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fixed het/hom node bugs

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chhylp123
2022-12-08 03:07:14 -05:00
parent a3b72457f0
commit a674110b23
6 changed files with 67 additions and 21 deletions
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Overlaps.cpp
+13 -13
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@@ -3594,7 +3594,7 @@ uint32_t startNode, uint32_t endNode, int max_dist, buf_t* bub)
{
Ns_first[0] = av[0].v; Ns_first[1] = av[1].v;
f1 = asg_bub_end_finder_with_del_advance(g, Ns_first, 2, max_dist,
bub, 0, (u_int32_t)-1, &convex1);
bub, 0, (uint32_t)-1, &convex1);
l1 = min_thres + 10;
}
@@ -3602,7 +3602,7 @@ uint32_t startNode, uint32_t endNode, int max_dist, buf_t* bub)
{
Ns_second[0] = aw[0].v; Ns_second[1] = aw[1].v;
f2 = asg_bub_end_finder_with_del_advance(g, Ns_second, 2, max_dist,
bub, 0, (u_int32_t)-1, &convex2);
bub, 0, (uint32_t)-1, &convex2);
l2 = min_thres + 10;
}
@@ -4034,7 +4034,7 @@ uint32_t startNode, uint32_t endNode, int max_dist, buf_t* bub)
{
Ns_first[0] = Nodes1[0]^1; Ns_first[1] = Nodes2[1]^1;
f1 = asg_bub_end_finder_with_del_advance(g, Ns_first, 2, max_dist,
bub, 0, (u_int32_t)-1, &convex1);
bub, 0, (uint32_t)-1, &convex1);
l1 = min_thres + 10;
}
@@ -4042,7 +4042,7 @@ uint32_t startNode, uint32_t endNode, int max_dist, buf_t* bub)
{
Ns_second[0] = Nodes2[0]^1; Ns_second[1] = Nodes1[1]^1;
f2 = asg_bub_end_finder_with_del_advance(g, Ns_second, 2, max_dist,
bub, 0, (u_int32_t)-1, &convex2);
bub, 0, (uint32_t)-1, &convex2);
l2 = min_thres + 10;
}
@@ -6896,7 +6896,7 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen, R_to_U* ruIndex)
kv_push(uint32_t, b_r, w);
aw = asg_arc_a(g, w);
min_edge = (u_int32_t)-1;
min_edge = (uint32_t)-1;
for (t = 0; t < nw; t++)
{
if(aw[t].del) continue;
@@ -6996,7 +6996,7 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen, R_to_U* ruIndex)
}
//check the length
if(to_del_l == 0 && asg_bub_end_finder_with_del_advance(g,
b_f.a, b_f.n, max_dist, &bub, 0, (u_int32_t)-1, &sink)==1)
b_f.a, b_f.n, max_dist, &bub, 0, (uint32_t)-1, &sink)==1)
{
to_del_l = 1;
}
@@ -7143,7 +7143,7 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen, R_to_U* ruIndex)
kv_push(uint32_t, b_r, w);
aw = asg_arc_a(g, w);
min_edge = (u_int32_t)-1;
min_edge = (uint32_t)-1;
for (t = 0; t < nw; t++)
{
if(aw[t].del) continue;
@@ -7187,7 +7187,7 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen, R_to_U* ruIndex)
kv_push(uint32_t, b_r, w);
aw = asg_arc_a(g, w);
min_edge = (u_int32_t)-1;
min_edge = (uint32_t)-1;
for (t = 0; t < nw; t++)
{
if(aw[t].del) continue;
@@ -7288,7 +7288,7 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen, R_to_U* ruIndex)
}
//check the length
if(to_del_l == 0 && asg_bub_end_finder_with_del_advance(g,
b_f.a, b_f.n, max_dist, &bub, 0, (u_int32_t)-1, &sink)==1)
b_f.a, b_f.n, max_dist, &bub, 0, (uint32_t)-1, &sink)==1)
{
to_del_l = 1;
}
@@ -7431,7 +7431,7 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen, R_to_U* ruIndex)
kv_push(uint32_t, b_r, w);
aw = asg_arc_a(g, w);
min_edge = (u_int32_t)-1;
min_edge = (uint32_t)-1;
for (t = 0; t < nw; t++)
{
if(aw[t].del) continue;
@@ -7475,7 +7475,7 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen, R_to_U* ruIndex)
kv_push(uint32_t, b_r, w);
aw = asg_arc_a(g, w);
min_edge = (u_int32_t)-1;
min_edge = (uint32_t)-1;
for (t = 0; t < nw; t++)
{
if(aw[t].del) continue;
@@ -7575,7 +7575,7 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen, R_to_U* ruIndex)
}
//check the length
if(to_del_l == 0 && asg_bub_end_finder_with_del_advance(g,
b_f.a, b_f.n, max_dist, &bub, 0, (u_int32_t)-1, &sink)==1)
b_f.a, b_f.n, max_dist, &bub, 0, (uint32_t)-1, &sink)==1)
{
to_del_l = 1;
}
@@ -31884,7 +31884,7 @@ int64_t max_tip, bub_label_t *b_mask_t, uint32_t is_trio, char *o_file)
nopt.cov = coverage_cut; nopt.b_mask_t = b_mask_t;
nopt.max_hang = max_hang_length; nopt.mini_ovlp = mini_overlap_length;
ul_realignment_gfa(uopt, *sg, clean_round, min_ovlp_drop_ratio, max_ovlp_drop_ratio,
asm_opt.max_short_tip, b_mask_t, ha_opt_triobin(&asm_opt), o_file, &nopt);;
asm_opt.max_short_tip, asm_opt.max_short_ul_tip, b_mask_t, ha_opt_triobin(&asm_opt), o_file, &nopt);;
// ma_ug_t *iug = ul_realignment_gfa(uopt, *sg, clean_round, min_ovlp_drop_ratio, max_ovlp_drop_ratio,
// asm_opt.max_short_tip, b_mask_t, ha_opt_triobin(&asm_opt), o_file);
// asg_t *ng = gen_ng(iug, *sg, uopt, coverage_cut, ruIndex, 256);