g, asg64_v *b64, uint64_t g_s, uint64_t g_e, uint64_t *integer_seq, uint8_t *f, uint64_t max_ext)
uint32_t ava_pass_unique_bridge_tips(usg_t *g, asg64_v *b64, uint64_t g_s, uint64_t g_e, uint64_t *integer_seq, uint8_t *f, uint64_t max_ext, double max_ext_rate, uint64_t ext_up)
{
uint64_t i, k, z, s, e, v, nv, bn = b64->n, kv, n_ext = 0; usg_arc_t *av;
uint64_t i, k, z, s, e, v, nv, bn = b64->n, kv, n_ext = 0, nkeep = 0, ncut = 0; usg_arc_t *av;
for (i = g_s; i < g_e; i++) {///available intervals within the same cluster
s = b64->a[((uint32_t)b64->a[i])]>>32; e = ((uint32_t)b64->a[((uint32_t)b64->a[i])]); assert(s < e);
for (k = s + 1; k < e; k++) {///note: here is [s, e]
f[integer_seq[k]] = f[integer_seq[k]^1] = 1;
f[integer_seq[k]] = f[integer_seq[k]^1] = 1;
nkeep += g->a[integer_seq[k]>>1].occ;
}
f[integer_seq[s]] = f[integer_seq[e]^1] = 1;
}
nkeep = nkeep*max_ext_rate;
///collect nodes within raw unitig graph that are linked by the clusters but not in the cluster
for (i = g_s; i < g_e; i++) {
@@ -11964,7 +11971,10 @@ uint32_t ava_pass_unique_bridge_tips(usg_t *g, asg64_v *b64, uint64_t g_s, uint6
}
}
while (b64->n > bn && n_ext < max_ext) {
ncut = MAX(nkeep, max_ext);
if(ncut > ext_up) ncut = ext_up;
if(ncut < max_ext) ncut = max_ext;
while (b64->n > bn && n_ext < ncut) {
v = b64->a[--b64->n]; if(f[v]) continue;
av = usg_arc_a(g, v^1); nv = usg_arc_n(g, v^1);
for (i = kv = 0; i < nv && kv < 1; i++) {
@@ -12014,7 +12024,7 @@ uint32_t ava_pass_unique_bridge_tips(usg_t *g, asg64_v *b64, uint64_t g_s, uint6
}
}
}
if((n_ext < ncut) && (n_ext > max_ext - 1)) n_ext = max_ext - 1;
return n_ext;
}
@@ -12954,7 +12964,7 @@ uint8_t *ff, uint32_t *ng_occ, uint32_t max_ext)
n_clus = 0;
for (k = a_n + 1, i = a_n, mm = a_n; k <= b64->n; k++) {
if(k == b64->n || (b64->a[k]>>32) != (b64->a[i]>>32)) {
tip_l = ava_pass_unique_bridge_tips(ng, b64, i, k, int_a, ff, max_ext);
tip_l = ava_pass_unique_bridge_tips(ng, b64, i, k, int_a, ff, max_ext, 0.03, 16);
if(tip_l < max_ext) {///no long tip
if(/**(!tip_l) || (**/ava_pass_unique_bridge_cov(uidx, ng, b64, i, k, int_a, tip_l)) {
for (z = i; z < k; z++) {
@@ -15934,11 +15944,14 @@ void u2g_clean(ul_resolve_t *uidx, ulg_opt_t *ulopt, uint32_t keep_raw_utg, uint
// char sb[1000];
// output_integer_graph(uidx, iug, "ig_h0", 0);
// fprintf(stderr, "\n[M::%s::] max_path_drop_ratio::%f, min_path_drop_ratio::%f\n", __func__, ulopt->max_path_drop_ratio, ulopt->min_path_drop_ratio);
// fprintf(stderr, "\n[M::%s::] max_path_drop_ratio::%f, min_path_drop_ratio::%f, max_tip_hifi::%ld, max_tip::%ld\n",
// __func__, ulopt->max_path_drop_ratio, ulopt->min_path_drop_ratio,
// ulopt->max_tip_hifi, ulopt->max_tip);
for (ss = 0; ss < 2; ss++) {
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, "[M::%s::] Starting round-%ld, drop::%f\n", __func__, i, drop);
// fprintf(stderr, "[M::%s::] Starting round-%ld, drop::%f, max_tip_hifi::%ld\n",
// __func__, i, drop, ulopt->max_tip_hifi);
cnt = 1; topo_level = 2; mm_tip = ulopt->max_tip;
while (cnt) {
cnt = 0;