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code clean
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chhylp123
-130
@@ -13496,34 +13496,6 @@ char* output_file_name)
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}
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// in a resolved bubble, mark unused vertices and arcs as "reduced"
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static void asg_bub_backtrack(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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///assert(b->S.n == 1);
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///first remove all nodes in this bubble
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for (i = 0; i < b->b.n; ++i)
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g->seq[b->b.a[i]>>1].del = 1;
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///second 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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///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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// count the number of outgoing arcs, excluding reduced arcs
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@@ -13536,109 +13508,7 @@ static inline int count_out(const asg_t *g, uint32_t v)
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return n;
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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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static uint64_t asg_bub_pop1(asg_t *g, uint32_t v0, int max_dist, buf_t *b)
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{
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uint32_t i, n_pending = 0;
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uint64_t n_pop = 0;
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///if this node has been deleted
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if (g->seq[v0>>1].del) return 0; // already deleted
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///asg_arc_n(n0)
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if ((uint32_t)g->idx[v0] < 2) return 0; // no bubbles
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///S saves nodes with all incoming edges visited
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b->S.n = b->T.n = b->b.n = b->e.n = 0;
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///for each node, b->a saves all related information
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b->a[v0].c = b->a[v0].d = 0;
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///b->S is the nodes with all incoming edges visited
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kv_push(uint32_t, b->S, v0);
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do {
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///v is a node that all incoming edges have been visited
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///d is the distance from v0 to v
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uint32_t v = kv_pop(b->S), d = b->a[v].d, c = b->a[v].c;
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uint32_t nv = asg_arc_n(g, v);
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asg_arc_t *av = asg_arc_a(g, v);
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///why we have this assert?
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///assert(nv > 0);
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///all out-edges of v
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for (i = 0; i < nv; ++i) { // loop through v's neighbors
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/**
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p->ul: |____________31__________|__________1___________|______________32_____________|
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qn direction of overlap length of this node (not overlap length)
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(in the view of query)
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p->v : |___________31___________|__________1___________|
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tn reverse direction of overlap
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(in the view of target)
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p->ol: overlap length
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**/
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uint32_t w = av[i].v, l = (uint32_t)av[i].ul; // v->w with length l
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binfo_t *t = &b->a[w];
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///that means there is a circle, directly terminate the whole bubble poping
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///if (w == v0) goto pop_reset;
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if ((w>>1) == (v0>>1)) goto pop_reset;
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///if this edge has been deleted
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if (av[i].del) continue;
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///push the edge
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///high 32-bit of g->idx[v] is the start point of v's edges
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//so here is the point of this specfic edge
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kv_push(uint32_t, b->e, (g->idx[v]>>32) + i);
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///find a too far path? directly terminate the whole bubble poping
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if (d + l > (uint32_t)max_dist) break; // too far
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///if this node
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if (t->s == 0) { // this vertex has never been visited
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kv_push(uint32_t, b->b, w); // save it for revert
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///t->p is the parent node of
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///t->s = 1 means w has been visited
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///d is len(v0->v), l is len(v->w), so t->d is len(v0->w)
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t->p = v, t->s = 1, t->d = d + l, t->c = c + 1;
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///incoming edges of w
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t->r = count_out(g, w^1);
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++n_pending;
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} else { // visited before
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///c is the weight (is very likely the number of node in this edge) of the parent node
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///select the longest edge (longest meams most reads/longest edge)
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if (c + 1 > t->c || (c + 1 == t->c && d + l > t->d)) t->p = v;
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if (c + 1 > t->c) t->c = c + 1;
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///update len(v0->w)
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///node: t->d is not the length from this node's parent
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///it is the shortest edge
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if (d + l < t->d) t->d = d + l; // update dist
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}
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///assert(t->r > 0);
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//if all incoming edges of w have visited
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//push it to b->S
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if (--(t->r) == 0) {
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uint32_t x = asg_arc_n(g, w);
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if (x) kv_push(uint32_t, b->S, w);
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///else kv_push(uint32_t, b->T, w); // a tip
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else goto pop_reset;
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--n_pending;
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}
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}
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///if i < nv, that means (d + l > max_dist)
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if (i < nv || b->S.n == 0) goto pop_reset;
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} while (b->S.n > 1 || n_pending);
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///fprintf(stderr, "\nbeg>>1: %u, sink>>1: %u, num nodes: %d\n", v0>>1, (b->S.a[0])>>1, b->b.n);
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asg_bub_backtrack(g, v0, b);
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///n_pop = 1 | (uint64_t)b->T.n<<32;
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n_pop = 1;
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// for (i = 0; i < b->b.n; ++i)
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// {
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// fprintf(stderr, "b->b.a[%d]: %d\n", i, b->b.a[i]>>1);
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// }
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pop_reset:
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for (i = 0; i < b->b.n; ++i) { // clear the states of visited vertices
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binfo_t *t = &b->a[b->b.a[i]];
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t->s = t->c = t->d = 0;
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}
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return n_pop;
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}
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// in a resolved bubble, mark unused vertices and arcs as "reduced"
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