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fix bug at r_utg

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chhylp123
2020-08-04 16:43:50 -04:00
parent ef5ba0cc2c
commit 320dc58127
2 changed files with 32 additions and 23 deletions
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Overlaps.cpp
+31 -22
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@@ -6618,7 +6618,7 @@ uint8_t get_tip_trio_infor(asg_t *sg, uint32_t begNode)
{
uint32_t v = begNode, w;
uint32_t kv;
uint32_t eLen = 0;
uint32_t eLen = 0, uLen = 0;
uint32_t father_occ = 0, mother_occ = 0, ambigious_occ = 0;
while (1)
@@ -6647,10 +6647,17 @@ uint8_t get_tip_trio_infor(asg_t *sg, uint32_t begNode)
if(v == begNode) break;
}
uLen = eLen;
eLen = father_occ + mother_occ;
if(father_occ >= TRIO_THRES*eLen) return FATHER;
if(mother_occ >= TRIO_THRES*eLen) return MOTHER;
if(eLen == 0) return AMBIGU;
if(father_occ >= mother_occ)
{
if((father_occ > TRIO_THRES*eLen) && (father_occ >= DOUBLE_CHECK_THRES*uLen)) return FATHER;
}
else
{
if((mother_occ > TRIO_THRES*eLen) && (mother_occ >= DOUBLE_CHECK_THRES*uLen)) return MOTHER;
}
return AMBIGU;
}
@@ -6697,28 +6704,30 @@ int if_skip_bubble, int if_drop, int if_check_hap, R_to_U* ruIndex)
kv = get_real_length(g, v, NULL);
kw = get_real_length(g, w, NULL);
if (kv <= 1 && kw <= 1) continue;
trio_flag = get_tip_trio_infor(g, v);
trio_flag = get_tip_trio_infor(g, v^1);
non_trio_flag = (uint32_t)-1;
if(trio_flag == FATHER) non_trio_flag = MOTHER;
if(trio_flag == MOTHER) non_trio_flag = FATHER;
///calculate the longest edge for v and w
for (i = 0, kv = 0; i < nv; ++i) {
if (av[i].del) continue;
kv++;
if(get_tip_trio_infor(g, av[i].v) == non_trio_flag) continue;
if (ov_max < av[i].ol) ov_max = av[i].ol, ov_max_i = i;
kv++;
///kv++;
}
if (kv >= 2 && a->ol > ov_max * drop_ratio) continue;
for (i = 0, kw = 0; i < nw; ++i) {
if (aw[i].del) continue;
kw++;
if (get_tip_trio_infor(g, aw[i].v) == non_trio_flag) continue;
if (ow_max < aw[i].ol) ow_max = aw[i].ol, ow_max_i = i;
kw++;
///kw++;
}
if (kw >= 2 && a->ol > ow_max * drop_ratio) continue;
if (kv <= 1 && kw <= 1) continue;
///to see which one is the current edge (from v and w)
@@ -7999,7 +8008,7 @@ int asg_arc_del_short_diploid_by_exact_trio(asg_t *g, int max_ext, ma_hit_t_allo
kv = get_real_length(g, v, NULL);
kw = get_real_length(g, w, NULL);
if (kv <= 1 && kw <= 1) continue;
trio_flag = get_tip_trio_infor(g, v);
trio_flag = get_tip_trio_infor(g, v^1);
non_trio_flag = (uint32_t)-1;
if(trio_flag == FATHER) non_trio_flag = MOTHER;
if(trio_flag == MOTHER) non_trio_flag = FATHER;
@@ -8008,25 +8017,27 @@ int asg_arc_del_short_diploid_by_exact_trio(asg_t *g, int max_ext, ma_hit_t_allo
///calculate the longest edge for v and w
for (i = 0, kv = 0; i < nv; ++i) {
if (av[i].del) continue;
++kv;
if(get_tip_trio_infor(g, av[i].v) == non_trio_flag) continue;
if (ov_max < av[i].ol)
{
ov_max = av[i].ol;
ov_max_i = i;
}
++kv;
///++kv;
}
if (kv >= 2 && a->ol == ov_max) continue;
for (i = 0, kw = 0; i < nw; ++i) {
if (aw[i].del) continue;
++kw;
if (get_tip_trio_infor(g, aw[i].v) == non_trio_flag) continue;
if (ow_max < aw[i].ol)
{
ow_max = aw[i].ol;
}
++kw;
///++kw;
}
if (kw >= 2 && a->ol == ow_max) continue;
if (kv <= 1 && kw <= 1) continue;
@@ -9571,20 +9582,20 @@ void clean_weak_ma_hit_t(ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_source
void debug_info_of_specfic_node(char* name, asg_t *g, char* command)
void debug_info_of_specfic_node(const char* name, asg_t *g, char* command)
{
fprintf(stderr, "\n\n\n");
uint32_t v, n_vtx = g->n_seq * 2;
uint32_t v, n_vtx = g->n_seq * 2, queryLen = strlen(name);
for (v = 0; v < n_vtx; ++v)
{
if(memcmp(name, Get_NAME(R_INF, (v>>1)), Get_NAME_LENGTH(R_INF, (v>>1))) == 0)
if(queryLen == Get_NAME_LENGTH(R_INF, (v>>1)) && memcmp(name, Get_NAME(R_INF, (v>>1)), Get_NAME_LENGTH(R_INF, (v>>1))) == 0)
{
fprintf(stderr, "\nafter %s\n****************graph ref_read: %.*s, dir: %u****************\n",
command, (int)Get_NAME_LENGTH(R_INF, (v>>1)), Get_NAME(R_INF, (v>>1)), v&1);
if(g->seq[v>>1].del)
{
fprintf(stderr, "read has already been deleted.\n");
continue;
return;
}
asg_arc_t *av = asg_arc_a(g, v);
@@ -9596,6 +9607,7 @@ void debug_info_of_specfic_node(char* name, asg_t *g, char* command)
Get_NAME(R_INF, (av[i].v>>1)),
av[i].el, av[i].strong, av[i].ol, av[i].del);
}
return;
}
}
}
@@ -11356,6 +11368,7 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp)
kvec_asg_arc_t_warp new_rtg_edges;
kv_init(new_rtg_edges.a);
if(ug == NULL) ug = ma_ug_gen(read_g);
uint32_t i;
for (i = 0; i < ug->u.n; ++i)
@@ -26846,6 +26859,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
asg_cut_tip(sg, asm_opt.max_short_tip);
///drop_inexact_edegs_at_bubbles(sg, bubble_dist);
///debug_info_of_specfic_node("m54329U_190617_231905/176226420/ccs", sg, "complex_false_link");
if(clean_round > 0)
{
@@ -26862,7 +26876,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
int i = 0;
for (i = 0; i < clean_round; i++, drop_ratio += cut_step)
{
if(drop_ratio > max_ovlp_drop_ratio)
{
drop_ratio = max_ovlp_drop_ratio;
@@ -26876,7 +26889,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
///just topological clean
pre_clean(sources, coverage_cut, sg, bubble_dist);
///asg_arc_del_orthology(sg, reverse_sources, drop_ratio, asm_opt.max_short_tip);
// asg_arc_del_orthology_multiple_way(sg, reverse_sources, drop_ratio, asm_opt.max_short_tip);
// asg_cut_tip(sg, asm_opt.max_short_tip);
@@ -26887,7 +26899,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
asg_arc_del_false_node(sg, asm_opt.max_short_tip);
asg_cut_tip(sg, asm_opt.max_short_tip);
/****************************may have bugs********************************/
/****************************may have bugs********************************/
///asg_arc_identify_simple_bubbles_multi(sg, 1);
asg_arc_identify_simple_bubbles_multi(sg, 0);
@@ -26902,8 +26913,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
}
asg_cut_tip(sg, asm_opt.max_short_tip);
/****************************may have bugs********************************/
asg_arc_identify_simple_bubbles_multi(sg, 1);
if (ha_opt_triobin(&asm_opt))
{
@@ -26919,7 +26928,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
asg_arc_identify_simple_bubbles_multi(sg, 1);
asg_arc_del_short_false_link(sg, 0.6, 0.85, bubble_dist, reverse_sources,
asm_opt.max_short_tip, ruIndex);
asm_opt.max_short_tip, ruIndex);
asg_arc_identify_simple_bubbles_multi(sg, 1);
asg_arc_del_complex_false_link(sg, 0.6, 0.85, bubble_dist, reverse_sources, asm_opt.max_short_tip);