mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-10-01 16:38:13 +08:00
Merge branch 'master' into dev-lh3
This commit is contained in:
Heng Li
-262
@@ -7654,257 +7654,6 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen, R_to_U* ruIndex)
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}
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int asg_arc_del_tri_link(asg_t *g, int max_dist)
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{
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double startTime = Get_T();
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kvec_t(uint64_t) b;
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memset(&b, 0, sizeof(b));
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kvec_t(uint32_t) b_f;
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memset(&b_f, 0, sizeof(b_f));
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kvec_t(uint32_t) b_r;
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memset(&b_r, 0, sizeof(b_r));
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uint32_t v, w, n_vtx = g->n_seq * 2, n_cut = 0;
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buf_t bub;
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if (!g->is_symm) asg_symm(g);
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memset(&bub, 0, sizeof(buf_t));
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bub.a = (binfo_t*)calloc(n_vtx, sizeof(binfo_t));
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uint32_t Ns_first[3];
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uint32_t Ns_second[3];
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long long NodeLen_first[3];
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long long NodeLen_second[3];
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for (v = 0; v < n_vtx; ++v)
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{
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if(g->seq_vis[v] == 0)
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{
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asg_arc_t *av = asg_arc_a(g, v);
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uint32_t nv = asg_arc_n(g, v);
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if(nv != 2) continue;
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if(av[0].v == av[1].v) continue;
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/**********************test first node************************/
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NodeLen_first[0] = NodeLen_first[1] = NodeLen_first[2] = -1;
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if(asg_is_single_edge(g, av[0].v, v>>1) <= 2 && asg_is_single_edge(g, av[1].v, v>>1) <= 2)
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{
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NodeLen_first[asg_is_single_edge(g, av[0].v, v>>1)] = 0;
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NodeLen_first[asg_is_single_edge(g, av[1].v, v>>1)] = 1;
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}
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///one node has one out-edge, another node has two out-edges
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if(NodeLen_first[1] == -1 || NodeLen_first[2] == -1)
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{
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continue;
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}
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/**********************test first node************************/
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/**********************test second node************************/
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w = av[NodeLen_first[2]].v^1;
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asg_arc_t *aw = asg_arc_a(g, w);
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uint32_t nw = asg_arc_n(g, w);
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if(nw != 2)
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{
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fprintf(stderr, "error\n");
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}
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NodeLen_second[0] = NodeLen_second[1] = NodeLen_second[2] = -1;
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if(asg_is_single_edge(g, aw[0].v, w>>1) <= 2 && asg_is_single_edge(g, aw[1].v, w>>1) <= 2)
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{
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NodeLen_second[asg_is_single_edge(g, aw[0].v, w>>1)] = 0;
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NodeLen_second[asg_is_single_edge(g, aw[1].v, w>>1)] = 1;
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}
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///one node has one out-edge, another node has two out-edges
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if(NodeLen_second[1] == -1 || NodeLen_second[2] == -1)
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{
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continue;
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}
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/**********************test second node************************/
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uint64_t t_ol = av[NodeLen_first[2]].ol;
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kv_push(uint64_t, b, (uint64_t)(t_ol << 32 | v));
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}
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}
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radix_sort_arch64(b.a, b.a + b.n);
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uint64_t k;
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for (k = 0; k < b.n; k++)
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{
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///v is the node
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v = (uint32_t)b.a[k];
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if (g->seq[v>>1].del) continue;
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uint32_t nv = asg_arc_n(g, v), nw, to_del;
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uint32_t kv = get_real_length(g, v, NULL), kw;
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///at the begining, the nv of all nodes must be == 2;
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///here kv == 2, that means all edges are kept
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///so we can use normal method to delete edges
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if (nv != 2) continue;
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if (kv != 2) continue;
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asg_arc_t *av = asg_arc_a(g, v), *aw;
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if(av[0].v == av[1].v)
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{
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continue;
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}
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/**********************test first node************************/
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NodeLen_first[0] = NodeLen_first[1] = NodeLen_first[2] = -1;
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if(asg_is_single_edge(g, av[0].v, v>>1) <= 2 && asg_is_single_edge(g, av[1].v, v>>1) <= 2)
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{
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NodeLen_first[asg_is_single_edge(g, av[0].v, v>>1)] = 0;
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NodeLen_first[asg_is_single_edge(g, av[1].v, v>>1)] = 1;
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}
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///one node has one out-edge, another node has two out-edges
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if(NodeLen_first[1] == -1 || NodeLen_first[2] == -1)
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{
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continue;
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}
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/**********************test first node************************/
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/**********************test second node************************/
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w = av[NodeLen_first[2]].v^1;
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aw = asg_arc_a(g, w);
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nw = asg_arc_n(g, w);
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kw = get_real_length(g, w, NULL);
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///at the begining, the nw of all nodes must be == 2;
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///here kw == 2, that means all edges are kept
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///so we can use normal method to delete edges
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if(nw != 2) continue;
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if(kw != 2) continue;
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NodeLen_second[0] = NodeLen_second[1] = NodeLen_second[2] = -1;
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if(asg_is_single_edge(g, aw[0].v, w>>1) <= 2 && asg_is_single_edge(g, aw[1].v, w>>1) <= 2)
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{
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NodeLen_second[asg_is_single_edge(g, aw[0].v, w>>1)] = 0;
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NodeLen_second[asg_is_single_edge(g, aw[1].v, w>>1)] = 1;
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}
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///one node has one out-edge, another node has two out-edges
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if(NodeLen_second[1] == -1 || NodeLen_second[2] == -1)
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{
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continue;
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}
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/**********************test second node************************/
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uint32_t convex1, convex2, f1, f2;
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long long l1, l2;
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to_del = 0;
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f1 = detect_bubble_end_with_bubbles(g, av[0].v, av[1].v, &convex1, &l1, NULL);
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f2 = detect_bubble_end_with_bubbles(g, aw[0].v, aw[1].v, &convex2, &l2, NULL);
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if(f1 && f2)
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{
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if((l1 <= min_thres) || (l2 <= min_thres))
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{
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continue;
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}
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to_del = 1;
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}
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else if(f1)
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{
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if(l1 <= min_thres)
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{
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continue;
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}
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to_del = 1;
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}
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else if(f2)
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{
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if(l2 <= min_thres)
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{
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continue;
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}
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to_del = 1;
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}
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///here both f1 and f2 must be false
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if(to_del == 0)
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{
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if(!f1)
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{
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Ns_first[0] = av[0].v; Ns_first[1] = av[1].v;
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f1 = asg_bub_end_finder_with_del_advance(g, Ns_first, 2, max_dist,
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&bub, 0, (u_int32_t)-1, &convex1);
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l1 = min_thres + 10;
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}
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if(!f2)
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{
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Ns_second[0] = aw[0].v; Ns_second[1] = aw[1].v;
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f2 = asg_bub_end_finder_with_del_advance(g, Ns_second, 2, max_dist,
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&bub, 0, (u_int32_t)-1, &convex2);
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l2 = min_thres + 10;
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}
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///since both f1 and f2 must be false before 'if(to_del == 0)'
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///here l1 = min_thres + 10, l2 = min_thres + 10
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if(f1 && f2)
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{
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// if(l1 <= min_thres || l2 <= min_thres) // TODO: check this block: it is always false
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// {
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// continue;
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// }
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to_del = 1;
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}
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else if(f1)
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{
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if(l1 <= min_thres)
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{
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continue;
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}
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to_del = 1;
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}
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else if(f2)
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{
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if(l2 <= min_thres)
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{
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continue;
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}
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to_del = 1;
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}
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}
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if (to_del)
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{
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++n_cut;
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av[NodeLen_first[2]].del = 1;
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asg_arc_del(g, av[NodeLen_first[2]].v^1, av[NodeLen_first[2]].ul>>32^1, 1);
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}
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}
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free(b.a); free(b_f.a); free(b_r.a);
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free(bub.a); free(bub.S.a); free(bub.T.a); free(bub.b.a); free(bub.e.a);
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if (n_cut)
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{
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asg_cleanup(g);
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asg_symm(g);
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}
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fprintf(stderr, "[M::%s] removed %d false overlaps\n", __func__, n_cut);
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fprintf(stderr, "[M::%s] takes %0.2f s\n\n", __func__, Get_T()-startTime);
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return n_cut;
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}
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int asg_arc_del_complex_false_link(asg_t *g, float drop_ratio, float o_drop_ratio, int max_dist,
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ma_hit_t_alloc* reverse_sources, long long miniedgeLen)
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{
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@@ -13454,11 +13203,6 @@ kvec_asg_arc_t_warp* new_rtg_edges)
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delete_useless_nodes(ug);
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// purge_dups(*ug, read_g, coverage_cut, reverse_sources, ruIndex, new_rtg_edges, 0.75, 50, 50, 0.5, max_hang,
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// min_ovlp, bubble_dist, drop_ratio, 1);
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// deduplicate(*ug, read_g, reverse_sources, 20, 100, 0.05, 0.2, ruIndex, 1);
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// delete_useless_nodes(ug);
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update_unitig_graph((*ug), read_g, reverse_sources, ruIndex, flag, drop_rate);
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renew_utg(ug, read_g, new_rtg_edges);
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@@ -22264,19 +22008,13 @@ kvec_asg_arc_t_warp* new_rtg_edges)
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renew_utg(ug, read_g, new_rtg_edges);
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///enable_debug_mode(1);
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purge_dups(*ug, read_g, coverage_cut, reverse_sources, ruIndex, new_rtg_edges, 0.75, 50, 50, 0.5, max_hang,
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min_ovlp, bubble_dist, drop_ratio, 0);
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delete_useless_nodes(ug);
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renew_utg(ug, read_g, new_rtg_edges);
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rescue_missing_overlaps_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang,
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min_ovlp, 0, 0, 1, NULL);
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renew_utg(ug, read_g, new_rtg_edges);
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+3
-1
@@ -1599,6 +1599,7 @@ hap_overlaps_list* all_ovlp)
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asg_arc_t t;
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asg_arc_t_offset t_offset;
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hap_candidates hap_can;
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memset(&hap_can, 0, sizeof(hap_candidates));
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hap_overlaps hap_align;
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xUid = Input_uId;
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if(nsg->seq[xUid].del || nsg->seq[xUid].c == ALTER_LABLE) return;
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@@ -2161,7 +2162,8 @@ void hap_alignment_worker(void *_data, long eid, int tid)
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int32_t r;
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asg_arc_t t;
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asg_arc_t_offset t_offset;
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hap_candidates hap_can;
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hap_candidates hap_can;
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memset(&hap_can, 0, sizeof(hap_candidates));
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hap_overlaps hap_align;
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xUid = Input_uId;
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if(nsg->seq[xUid].del || nsg->seq[xUid].c == ALTER_LABLE) return;
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