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integer correction

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chhylp123
2022-06-07 16:56:28 -04:00
parent 8f1c59a5da
commit 98bb89227e
5 changed files with 2129 additions and 49 deletions
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hic.cpp
+22 -19
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@@ -6416,15 +6416,15 @@ asg_arc_t *p, uint32_t check_het)
if(x_1_b_id) id1 = (*x_1_b_id);
if((x_0 != (uint32_t)-1) && (x_1 != (uint32_t)-1))
{
if(((x_0>>1) == (x_1>>1)))
if(((x_0>>1) == (x_1>>1)))///if we would like to find a edge bridging two nearby bubbles
{
if(x_0_b_id == NULL && x_1_b_id == NULL)
{
get_bub_id(bub, x_0>>1, &id0, &id1, check_het);
}
get_bubbles(bub, id0, &beg_0, &sink_0, &a, &n, NULL);
get_bubbles(bub, id1, &beg_1, &sink_1, &a, &n, NULL);
get_bubbles(bub, id0, &beg_0, &sink_0, &a, &n, NULL);//first bubble
get_bubbles(bub, id1, &beg_1, &sink_1, &a, &n, NULL);//second bubble
ori_0 = (uint64_t)-1;
@@ -6716,10 +6716,11 @@ void detect_bub_graph(bubble_type* bub, asg_t *untig_sg)
uint64_t pLen, rLEN, r_hetLen;
ma_utg_t *u = NULL;
asg_arc_t *t = NULL;
for (i = 0; i < ug->u.n; i++)
for (i = 0; i < ug->u.n; i++)///bubble chain graph; bubbles within the same chain have been merged
{
u = &(ug->u.a[i]);
if(u->n == 0) continue;
///u is a bubble chain
for (k = pLen = rLEN = r_hetLen = beg_idx = 0, end_idx = -1; k < u->n; k++)
{
rId = u->a[k]>>33;
@@ -6727,7 +6728,7 @@ void detect_bub_graph(bubble_type* bub, asg_t *untig_sg)
get_bubbles(bub, rId, ori == 1?&root:&r_root, ori == 0?&root:&r_root, NULL, NULL, NULL);
t = NULL;
if(k+1 < u->n) t = &(arc_first(bg, u->a[k]>>32));
if(k+1 < u->n) t = &(arc_first(bg, u->a[k]>>32));//edge between two bubbles within the same chain
pLen += bg->seq[rId].len;///path length in bubble
if(end_idx < beg_idx) ///first bubble
@@ -6739,7 +6740,7 @@ void detect_bub_graph(bubble_type* bub, asg_t *untig_sg)
if(t)
{
if(t->el == 0)
if(t->el == 0)///there is tangle between two bubbles
{
if(end_idx >= beg_idx)
{
@@ -6752,7 +6753,7 @@ void detect_bub_graph(bubble_type* bub, asg_t *untig_sg)
pLen = rLEN = r_hetLen = 0;
beg_idx = k + 1; end_idx = k;
}
else
else///two bubbles directly connected with each other
{
pLen += t->ol;
rLEN += t->ol;
@@ -6784,7 +6785,7 @@ void get_bub_graph(ma_ug_t* ug, bubble_type* bub)
uint32_t *pre = NULL; MALLOC(pre, n_vtx);
uint32_t pre_id, adjecent, bub_occ;
asg_t *bub_g = asg_init();
for (v = 0; v < bub->f_bub; v++)
for (v = 0; v < bub->f_bub; v++)///all bubbles
{
uint64_t pathbase;
uint32_t beg, sink;
@@ -6793,11 +6794,12 @@ void get_bub_graph(ma_ug_t* ug, bubble_type* bub)
bub_g->seq[v].c = PRIMARY_LABLE;
}
//check all unitigs
//check all unitigs, instead of bubble nodes
for (v = 0; v < n_vtx; ++v)
{
if(sg->seq[v>>1].del) continue;
if(bub->b_s_idx.a[v>>1] == (uint64_t)-1) continue; ///if (v>>1) is not a beg or sink of bubbles
///one node might be the beg/sink node of at most two bubbles
bub_occ = connect_bub_occ(bub, v>>1, bub->check_het);
if(bub_occ == 0) continue;
if(bub_occ == 2)
@@ -6812,6 +6814,7 @@ void get_bub_graph(ma_ug_t* ug, bubble_type* bub)
}
if(ma_2_bub_arc(bub, v, NULL, (uint32_t)-1, NULL, &t, bub->check_het) == 0) continue;
///v is the beg/sink node of only one bubble
get_shortest_path(v, &pq, sg, pre);
for (k = 0; k < pq.dis.n; k++)
{
@@ -6833,7 +6836,7 @@ void get_bub_graph(ma_ug_t* ug, bubble_type* bub)
if(adjecent == 0)
{
if(ma_2_bub_arc(bub, v, NULL, k^1, NULL, &t, bub->check_het))
if(ma_2_bub_arc(bub, v, NULL, k^1, NULL, &t, bub->check_het))///edges spanning tangles
{
t.el = 0; t.ol = pq.dis.a[k] + sg->seq[k>>1].len;
p = asg_arc_pushp(bub_g);
@@ -6963,7 +6966,7 @@ uint8_t* vis_flag, uint32_t vis_flag_n, kvec_t_u32_warp* stack, asg_t *bsg, asg_
radix_sort_u32(broken->a.a, broken->a.a + broken->a.n);
for (i = n = 0, pre = (uint32_t)-1; i < broken->a.n; i++)
{
if((broken->a.a[i]>>1) == (pre>>1)) continue;
if((broken->a.a[i]>>1) == (pre>>1)) continue;///skip same node like v and v^1
pre = broken->a.a[i];
broken->a.a[n] = pre;
n++;
@@ -8046,7 +8049,7 @@ void resolve_bubble_chain_tangle(ma_ug_t* ug, bubble_type* bub)
occ_idx.a[occ_idx.n - k - 1] = tmp;
}
for (k = 0; k < bub_ug->g->n_seq; k++)
for (k = 0; k < bub_ug->g->n_seq; k++)///start from the longest chain
{
v = ((uint32_t)(occ_idx.a[k]))<<1;
if(is_used[v] == 0 && asg_arc_n(bub_ug->g, v) > 0)
@@ -8192,9 +8195,9 @@ void update_bubble_chain(ma_ug_t* ug, bubble_type* bub, uint32_t is_middle, uint
///uint64_t end_thres;
uint8_t *bsg_idx = NULL; CALLOC(bsg_idx, n_vtx>>1);
for (i = 0; i < bub_ug->u.n; i++)
for (i = 0; i < bub_ug->u.n; i++)///label all unitigs within the bubble chains
{
u = &(bub_ug->u.a[i]);
u = &(bub_ug->u.a[i]);///a bubble chain
if(u->n == 0) continue;
for (k_i = 0; k_i < u->n; k_i++)
{
@@ -8213,7 +8216,7 @@ void update_bubble_chain(ma_ug_t* ug, bubble_type* bub, uint32_t is_middle, uint
new_bub = bub->b_g->n_seq;
for (i = 0; i < bub_ug->u.n; i++)
{
u = &(bub_ug->u.a[i]);
u = &(bub_ug->u.a[i]);///bubble chain
if(u->n == 0) continue;
///end_thres = calculate_chain_weight(u, bub, ug, &x);
if(is_middle)
@@ -8223,7 +8226,7 @@ void update_bubble_chain(ma_ug_t* ug, bubble_type* bub, uint32_t is_middle, uint
if(k_i+1 >= u->n) continue;
///note: must igore .del here, since bsg might be changed
t = &(arc_first(bsg, u->a[k_i]>>32));
if(t->el == 1) continue;
if(t->el == 1) continue;///if a[k_i] and a[k_i+1] are directly connected without any tangle involoved
rId_0 = u->a[k_i]>>33;
ori_0 = u->a[k_i]>>32&1;
@@ -8233,7 +8236,7 @@ void update_bubble_chain(ma_ug_t* ug, bubble_type* bub, uint32_t is_middle, uint
ori_1 = (u->a[k_i+1]>>32&1)^1;
get_bubbles(bub, rId_1, ori_1 == 1?&root_1:NULL, ori_1 == 0?&root_1:NULL, NULL, NULL, NULL);
broken.a.n = 0;
broken.a.n = 0;///just collect all nodes between root_0 and root_1
get_related_bub_nodes(&broken, bub, &pq, sg, pre, root_0, root_1, NULL);
get_related_bub_nodes(&broken, bub, &pq, sg, pre, root_1, root_0, NULL);
///no need to cut the edge, we still have chance to flip by chain
@@ -9353,8 +9356,8 @@ void build_bub_graph(ma_ug_t* ug, bubble_type* bub)
// detect_bub_graph(bub, ug->g, 1);
update_bubble_chain(ug, bub, 1, 0);
///print_bubble_chain(bub, "second round");
update_bubble_chain(ug, bub, 0, 1);
resolve_bubble_chain_tangle(ug, bub);
update_bubble_chain(ug, bub, 0, 1);///resolve tangles within bubble chains
resolve_bubble_chain_tangle(ug, bub);///resolve tangles between bubble chains
}
void get_forward_distance(uint32_t src, uint32_t dest, asg_t *sg, hc_links* link, MT* M)