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fix cross-chr bugs

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This commit is contained in:
Haoyu Cheng
2019-11-30 16:01:37 -05:00
parent f95691db3a
commit fca9c8db15
1 changed files with 129 additions and 23 deletions
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152
Overlaps.cpp
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@@ -6187,7 +6187,8 @@ int asg_arc_del_short_false_link_back(asg_t *g, float drop_ratio, int max_ext)
}
int asg_arc_del_short_false_link(asg_t *g, float drop_ratio, int max_dist)
int asg_arc_del_short_false_link(asg_t *g, float drop_ratio, float o_drop_ratio, int max_dist,
ma_hit_t_alloc* reverse_sources, long long miniedgeLen)
{
double startTime = Get_T();
@@ -6212,27 +6213,12 @@ int asg_arc_del_short_false_link(asg_t *g, float drop_ratio, int max_dist)
for (v = 0; v < n_vtx; ++v)
{
// if(v>>1 == 4581428)
// {
// fprintf(stderr, "%.*s, vis: %d\n", Get_NAME_LENGTH(R_INF, v>>1), Get_NAME(R_INF, v>>1),
// g->seq_vis[v]);
// }
if(g->seq_vis[v] == 0)
{
asg_arc_t *av = asg_arc_a(g, v);
uint32_t nv = asg_arc_n(g, v);
// if(v>>1 == 4581428)
// {
// fprintf(stderr, "nv: %d, rnv: %d\n", nv, asg_arc_n(g, v^1));
// }
if(nv == 1 && asg_arc_n(g, v^1) == 1) continue;
uint64_t t_ol = 0;
long long i;
for (i = 0; i < nv; ++i)
@@ -6296,6 +6282,112 @@ int asg_arc_del_short_false_link(asg_t *g, float drop_ratio, int max_dist)
if(av[i].ol < min_edge * drop_ratio) to_del_l++;
}
/****************************may have bugs********************************/
/**
if(to_del_l != kv)
{
b_f.n = 0;
b_r.n = 0;
to_del_l = 0;
for (i = 0; i < nv; i++)
{
if (av[i].del) continue;
w = av[i].v^1;
nw = asg_arc_n(g, w);
if(nw < 2) break;
kw = get_real_length(g, w, NULL);
if(kw < 2) break;
kv_push(uint32_t, b_f, av[i].v);
kv_push(uint32_t, b_r, w);
aw = asg_arc_a(g, w);
min_edge = (u_int32_t)-1;
for (t = 0; t < nw; t++)
{
if(aw[t].del) continue;
if((aw[t].v>>1) == (v>>1)) continue;
if(aw[t].ol < min_edge) min_edge = aw[t].ol;
}
if(av[i].ol < min_edge * o_drop_ratio) to_del_l++;
}
if(to_del_l == kv)
{
///forward
to_del_l = 1;
for (i = 1; i < b_f.n; i++)
{
if(check_if_diploid(b_f.a[0], b_f.a[i], g, reverse_sources, miniedgeLen) == 1)
{
to_del_l++;
}
}
///backward
if(to_del_l != kv && b_r.n >= 2)
{
to_del_l = 0;
uint32_t w0, w1;
w = b_r.a[0];
kw = get_real_length(g, w, NULL);
if(kw != 2) goto terminal;
aw = asg_arc_a(g, w);
nw = asg_arc_n(g, w);
for (t = 0; t < nw; t++)
{
if(aw[t].del) continue;
if((aw[t].v>>1) == (v>>1)) continue;
w0 = aw[t].v;
}
to_del_l = 1;
for (i = 1; i < b_r.n; i++)
{
w = b_r.a[i];
kw = get_real_length(g, w, NULL);
if(kw != 2) goto terminal;
aw = asg_arc_a(g, w);
nw = asg_arc_n(g, w);
for (t = 0; t < nw; t++)
{
if(aw[t].del) continue;
if((aw[t].v>>1) == (v>>1)) continue;
w1 = aw[t].v;
}
if(check_if_diploid(w0, w1, g, reverse_sources, miniedgeLen) == 1)
{
to_del_l++;
}
}
}
}
}
terminal:
**/
/****************************may have bugs********************************/
if(to_del_l != kv) continue;
@@ -6671,7 +6763,8 @@ int asg_arc_del_tri_link(asg_t *g, int max_dist)
return n_cut;
}
int asg_arc_del_complex_false_link(asg_t *g, float drop_ratio, int max_dist)
int asg_arc_del_complex_false_link(asg_t *g, float drop_ratio, float o_drop_ratio, int max_dist,
ma_hit_t_alloc* reverse_sources, long long miniedgeLen)
{
double startTime = Get_T();
@@ -8434,7 +8527,8 @@ static uint64_t asg_bub_pop1(asg_t *g, uint32_t v0, int max_dist, buf_t *b)
uint32_t w = av[i].v, l = (uint32_t)av[i].ul; // v->w with length l
binfo_t *t = &b->a[w];
///that means there is a circle, directly terminate the whole bubble poping
if (w == v0) goto pop_reset;
///if (w == v0) goto pop_reset;
if ((w>>1) == (v0>>1)) goto pop_reset;
///if this edge has been deleted
if (av[i].del) continue;
@@ -8480,10 +8574,16 @@ static uint64_t asg_bub_pop1(asg_t *g, uint32_t v0, int max_dist, buf_t *b)
///if i < nv, that means (d + l > max_dist)
if (i < nv || b->S.n == 0) goto pop_reset;
} while (b->S.n > 1 || n_pending);
///fprintf(stderr, "\nbeg>>1: %u, sink>>1: %u, num nodes: %d\n", v0>>1, (b->S.a[0])>>1, b->b.n);
asg_bub_backtrack(g, v0, b);
///n_pop = 1 | (uint64_t)b->T.n<<32;
n_pop = 1;
///fprintf(stderr, "v>>1: %u, num nodes: %d\n", v0>>1, b->b.n);
// for (i = 0; i < b->b.n; ++i)
// {
// fprintf(stderr, "b->b.a[%d]: %d\n", i, b->b.a[i]>>1);
// }
pop_reset:
for (i = 0; i < b->b.n; ++i) { // clear the states of visited vertices
binfo_t *t = &b->a[b->b.a[i]];
@@ -8938,6 +9038,12 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen)
cur_cons = sg->n_seq + sg->n_arc;
}
/**
fprintf(stderr, "pop bubbles: %d, sg->n_seq + sg->n_arc: %d\n",
asg_pop_bubble(sg, bubble_dist), sg->n_seq + sg->n_arc);
fprintf(stderr, "pop bubbles: %d, sg->n_seq + sg->n_arc: %d\n",
asg_pop_bubble(sg, bubble_dist), sg->n_seq + sg->n_arc);
**/
///asg_arc_del_self_circle_untig(sg, circleLen);
@@ -9152,11 +9258,11 @@ char* output_file_name, long long bubble_dist, int read_graph, int write)
asg_arc_del_short_diploid_by_length(sg, drop_ratio, MAX_SHORT_TIPS, reverse_sources, MAX_SHORT_TIPS);
asg_cut_tip(sg, MAX_SHORT_TIPS);
asg_arc_identify_simple_bubbles_multi(sg, 0);
asg_arc_del_short_false_link(sg, 0.6, bubble_dist);
asg_arc_identify_simple_bubbles_multi(sg, 1);
asg_arc_del_short_false_link(sg, 0.6, 0.85, bubble_dist, reverse_sources, MAX_SHORT_TIPS);
asg_arc_identify_simple_bubbles_multi(sg, 0);
asg_arc_del_complex_false_link(sg, 0.6, bubble_dist);
asg_arc_identify_simple_bubbles_multi(sg, 1);
asg_arc_del_complex_false_link(sg, 0.6, 0.85, bubble_dist, reverse_sources, MAX_SHORT_TIPS);
asg_cut_tip(sg, MAX_SHORT_TIPS);
}