xxay/hifiasm
1
0
Fork 0
mirror of https://github.com/chhylp123/hifiasm.git synced 2026-09-27 21:38:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

for hic

Browse Source
This commit is contained in:
chhylp123
2020-12-17 02:53:31 -05:00
parent 73b5ef6769
commit f3e390eee8
7 changed files with 1362 additions and 223 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Overlaps.cpp
+178 -46
View File
@@ -9795,6 +9795,74 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, uint8_t* r_flag)
return C_bases/R_bases;
}
uint32_t get_ug_coverage_aggressive(ma_ug_t *ug, uint32_t uID, asg_t* read_g,
const ma_sub_t* coverage_cut, ma_hit_t_alloc* sources, R_to_U* ruIndex, uint8_t* r_flag)
{
ma_utg_t* u = &(ug->u.a[uID]);
uint32_t k, j, rId, tn, is_Unitig;
long long R_bases = 0, C_bases = 0;
ma_hit_t *h;
if(u->m == 0) return 0;
for (k = 0; k < u->n; k++)
{
rId = u->a[k]>>33;
r_flag[rId] = 1;
}
uint32_t nv, i;
asg_arc_t *av = NULL;
for (i = 0; i < 2; i++)
{
nv = asg_arc_n(ug->g, (uID<<1)+i);
av = asg_arc_a(ug->g, (uID<<1)+i);
for (j = 0; j < nv; j++)
{
u = &(ug->u.a[av[j].v>>1]);
for (k = 0; k < u->n; k++)
{
rId = u->a[k]>>33;
r_flag[rId] = 1;
}
}
}
u = &(ug->u.a[uID]);
for (k = 0; k < u->n; k++)
{
rId = u->a[k]>>33;
R_bases += (coverage_cut[rId].e - coverage_cut[rId].s);
for (j = 0; j < (uint64_t)(sources[rId].length); j++)
{
h = &(sources[rId].buffer[j]);
if(h->el != 1) continue;
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(r_flag[tn] != 1) continue;
C_bases += (Get_qe((*h)) - Get_qs((*h)));
}
}
for (k = 0; k < u->n; k++)
{
rId = u->a[k]>>33;
r_flag[rId] = 0;
}
return C_bases/R_bases;
}
void ma_ug_print2(const ma_ug_t *ug, All_reads *RNF, asg_t* read_g, const ma_sub_t *coverage_cut,
ma_hit_t_alloc* sources, R_to_U* ruIndex, int print_seq, const char* prefix, FILE *fp)
{
@@ -10889,8 +10957,50 @@ uint32_t get_num_trio_flag(ma_ug_t *ug, uint32_t v, uint32_t flag)
return flag_occ;
}
void set_pre_uid(buf_t* b, hc_links* link, ma_ug_t *ug)
{
uint32_t k = 0, i = 0, m = 0, rId, pre = (uint32_t)-1;
ma_utg_t* u = NULL;
for (i = 0; i < b->b.n; i++)
{
u = &(ug->u.a[b->b.a[i]>>1]);
if(u->m == 0) continue;
for (k = 0; k < u->m; k++)
{
rId = u->a[k]>>33;
if(link->u_idx[rId] == (uint32_t)-1) continue;
if(pre == link->u_idx[rId]) continue;
pre = link->u_idx[rId];
b->b.a[m] = link->u_idx[rId];
m++;
}
}
b->b.n = m;
}
void collect_reverse_unitigs(buf_t* b_0, buf_t* b_1, hc_links* link, ma_ug_t *ug)
{
uint32_t k, m;
uint64_t d = (uint64_t)-1;
set_pre_uid(b_0, link, ug);
set_pre_uid(b_1, link, ug);
for (k = 0; k < b_0->b.n; k++)
{
for (m = 0; m < b_1->b.n; m++)
{
if(b_0->b.a[k] == b_1->b.a[m]) continue;
push_hc_edge(&(link->a.a[b_0->b.a[k]]), b_1->b.a[m], 1, 1, &d);
push_hc_edge(&(link->a.a[b_1->b.a[m]]), b_0->b.a[k], 1, 1, &d);
}
}
}
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)
long long miniedgeLen, R_to_U* ruIndex, uint32_t positive_flag, uint32_t negative_flag, hc_links* link)
{
asg_t *g = ug->g;
double startTime = Get_T();
@@ -11018,6 +11128,8 @@ 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);
is_hap++;
}
}
@@ -11639,8 +11751,8 @@ kvec_asg_arc_t_warp* new_rtg_edges, int max_hang, int min_ovlp)
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);
dip_thres = ((double)asm_opt.hom_global_coverage)/((double)HOM_PEAK_RATE)*0.6;
asm_opt.purge_simi_rate, asm_opt.purge_overlap_len, max_hang, min_ovlp, 0, 0, 0, 1, NULL);
dip_thres = ((double)asm_opt.hom_global_coverage)/((double)HOM_PEAK_RATE)*0.75;
asm_opt.hom_global_coverage = tmp_cov;
for (i = 0; i < ug->g->n_seq; i++)
@@ -11648,6 +11760,10 @@ kvec_asg_arc_t_warp* new_rtg_edges, int max_hang, int min_ovlp)
if(get_ug_coverage(&ug->u.a[i], sg, coverage_cut, sources, ruIndex, primary_flag)<dip_thres)
{
ug->g->seq[i].c = 1;
if(get_ug_coverage_aggressive(ug, i, sg, coverage_cut, sources, ruIndex, primary_flag)<dip_thres)
{
ug->g->seq[i].c = 2;
}
}
else
{
@@ -12268,8 +12384,9 @@ asg_t *read_sg, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex, uint32_t min_e
return cnt;
}
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)
R_to_U* ruIndex, uint32_t min_edge_length, float drop_ratio, hc_links* link)
{
double startTime = Get_T();
///the reason is that each read has two direction (query->target, target->query)
@@ -12370,6 +12487,8 @@ R_to_U* ruIndex, uint32_t min_edge_length, float drop_ratio)
}
if(link && operation != CUT) collect_reverse_unitigs(&b_0, &b_1, link, ug);
}
}
}
@@ -12392,7 +12511,7 @@ R_to_U* ruIndex, uint32_t min_edge_length, float drop_ratio)
}
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)
R_to_U* ruIndex, uint32_t min_edge_length, float drop_ratio, uint32_t stops_threshold, hc_links* link)
{
double startTime = Get_T();
uint32_t v, n_vtx = g->n_seq * 2, n_reduced = 0, convex, in, flag, operation;
@@ -12493,6 +12612,8 @@ 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);
break;
}
}
@@ -12590,7 +12711,8 @@ 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)
ma_hit_t_alloc* reverse_sources, long long miniedgeLen, R_to_U* ruIndex, uint32_t trio_flag,
hc_links* link)
{
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;
@@ -12677,6 +12799,8 @@ 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);
is_hap++;
}
@@ -12908,7 +13032,7 @@ 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)
ma_hit_t_alloc* reverse_sources, long long miniedgeLen, R_to_U* ruIndex, uint32_t stops_threshold, hc_links* link)
{
double startTime = Get_T();
uint32_t v, n_vtx = g->n_seq * 2, n_reduced = 0, convex, in, flag;
@@ -13001,6 +13125,7 @@ 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);
///lable the primary one
b_0.b.n = 0;
@@ -13369,7 +13494,7 @@ float drop_ratio, uint32_t trio_flag, float trio_drop_rate)
///print_untig((ug), 61955, "i-0:", 0);
asg_pop_bubble_primary_trio(ug, bubble_dist, trio_flag, DROP);
untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, trio_flag, DROP);
untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, trio_flag, DROP, NULL);
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**********/
@@ -13392,12 +13517,10 @@ float drop_ratio, uint32_t trio_flag, float trio_drop_rate)
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);
asg_arc_cut_trio_long_equal_tips_assembly(g, ug, read_g, reverse_sources, 2, ruIndex, trio_flag);
asg_arc_cut_trio_long_tip_primary_complex(g, ug, read_g, reverse_sources, ruIndex,
2, tip_drop_ratio, stops_threshold);
asg_arc_cut_trio_long_equal_tips_assembly_complex(g, ug, read_g, reverse_sources,
2, ruIndex, stops_threshold);
asg_arc_cut_trio_long_tip_primary(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, NULL);
asg_arc_cut_trio_long_equal_tips_assembly(g, ug, read_g, reverse_sources, 2, ruIndex, trio_flag, NULL);
asg_arc_cut_trio_long_tip_primary_complex(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, stops_threshold, NULL);
asg_arc_cut_trio_long_equal_tips_assembly_complex(g, ug, read_g, reverse_sources, 2, ruIndex, stops_threshold, NULL);
///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);
@@ -13407,7 +13530,7 @@ float drop_ratio, uint32_t trio_flag, float trio_drop_rate)
/**********debug**********/
cur_cons = get_graph_statistic(g);
}
untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, trio_flag, DROP);
untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, trio_flag, DROP, NULL);
if(just_bubble_pop == 0)
{
@@ -13433,7 +13556,7 @@ 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)
float drop_ratio, hc_links* link)
{
#define T_ROUND 2
asg_t *g = ug->g;
@@ -13442,7 +13565,7 @@ float drop_ratio)
redo:
asg_pop_bubble_primary_trio(ug, bubble_dist, (uint32_t)-1, DROP);
untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, (uint32_t)-1, DROP);
untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, (uint32_t)-1, DROP, link);
if(just_bubble_pop == 0)
{
@@ -13460,15 +13583,11 @@ float drop_ratio)
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);
asg_arc_cut_trio_long_equal_tips_assembly(g, ug, read_g, reverse_sources, 2, ruIndex, (uint32_t)-1);
asg_arc_cut_trio_long_tip_primary_complex(g, ug, read_g, reverse_sources, ruIndex,
2, tip_drop_ratio, stops_threshold);
asg_arc_cut_trio_long_equal_tips_assembly_complex(g, ug, read_g, reverse_sources,
2, ruIndex, stops_threshold);
detect_chimeric_by_topo(g, ug, read_g, reverse_sources, 2, stops_threshold, chimeric_rate,
ruIndex);
asg_arc_cut_trio_long_tip_primary(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, link);
asg_arc_cut_trio_long_equal_tips_assembly(g, ug, read_g, reverse_sources, 2, ruIndex, (uint32_t)-1, link);
asg_arc_cut_trio_long_tip_primary_complex(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, stops_threshold, link);
asg_arc_cut_trio_long_equal_tips_assembly_complex(g, ug, read_g, reverse_sources, 2, ruIndex, stops_threshold, link);
detect_chimeric_by_topo(g, ug, read_g, reverse_sources, 2, stops_threshold, chimeric_rate, ruIndex);
if(round != T_ROUND)
{
@@ -13478,7 +13597,7 @@ float drop_ratio)
}
cur_cons = get_graph_statistic(g);
}
untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, (uint32_t)-1, DROP);
untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, (uint32_t)-1, DROP, link);
if(just_bubble_pop == 0)
{
@@ -14011,6 +14130,7 @@ void drop_semi_circle(ma_ug_t *ug, asg_t* nsg, asg_t* read_g, ma_hit_t_alloc* re
{
av[i].del = 1;
asg_arc_del(nsg, av[i].v^1, v^1, 1);
///fprintf(stderr, "****, v>>1: %u, av[i].v>>1: %u\n", v>>1, av[i].v>>1);
}
}
@@ -14152,7 +14272,7 @@ 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, 1);
drop_ratio, 1, 1, NULL);
if(asm_opt.recover_atg_cov_min == -1024)
{
asm_opt.recover_atg_cov_max = asm_opt.hom_global_coverage/HOM_PEAK_RATE;
@@ -14230,7 +14350,7 @@ 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);
drop_ratio, 1, 0, NULL);
///delete_useless_nodes(ug);
delete_useless_trio_nodes(ug, read_g, coverage_cut, sources, ruIndex);
}
@@ -23214,7 +23334,7 @@ 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)
kvec_asg_arc_t_warp* new_rtg_edges, hc_links* link)
{
asg_t* nsg = (*ug)->g;
uint32_t v, n_vtx = nsg->n_seq, k, rId, just_contain;
@@ -23222,10 +23342,23 @@ kvec_asg_arc_t_warp* new_rtg_edges)
///print_utg_coverage(*ug, coverage_cut, 440, sources);
///exit(0);
/**
kvec_t_u32_warp new_rtg_nodes;
kv_init(new_rtg_nodes.a);
**/
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;
link->u_idx[rId] = v;
}
}
}
drop_semi_circle((*ug), nsg, read_g, reverse_sources, ruIndex);
asg_cleanup(nsg);
@@ -23242,7 +23375,7 @@ kvec_asg_arc_t_warp* new_rtg_edges)
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);
chimeric_rate, 0, 0, drop_ratio, link);
delete_useless_nodes(ug);
renew_utg(ug, read_g, new_rtg_edges);
@@ -23254,7 +23387,7 @@ 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, just_contain, 0);
drop_ratio, just_contain, 0, link);
delete_useless_nodes(ug);
renew_utg(ug, read_g, new_rtg_edges);
}
@@ -23277,7 +23410,7 @@ 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, just_contain, 0);
drop_ratio, just_contain, 0, link);
delete_useless_nodes(ug);
renew_utg(ug, read_g, new_rtg_edges);
}
@@ -23287,7 +23420,7 @@ 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, 0, 1);
drop_ratio, 0, 1, link);
}
n_vtx = read_g->n_seq;
@@ -23341,10 +23474,7 @@ kvec_asg_arc_t_warp* new_rtg_edges)
}
recover_utg_by_coverage(ug, read_g, coverage_cut, sources, ruIndex);
/**
kv_destroy(new_rtg_nodes.a);
**/
}
@@ -23414,7 +23544,7 @@ R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ov
adjust_utg_by_primary(&ug, sg, TRIO_THRES, sources, reverse_sources, coverage_cut,
bubble_dist, tipsLen, tip_drop_ratio, stops_threshold, ruIndex, chimeric_rate, drop_ratio,
max_hang, min_ovlp, &new_rtg_edges);
max_hang, min_ovlp, &new_rtg_edges, NULL);
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp);
@@ -27356,7 +27486,9 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
ma_hit_contained_advance(sources, n_read, coverage_cut, ruIndex, max_hang_length, mini_overlap_length);
sg = ma_sg_gen(sources, n_read, coverage_cut, max_hang_length, mini_overlap_length);
///debug_info_of_specfic_node((char*)"m64062_190804_172951/130483063/ccs", sg, ruIndex, (char*)"sbsbsb");
///debug_info_of_specfic_node((char*)"m64043_200504_050026/93784180/ccs", sg, ruIndex, (char*)"sbsbsb");
asg_arc_del_trans(sg, gap_fuzz);
@@ -27371,8 +27503,9 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
}
asg_cut_tip(sg, asm_opt.max_short_tip);
///debug_info_of_specfic_node("m64062_190803_042216/15205346/ccs", sg, "inner_1");
///debug_info_of_specfic_node("m64043_200505_112554/8849050/ccs", sg, "inner_1");
///drop_inexact_edegs_at_bubbles(sg, bubble_dist);
if(clean_round > 0)
{
@@ -27587,7 +27720,6 @@ long long bubble_dist, int read_graph, int write)
}
///debug_info_of_specfic_read("m64062_190803_042216/177341795/ccs", sources, reverse_sources, -1, "beg");
// debug_info_of_specfic_read("m64062_190807_194840/126682874/ccs", sources, reverse_sources, -1, "beg");
if (!(asm_opt.flag & HA_F_BAN_ASSEMBLY))
{