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update trans chain

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chhylp123
2021-03-10 22:46:50 -05:00
parent 8aa87fdce8
commit 4c2ce6fc6b
6 changed files with 1363 additions and 334 deletions
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Overlaps.cpp
+198 -72
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@@ -11328,7 +11328,7 @@ void collect_trans_cov(buf_t* pri, buf_t* aux, ma_ug_t *ug, asg_t *read_sg, hap_
}
int untig_asg_arc_simple_large_bubbles_trio(ma_ug_t *ug, asg_t *read_sg, ma_hit_t_alloc* reverse_sources,
long long miniedgeLen, R_to_U* ruIndex, uint32_t positive_flag, uint32_t negative_flag, hc_links* link, hap_cov_t *cov)
long long miniedgeLen, R_to_U* ruIndex, uint32_t positive_flag, uint32_t negative_flag, hap_cov_t *cov)
{
asg_t *g = ug->g;
double startTime = Get_T();
@@ -11452,7 +11452,7 @@ long long miniedgeLen, R_to_U* ruIndex, uint32_t positive_flag, uint32_t negativ
asg_seq_drop(g, buffer.b.a[k]>>1);
}
if(link) collect_reverse_unitigs(&b_0, &b_1, link, ug, read_sg);
if(cov->link) collect_reverse_unitigs(&b_0, &b_1, cov->link, ug, read_sg);
if(cov) collect_trans_cov(&b_0, &b_1, ug, read_sg, cov);
is_hap++;
@@ -11645,13 +11645,13 @@ kvec_asg_arc_t_warp* new_rtg_edges, int max_hang, int min_ovlp)
{
uint64_t i, dip_thre_max, dip_thres, n_utg;
uint8_t* primary_flag = (uint8_t*)calloc(sg->n_seq, sizeof(uint8_t));
hap_cov_t *cov = init_hap_cov_t(ug, sg, sources, ruIndex, reverse_sources, coverage_cut, max_hang, min_ovlp);
hap_cov_t *cov = init_hap_cov_t(ug, sg, sources, ruIndex, reverse_sources, coverage_cut, max_hang, min_ovlp, NULL);
int tmp_cov = asm_opt.hom_global_coverage;
asm_opt.hom_global_coverage = -1;
purge_dups(ug, sg, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges,
asm_opt.purge_simi_rate, asm_opt.purge_overlap_len, max_hang, min_ovlp, 0, 0, 0, 1, NULL, cov);
asm_opt.purge_simi_rate, asm_opt.purge_overlap_len, max_hang, min_ovlp, 0, 0, 0, 1, cov);
dip_thre_max = ((double)asm_opt.hom_global_coverage)/((double)HOM_PEAK_RATE)*0.70;
asm_opt.hom_global_coverage = tmp_cov;
///fprintf(stderr, "dip_thre_max: %lu\n", dip_thre_max);
@@ -12523,7 +12523,7 @@ asg_t *read_sg, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex, uint32_t min_e
int asg_arc_cut_trio_long_tip_primary(asg_t *g, ma_ug_t *ug, asg_t *read_sg, ma_hit_t_alloc* reverse_sources,
R_to_U* ruIndex, uint32_t min_edge_length, float drop_ratio, hc_links* link, hap_cov_t *cov)
R_to_U* ruIndex, uint32_t min_edge_length, float drop_ratio, hap_cov_t *cov)
{
double startTime = Get_T();
///the reason is that each read has two direction (query->target, target->query)
@@ -12622,7 +12622,7 @@ R_to_U* ruIndex, uint32_t min_edge_length, float drop_ratio, hc_links* link, hap
}
}
if(link && operation != CUT) collect_reverse_unitigs(&b_0, &b_1, link, ug, read_sg);
if(cov->link && operation != CUT) collect_reverse_unitigs(&b_0, &b_1, cov->link, ug, read_sg);
if(cov && operation != CUT) collect_trans_cov(&b_0, &b_1, ug, read_sg, cov);
}
}
@@ -12646,7 +12646,7 @@ R_to_U* ruIndex, uint32_t min_edge_length, float drop_ratio, hc_links* link, hap
}
int asg_arc_cut_trio_long_tip_primary_complex(asg_t *g, ma_ug_t *ug, asg_t *read_sg, ma_hit_t_alloc* reverse_sources,
R_to_U* ruIndex, uint32_t min_edge_length, float drop_ratio, uint32_t stops_threshold, hc_links* link, hap_cov_t *cov)
R_to_U* ruIndex, uint32_t min_edge_length, float drop_ratio, uint32_t stops_threshold, hap_cov_t *cov)
{
double startTime = Get_T();
uint32_t v, n_vtx = g->n_seq * 2, n_reduced = 0, convex, in, flag, operation;
@@ -12721,7 +12721,7 @@ R_to_U* ruIndex, uint32_t min_edge_length, float drop_ratio, uint32_t stops_thre
}
}
if(link && operation != CUT) collect_reverse_unitigs(&b_0, &b_1, link, ug, read_sg);
if(cov->link && operation != CUT) collect_reverse_unitigs(&b_0, &b_1, cov->link, ug, read_sg);
if(cov && operation != CUT) collect_trans_cov(&b_0, &b_1, ug, read_sg, cov);
break;
@@ -12822,7 +12822,7 @@ long long* base_maxLen, long long* base_maxLen_i, uint32_t stops_threshold, buf_
int asg_arc_cut_trio_long_equal_tips_assembly(asg_t *g, ma_ug_t *ug, asg_t *read_sg,
ma_hit_t_alloc* reverse_sources, long long miniedgeLen, R_to_U* ruIndex, uint32_t trio_flag,
hc_links* link, hap_cov_t *cov)
hap_cov_t *cov)
{
double startTime = Get_T();
uint32_t v, n_vtx = g->n_seq * 2, n_reduced = 0, convex, flag, is_hap, n_tips, return_flag, k;
@@ -12909,7 +12909,7 @@ hc_links* link, hap_cov_t *cov)
asg_seq_drop(g, b.b.a[k]>>1);
}
if(link) collect_reverse_unitigs(&b_0, &b_1, link, ug, read_sg);
if(cov->link) collect_reverse_unitigs(&b_0, &b_1, cov->link, ug, read_sg);
if(cov) collect_trans_cov(&b_0, &b_1, ug, read_sg, cov);
is_hap++;
@@ -13143,7 +13143,7 @@ R_to_U* ruIndex, uint32_t positive_flag, float drop_rate)
}
int asg_arc_cut_trio_long_equal_tips_assembly_complex(asg_t *g, ma_ug_t *ug, asg_t *read_sg,
ma_hit_t_alloc* reverse_sources, long long miniedgeLen, R_to_U* ruIndex, uint32_t stops_threshold, hc_links* link, hap_cov_t *cov)
ma_hit_t_alloc* reverse_sources, long long miniedgeLen, R_to_U* ruIndex, uint32_t stops_threshold, hap_cov_t *cov)
{
double startTime = Get_T();
uint32_t v, n_vtx = g->n_seq * 2, n_reduced = 0, convex, in, flag;
@@ -13211,7 +13211,7 @@ ma_hit_t_alloc* reverse_sources, long long miniedgeLen, R_to_U* ruIndex, uint32_
asg_seq_drop(g, b.b.a[k]>>1);
}
if(link) collect_reverse_unitigs(&b_0, &b_1, link, ug, read_sg);
if(cov->link) collect_reverse_unitigs(&b_0, &b_1, cov->link, ug, read_sg);
if(cov) collect_trans_cov(&b_0, &b_1, ug, read_sg, cov);
///lable the primary one
@@ -13606,7 +13606,7 @@ ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, long long bubble_dist,
long long tipsLen, float tip_drop_ratio, long long stops_threshold,
R_to_U* ruIndex, buf_t* b_0, uint8_t* visit, float density, uint32_t miniHapLen,
uint32_t miniBiGraph, float chimeric_rate, int is_final_clean, int just_bubble_pop,
float drop_ratio, uint32_t trio_flag, float trio_drop_rate)
float drop_ratio, uint32_t trio_flag, float trio_drop_rate, hap_cov_t *cov)
{
asg_t *g = ug->g;
uint32_t is_first = 1;
@@ -13614,15 +13614,14 @@ float drop_ratio, uint32_t trio_flag, float trio_drop_rate)
redo:
///print_untig((ug), 61955, "i-0:", 0);
asg_pop_bubble_primary_trio(ug, bubble_dist, trio_flag, DROP, NULL);
untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, trio_flag, DROP, NULL, NULL);
asg_pop_bubble_primary_trio(ug, bubble_dist, trio_flag, DROP, cov);
untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, trio_flag, DROP, cov);
magic_trio_phasing(g, ug, read_g, coverage_cut, sources, reverse_sources, 2, ruIndex, trio_flag, trio_drop_rate);
///drop_semi_circle(ug, g, read_g, reverse_sources, ruIndex);
/**********debug**********/
if(just_bubble_pop == 0)
{
cut_trio_tip_primary(g, ug, tipsLen, trio_flag, 0, read_g, reverse_sources, ruIndex,
2);
cut_trio_tip_primary(g, ug, tipsLen, trio_flag, 0, read_g, reverse_sources, ruIndex, 2);
}
/**********debug**********/
long long pre_cons = get_graph_statistic(g);
@@ -13631,30 +13630,28 @@ float drop_ratio, uint32_t trio_flag, float trio_drop_rate)
{
pre_cons = get_graph_statistic(g);
///need consider tangles
asg_pop_bubble_primary_trio(ug, bubble_dist, trio_flag, DROP, NULL);
asg_pop_bubble_primary_trio(ug, bubble_dist, trio_flag, DROP, cov);
/**********debug**********/
if(just_bubble_pop == 0)
{
///need consider tangles
asg_arc_cut_trio_long_tip_primary(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, NULL, NULL);
asg_arc_cut_trio_long_equal_tips_assembly(g, ug, read_g, reverse_sources, 2, ruIndex, trio_flag, NULL, NULL);
asg_arc_cut_trio_long_tip_primary_complex(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, stops_threshold, NULL, NULL);
asg_arc_cut_trio_long_equal_tips_assembly_complex(g, ug, read_g, reverse_sources, 2, ruIndex, stops_threshold, NULL, NULL);
asg_arc_cut_trio_long_tip_primary(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, cov);
asg_arc_cut_trio_long_equal_tips_assembly(g, ug, read_g, reverse_sources, 2, ruIndex, trio_flag, cov);
asg_arc_cut_trio_long_tip_primary_complex(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, stops_threshold, cov);
asg_arc_cut_trio_long_equal_tips_assembly_complex(g, ug, read_g, reverse_sources, 2, ruIndex, stops_threshold, cov);
///print_debug_gfa(read_g, ug, coverage_cut, "debug_chimeric", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);
detect_chimeric_by_topo(g, ug, read_g, reverse_sources, 2, stops_threshold, chimeric_rate,
ruIndex);
detect_chimeric_by_topo(g, ug, read_g, reverse_sources, 2, stops_threshold, chimeric_rate, ruIndex);
///need consider tangles
///note we need both the read graph and the untig graph
}
/**********debug**********/
cur_cons = get_graph_statistic(g);
}
untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, trio_flag, DROP, NULL, NULL);
untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, trio_flag, DROP, cov);
if(just_bubble_pop == 0)
{
cut_trio_tip_primary(g, ug, tipsLen, trio_flag, 0, read_g, reverse_sources, ruIndex,
2);
cut_trio_tip_primary(g, ug, tipsLen, trio_flag, 0, read_g, reverse_sources, ruIndex, 2);
}
resolve_tangles(ug, read_g, reverse_sources, 20, 100, 0.05, 0.2, ruIndex, trio_flag, drop_ratio);
@@ -13674,7 +13671,7 @@ void clean_primary_untig_graph(ma_ug_t *ug, asg_t *read_g, ma_hit_t_alloc* rever
long long bubble_dist, long long tipsLen, float tip_drop_ratio, long long stops_threshold,
R_to_U* ruIndex, buf_t* b_0, uint8_t* visit, float density, uint32_t miniHapLen,
uint32_t miniBiGraph, float chimeric_rate, int is_final_clean, int just_bubble_pop,
float drop_ratio, hc_links* link, hap_cov_t *cov)
float drop_ratio, hap_cov_t *cov)
{
#define T_ROUND 2
asg_t *g = ug->g;
@@ -13683,7 +13680,7 @@ float drop_ratio, hc_links* link, hap_cov_t *cov)
redo:
asg_pop_bubble_primary_trio(ug, bubble_dist, (uint32_t)-1, DROP, cov);
untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, (uint32_t)-1, DROP, link, cov);
untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, (uint32_t)-1, DROP, cov);
if(just_bubble_pop == 0)
{
cut_trio_tip_primary(g, ug, tipsLen, (uint32_t)-1, 0, read_g, reverse_sources, ruIndex,
@@ -13700,10 +13697,10 @@ float drop_ratio, hc_links* link, hap_cov_t *cov)
if(just_bubble_pop == 0)
{
///need consider tangles
asg_arc_cut_trio_long_tip_primary(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, link, cov);
asg_arc_cut_trio_long_equal_tips_assembly(g, ug, read_g, reverse_sources, 2, ruIndex, (uint32_t)-1, link, cov);
asg_arc_cut_trio_long_tip_primary_complex(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, stops_threshold, link, cov);
asg_arc_cut_trio_long_equal_tips_assembly_complex(g, ug, read_g, reverse_sources, 2, ruIndex, stops_threshold, link, cov);
asg_arc_cut_trio_long_tip_primary(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, cov);
asg_arc_cut_trio_long_equal_tips_assembly(g, ug, read_g, reverse_sources, 2, ruIndex, (uint32_t)-1, cov);
asg_arc_cut_trio_long_tip_primary_complex(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, stops_threshold, cov);
asg_arc_cut_trio_long_equal_tips_assembly_complex(g, ug, read_g, reverse_sources, 2, ruIndex, stops_threshold, cov);
detect_chimeric_by_topo(g, ug, read_g, reverse_sources, 2, stops_threshold, chimeric_rate, ruIndex);
if(round != T_ROUND)
{
@@ -13713,7 +13710,7 @@ float drop_ratio, hc_links* link, hap_cov_t *cov)
}
cur_cons = get_graph_statistic(g);
}
untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, (uint32_t)-1, DROP, link, cov);
untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, (uint32_t)-1, DROP, cov);
if(just_bubble_pop == 0)
{
cut_trio_tip_primary(g, ug, tipsLen, (uint32_t)-1, 0, read_g, reverse_sources, ruIndex,
@@ -14375,11 +14372,11 @@ kvec_asg_arc_t_warp* new_rtg_edges)
{
asg_t* nsg = (*ug)->g;
uint32_t v, n_vtx = nsg->n_seq;
hap_cov_t *cov = init_hap_cov_t(*ug, read_g, sources, ruIndex, reverse_sources, coverage_cut, max_hang, min_ovlp);
hap_cov_t *cov = init_hap_cov_t(*ug, read_g, sources, ruIndex, reverse_sources, coverage_cut, max_hang, min_ovlp, NULL);
purge_dups(*ug, read_g, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges,
asm_opt.purge_simi_rate, asm_opt.purge_overlap_len, max_hang, min_ovlp, bubble_dist,
drop_ratio, 1, 1, NULL, cov);
drop_ratio, 1, 1, cov);
if(asm_opt.recover_atg_cov_min == -1024)
{
asm_opt.recover_atg_cov_max = asm_opt.hom_global_coverage/HOM_PEAK_RATE;
@@ -14415,8 +14412,7 @@ kvec_asg_arc_t_warp* new_rtg_edges)
EvaluateLen((*ug)->u, v) = (*ug)->u.a[v].n;
}
clean_trio_untig_graph(*ug, read_g, coverage_cut, sources, reverse_sources, bubble_dist,
tipsLen, tip_drop_ratio, stops_threshold, ruIndex, NULL, NULL, 0, 0, 0,
chimeric_rate, 0, 0, drop_ratio, flag, drop_rate);
tipsLen, tip_drop_ratio, stops_threshold, ruIndex, NULL, NULL, 0, 0, 0, chimeric_rate, 0, 0, drop_ratio, flag, drop_rate, cov);
///if(flag == MOTHER) fprintf(stderr, "(o.1) c: %u, del: %u, n: %u\n", (*ug)->g->seq[28141].c, (*ug)->g->seq[28141].del, (*ug)->u.a[28141].n);
@@ -14460,7 +14456,7 @@ kvec_asg_arc_t_warp* new_rtg_edges)
{
purge_dups(*ug, read_g, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges,
asm_opt.purge_simi_rate, asm_opt.purge_overlap_len, max_hang, min_ovlp, bubble_dist,
drop_ratio, 1, 0, NULL, cov);
drop_ratio, 1, 0, cov);
///delete_useless_nodes(ug);
delete_useless_trio_nodes(ug, read_g, coverage_cut, sources, ruIndex);
}
@@ -20825,6 +20821,150 @@ char* output_file_name, ma_hit_t_alloc** reverse_sources, R_to_U* ruIndex)
}
hap_cov_t* init_hap_cov_t(ma_ug_t *ug, asg_t* read_g, ma_hit_t_alloc* sources, R_to_U* ruIndex,
ma_hit_t_alloc* reverse_sources, ma_sub_t *coverage_cut, int max_hang, int min_ovlp, hc_links* link)
{
uint32_t n_ux = ug->g->n_seq, i, k, j, v, rId, tn, is_Unitig, r_i, nv, w, C_bases;
uint8_t *set = NULL;
hap_cov_t *x = NULL; CALLOC(x, 1);
x->n = read_g->n_seq;
x->reverse_sources = reverse_sources;
x->coverage_cut = coverage_cut;
x->ruIndex = ruIndex;
x->max_hang = max_hang;
x->min_ovlp = min_ovlp;
x->read_g = read_g;
x->link = link;
kv_init(x->u_buffer.a);
kv_init(x->tailIndex.a);
kv_init(x->prevIndex.a);
ma_utg_t* u = NULL;
asg_arc_t *av = NULL;
ma_hit_t *h = NULL;
MALLOC(x->pos_idx, x->n); memset(x->pos_idx, -1, x->n*sizeof(uint64_t));
CALLOC(set, read_g->n_seq<<1);
CALLOC(x->cov, x->n);
for (i = 0; i < n_ux; i++)
{
if(ug->g->seq[i].del) continue;
u = &(ug->u.a[i]);
for (r_i = 0; r_i < u->n; r_i++) set[u->a[r_i]>>33] = 1;
v = i<<1;
nv = asg_arc_n(ug->g, v);
av = asg_arc_a(ug->g, v);
for (k = 0; k < nv; k++)
{
w = av[k].v;
if(av[k].del) continue;
if(ug->g->seq[w>>1].del) continue;
u = &(ug->u.a[w>>1]);
for (r_i = 0; r_i < u->n; r_i++) set[u->a[r_i]>>33] = 1;
}
v = (i<<1)+1;
nv = asg_arc_n(ug->g, v);
av = asg_arc_a(ug->g, v);
for (k = 0; k < nv; k++)
{
w = av[k].v;
if(av[k].del) continue;
if(ug->g->seq[w>>1].del) continue;
u = &(ug->u.a[w>>1]);
for (r_i = 0; r_i < u->n; r_i++) set[u->a[r_i]>>33] = 1;
}
u = &(ug->u.a[i]);
for (k = 0; k < u->n; k++)
{
C_bases = 0;
rId = u->a[k]>>33;
for (j = 0; j < (uint64_t)(sources[rId].length); j++)
{
h = &(sources[rId].buffer[j]);
tn = Get_tn((*h));
if(read_g->seq[tn].del == 1)
{
///get the id of read that contains it
get_R_to_U(ruIndex, tn, &tn, &is_Unitig);
if(tn == (uint32_t)-1 || is_Unitig == 1 || read_g->seq[tn].del == 1) continue;
}
if(read_g->seq[tn].del == 1) continue;
if(!set[tn]) continue;
C_bases += (Get_qe((*h)) - Get_qs((*h)));
}
x->cov[rId] = MAX(C_bases, x->cov[rId]);
}
u = &(ug->u.a[i]);
for (r_i = 0; r_i < u->n; r_i++) set[u->a[r_i]>>33] = 0;
v = i<<1;
nv = asg_arc_n(ug->g, v);
av = asg_arc_a(ug->g, v);
for (k = 0; k < nv; k++)
{
w = av[k].v;
if(av[k].del) continue;
if(ug->g->seq[w>>1].del) continue;
u = &(ug->u.a[w>>1]);
for (r_i = 0; r_i < u->n; r_i++) set[u->a[r_i]>>33] = 0;
}
v = (i<<1)+1;
nv = asg_arc_n(ug->g, v);
av = asg_arc_a(ug->g, v);
for (k = 0; k < nv; k++)
{
w = av[k].v;
if(av[k].del) continue;
if(ug->g->seq[w>>1].del) continue;
u = &(ug->u.a[w>>1]);
for (r_i = 0; r_i < u->n; r_i++) set[u->a[r_i]>>33] = 0;
}
}
if(set) free(set);
if(x->link)
{
memset(x->link->u_idx, -1, read_g->n_seq*sizeof(uint32_t));
asg_t* nsg = ug->g;
uint32_t n_vtx = nsg->n_seq;
for (v = 0; v < n_vtx; ++v)
{
if(nsg->seq[v].del) continue;
u = &(ug->u.a[v]);
if(u->m == 0) continue;
for (k = 0; k < u->n; k++)
{
rId = u->a[k]>>33;
///if(read_g->seq[rId].c == FAKE_LABLE) continue;
x->link->u_idx[rId] = v;
}
}
}
return x;
}
void destory_hap_cov_t(hap_cov_t **x)
{
if(*x)
{
free((*x)->cov);
free((*x)->pos_idx);
kv_destroy((*x)->u_buffer.a);
kv_destroy((*x)->tailIndex.a);
kv_destroy((*x)->prevIndex.a);
free((*x));
}
}
void print_utg_hap(ma_ug_t *ug, asg_t* read_g, uint32_t uid, ma_hit_t_alloc* reverse_sources,
@@ -21096,33 +21236,15 @@ void adjust_utg_by_primary(ma_ug_t **ug, asg_t* read_g, float drop_rate,
ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, ma_sub_t* coverage_cut,
long long bubble_dist, long long tipsLen, float tip_drop_ratio, long long stops_threshold,
R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp,
kvec_asg_arc_t_warp* new_rtg_edges, hc_links* link)
kvec_asg_arc_t_warp* new_rtg_edges, hc_links* lk)
{
asg_t* nsg = (*ug)->g;
uint32_t v, n_vtx = nsg->n_seq, k, rId, just_contain;
ma_utg_t* u = NULL;
hap_cov_t *cov = init_hap_cov_t(*ug, read_g, sources, ruIndex, reverse_sources, coverage_cut, max_hang, min_ovlp);
hap_cov_t *cov = init_hap_cov_t(*ug, read_g, sources, ruIndex, reverse_sources, coverage_cut, max_hang, min_ovlp, lk);
///print_utg_coverage(*ug, coverage_cut, 440, sources);
///exit(0);
if(link)
{
memset(link->u_idx, -1, R_INF.total_reads*sizeof(uint32_t));
nsg = (*ug)->g;
n_vtx = nsg->n_seq;
for (v = 0; v < n_vtx; ++v)
{
if(nsg->seq[v].del) continue;
u = &((*ug)->u.a[v]);
if(u->m == 0) continue;
for (k = 0; k < u->n; k++)
{
rId = u->a[k]>>33;
///if(read_g->seq[rId].c == FAKE_LABLE) continue;
link->u_idx[rId] = v;
}
}
}
drop_semi_circle((*ug), nsg, read_g, reverse_sources, ruIndex);
asg_cleanup(nsg);
@@ -21136,16 +21258,18 @@ kvec_asg_arc_t_warp* new_rtg_edges, hc_links* link)
EvaluateLen((*ug)->u, v) = (*ug)->u.a[v].n;
}
clean_primary_untig_graph(*ug, read_g, reverse_sources, bubble_dist, tipsLen, tip_drop_ratio,
stops_threshold, ruIndex, NULL, NULL, 0, 0, 0, chimeric_rate, 0, 0, drop_ratio, link, cov);
stops_threshold, ruIndex, NULL, NULL, 0, 0, 0, chimeric_rate, 0, 0, drop_ratio, cov);
delete_useless_nodes(ug);
renew_utg(ug, read_g, new_rtg_edges);
if(cov->link) goto skip_purge;
if(asm_opt.purge_level_primary > 0)
{
just_contain = 0;
if(asm_opt.purge_level_primary == 1) just_contain = 1;
purge_dups(*ug, read_g, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges,
asm_opt.purge_simi_rate, asm_opt.purge_overlap_len, max_hang, min_ovlp, bubble_dist,
drop_ratio, just_contain, 0, link, cov);
drop_ratio, just_contain, 0, cov);
delete_useless_nodes(ug);
renew_utg(ug, read_g, new_rtg_edges);
}
@@ -21165,7 +21289,7 @@ kvec_asg_arc_t_warp* new_rtg_edges, hc_links* link)
if(asm_opt.purge_level_primary == 1) just_contain = 1;
purge_dups(*ug, read_g, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges,
asm_opt.purge_simi_rate, asm_opt.purge_overlap_len, max_hang, min_ovlp, bubble_dist,
drop_ratio, just_contain, 0, link, cov);
drop_ratio, just_contain, 0, cov);
delete_useless_nodes(ug);
renew_utg(ug, read_g, new_rtg_edges);
}
@@ -21175,7 +21299,7 @@ kvec_asg_arc_t_warp* new_rtg_edges, hc_links* link)
{
purge_dups(*ug, read_g, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges,
asm_opt.purge_simi_rate, asm_opt.purge_overlap_len, max_hang, min_ovlp, bubble_dist,
drop_ratio, 0, 1, link, cov);
drop_ratio, 0, 1, cov);
}
n_vtx = read_g->n_seq;
@@ -21227,21 +21351,23 @@ kvec_asg_arc_t_warp* new_rtg_edges, hc_links* link)
fprintf(stderr, "[M::%s] primary contig coverage range: [%d, infinity]\n",
__func__, asm_opt.recover_atg_cov_min);
}
recover_utg_by_coverage(ug, read_g, coverage_cut, sources, ruIndex, link);
if(link)
skip_purge:
recover_utg_by_coverage(ug, read_g, coverage_cut, sources, ruIndex, lk);
if(lk)
{
uint32_t m;
for (v = 0; v < link->a.n; v++)
for (v = 0; v < lk->a.n; v++)
{
for (k = m = 0; k < link->a.a[v].f.n; k++)
for (k = m = 0; k < lk->a.a[v].f.n; k++)
{
if(link->a.a[v].f.a[k].del) continue;
link->a.a[v].f.a[m] = link->a.a[v].f.a[k];
if(lk->a.a[v].f.a[k].del) continue;
lk->a.a[v].f.a[m] = lk->a.a[v].f.a[k];
m++;
}
link->a.a[v].f.n = m;
lk->a.a[v].f.n = m;
}
}