mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-30 10:08:11 +08:00
fix bugs
This commit is contained in:
Haoyu Cheng
+126
-5
@@ -4596,6 +4596,94 @@ ma_hit_t_alloc* reverse_sources, long long min_edge_length)
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}
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long long check_if_diploid_primary(uint32_t v1, uint32_t v2, asg_t *g,
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ma_hit_t_alloc* reverse_sources, long long min_edge_length)
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{
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buf_t b_0, b_1;
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memset(&b_0, 0, sizeof(buf_t));
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memset(&b_1, 0, sizeof(buf_t));
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uint32_t convex1, convex2;
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long long l1, l2;
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b_0.b.n = 0;
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b_1.b.n = 0;
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///uint32_t flag1 = detect_single_path(g, v1, &convex1, &l1, &b_0);
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uint32_t flag1 = detect_single_path_with_dels(g, v1, &convex1, &l1, &b_0);
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///uint32_t flag2 = detect_single_path(g, v2, &convex2, &l2, &b_1);
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uint32_t flag2 = detect_single_path_with_dels(g, v2, &convex2, &l2, &b_1);
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if(flag1 == LOOP || flag2 == LOOP)
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{
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return -1;
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}
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if(flag1 != END_TIPS && flag1 != LONG_TIPS)
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{
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l1--;
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b_0.b.n--;
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}
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if(flag2 != END_TIPS && flag2 != LONG_TIPS)
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{
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l2--;
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b_1.b.n--;
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}
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if(l1 <= min_edge_length || l2 <= min_edge_length)
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{
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return -1;
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}
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buf_t* b_min;
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buf_t* b_max;
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if(l1<=l2)
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{
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b_min = &b_0;
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b_max = &b_1;
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}
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else
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{
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b_min = &b_1;
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b_max = &b_0;
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}
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long long i, j, k;
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double max_count = 0;
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double min_count = 0;
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uint32_t qn, tn;
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for (i = 0; i < (long long)b_min->b.n; i++)
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{
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qn = b_min->b.a[i];
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for (j = 0; j < (long long)reverse_sources[qn].length; j++)
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{
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tn = Get_tn(reverse_sources[qn].buffer[j]);
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if(g->seq[tn].del == 1 || g->seq[tn].c) continue;
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min_count++;
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for (k = 0; k < (long long)b_max->b.n; k++)
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{
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if(b_max->b.a[k]==tn)
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{
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max_count++;
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break;
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}
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}
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}
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}
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free(b_0.b.a);
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free(b_1.b.a);
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if(min_count == 0) return -1;
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if(max_count == 0) return 0;
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if(max_count/min_count>0.3) return 1;
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return 0;
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}
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long long check_if_diploid_aggressive(uint32_t v1, uint32_t v2, asg_t *g,
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ma_hit_t_alloc* reverse_sources, long long min_edge_length)
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@@ -7316,7 +7404,7 @@ int asg_arc_cut_long_equal_tips_assembly(asg_t *g, ma_hit_t_alloc* reverse_sourc
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continue;
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}
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//we can only cut tips
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if(check_if_diploid(av[base_maxLen_i].v, av[i].v, g,
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if(check_if_diploid_primary(av[base_maxLen_i].v, av[i].v, g,
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reverse_sources, miniedgeLen)==1)
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{
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n_reduced++;
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@@ -7730,7 +7818,7 @@ int asg_pop_bubble(asg_t *g, int max_dist)
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// in a resolved bubble, mark unused vertices and arcs as "reduced"
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static void asg_bub_backtrack_primary(asg_t *g, uint32_t v0, buf_t *b)
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{
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uint32_t i, v;
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uint32_t i, v, qn, tn;
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///assert(b->S.n == 1);
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///first remove all nodes in this bubble
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@@ -7748,6 +7836,38 @@ static void asg_bub_backtrack_primary(asg_t *g, uint32_t v0, buf_t *b)
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v = u;
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} while (v != v0);
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///remove all edges (self/reverse for each edge) in this bubble
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for (i = 0; i < b->e.n; ++i) {
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asg_arc_t *a = &g->arc[b->e.a[i]];
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qn = a->ul>>33;
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tn = a->v>>1;
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///there are three cases:
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///1. two nodes are at primary
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///2. two nodes are not at primary
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///3. one node is at primary, while another is not
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///for case 1 and case 3, we need to remove edges
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if(g->seq[qn].c == 1 && g->seq[tn].c == 1)
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{
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continue;
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}
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///remove this edge self
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a->del = 1;
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///remove the reverse direction
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asg_arc_del(g, a->v^1, a->ul>>32^1, 1);
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}
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///v is the sink of this bubble
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v = b->S.a[0];
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///recover node
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do {
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uint32_t u = b->a[v].p; // u->v
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g->seq[v>>1].del = 0;
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asg_arc_del(g, u, v, 0);
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asg_arc_del(g, v^1, u^1, 0);
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v = u;
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} while (v != v0);
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/**
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for (i = 0; i < b->b.n; ++i)
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{
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v = b->b.a[i];
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@@ -7757,6 +7877,7 @@ static void asg_bub_backtrack_primary(asg_t *g, uint32_t v0, buf_t *b)
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asg_seq_drop(g, v>>1);
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}
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}
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**/
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}
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// pop bubbles from vertex v0; the graph MJUST BE symmetric: if u->v present, v'->u' must be present as well
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@@ -8397,10 +8518,10 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen)
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n_ac += asg_arc_del_self_circle_untig(sg, circleLen, 0);
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n_ac += asg_arc_cut_long_tip(sg, tip_drop_ratio);
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n_ac += asg_arc_cut_long_equal_tips(sg, reverse_sources, 2);
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cur_cons = sg->n_seq + sg->n_arc;
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}
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asg_arc_identify_simple_bubbles_multi(sg, 1);
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asg_arc_del_short_false_link(sg, 0.6, 0.85, bubble_dist, reverse_sources, MAX_SHORT_TIPS, 0);
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@@ -8461,14 +8582,14 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen)
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n_ac += asg_arc_del_self_circle_untig(sg, circleLen, 1);
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n_ac += asg_arc_cut_long_tip_primary(sg, tip_drop_ratio);
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n_ac += asg_arc_cut_long_equal_tips_assembly(sg, reverse_sources, 2);
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cur_cons = get_graph_statistic(sg);
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}
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asg_arc_identify_simple_bubbles_multi(sg, 1);
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///we don't need a special function here since it just removes edges instead of nodes
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asg_arc_del_short_false_link(sg, 0.6, 0.85, bubble_dist, reverse_sources, MAX_SHORT_TIPS, 1);
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ma_ug_t *ug = NULL;
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ug = ma_ug_gen_primary(sg, 0);
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