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chhylp123
2021-05-31 18:16:20 -04:00
parent aa164949f2
commit ca67e7a9b3
2 changed files with 113 additions and 11 deletions
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2
CommandLines.h
View File

@@ -4,7 +4,7 @@
#include <pthread.h>
#include <stdint.h>
#define HA_VERSION "0.15.1-r334"
#define HA_VERSION "0.15.1-r336"
#define VERBOSE 0

122
Overlaps.cpp
View File

@@ -13111,6 +13111,104 @@ trans_chain* load_hc_trans(const char *fn)
return t_ch;
}
void hic_clean(asg_t* read_g)
{
uint32_t n_vtx, v, u;
uint64_t i, k, k_i, tLen, v_occ, u_occ, utg_occ;
double bub_rate = 0.1;
ma_ug_t *ug = NULL;
ug = ma_ug_gen_primary(read_g, PRIMARY_LABLE);
n_vtx = ug->g->n_seq * 2;
buf_t b; memset(&b, 0, sizeof(buf_t)); b.a = (binfo_t*)calloc(n_vtx, sizeof(binfo_t));
///for (i = 0, tLen = 1; i < ug->u.n; i++) tLen += ug->u.a[i].len;
tLen = get_bub_pop_max_dist_advance(ug->g, &b);
uint8_t* bs_flag = (uint8_t*)calloc(n_vtx, 1);
kvec_t(uint32_t) ax;
kv_init(ax);
for (v = 0; v < ug->g->n_seq; ++v)
{
if(ug->g->seq[v].del) continue;
ug->g->seq[v].c = PRIMARY_LABLE;
EvaluateLen(ug->u, v) = ug->u.a[v].n;
}
for (v = 0; v < n_vtx; ++v)
{
if(ug->g->seq[v>>1].del) continue;
if(asg_arc_n(ug->g, v) < 2) continue;
if(bs_flag[v] != 0) continue;
if(asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, NULL, NULL, NULL, 0, 0, NULL))
{
//beg is v, end is b.S.a[0]
//note b.b include end, does not include beg
for (i = 0; i < b.b.n; i++)
{
if(b.b.a[i]==v || b.b.a[i]==b.S.a[0]) continue;
bs_flag[b.b.a[i]] = bs_flag[b.b.a[i]^1] = 1;
}
bs_flag[v] = 2; bs_flag[b.S.a[0]^1] = 3;
}
}
for (v = 0; v < n_vtx; ++v)
{
if(bs_flag[v] !=2) continue;
if(asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, NULL, NULL, NULL, 0, 0, NULL))
{
//note b.b include end, does not include beg
for (i = v_occ = ax.n = 0; i < b.b.n; i++)
{
if(b.b.a[i]==v || b.b.a[i]==b.S.a[0]) continue;
v_occ += ug->u.a[b.b.a[i]>>1].n;
kv_push(uint32_t, ax, b.b.a[i]>>1);
}
for (i = 0; i < ax.n; i++)
{
for (k = 0; k < 2; k++)
{
u = (ax.a[i]<<1) + k;
if(asg_arc_n(ug->g, u) < 2) continue;
if(asg_bub_pop1_primary_trio(ug->g, NULL, u, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, NULL, NULL, NULL, 0, 0, NULL))
{
for (k_i = u_occ = utg_occ = 0; k_i < b.b.n; k_i++)
{
if(b.b.a[k_i]==u || b.b.a[k_i]==b.S.a[0]) continue;
u_occ += ug->u.a[b.b.a[k_i]>>1].n;
utg_occ++;
}
if(u_occ >= v_occ*bub_rate) continue;
if(u_occ > 3) continue;
if(utg_occ > 2) continue;
asg_bub_pop1_primary_trio(ug->g, NULL, u, tLen, &b, (uint32_t)-1, (uint32_t)-1, 1, NULL, NULL, NULL, 0, 0, NULL);
}
}
}
}
}
ma_utg_t* m = NULL;
for (v = 0; v < ug->g->n_seq; ++v)
{
if(ug->g->seq[v].del) continue;
if(ug->g->seq[v].c != ALTER_LABLE) continue;
m = &(ug->u.a[v]);
if(m->m == 0) continue;
for (k = 0; k < m->n; k++)
{
asg_seq_del(read_g, m->a[k]>>33);
}
}
asg_cleanup(read_g);
free(b.a); free(b.S.a); free(b.T.a); free(b.b.a); free(b.e.a); free(bs_flag);
ma_ug_destroy(ug);
kv_destroy(ax);
}
void output_contig_graph_alternative(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name,
ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp);
void clean_u_trans_t_idx(kv_u_trans_t *ta, ma_ug_t *ug, asg_t *read_g);
@@ -13120,6 +13218,7 @@ 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,
long long gap_fuzz, bub_label_t* b_mask_t)
{
hic_clean(sg);
ug_opt_t opt; memset(&opt, 0, sizeof(opt));
opt.coverage_cut = coverage_cut;
opt.sources = sources;
@@ -14101,6 +14200,7 @@ 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,
bub_label_t* b_mask_t)
{
hic_clean(sg);
kvec_asg_arc_t_warp new_rtg_edges;
kv_init(new_rtg_edges.a);
ma_ug_t *ug = NULL;
@@ -14747,7 +14847,7 @@ asg_t *read_sg, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex, uint32_t min_e
if(operation == CUT) break;
if(aw[i].del) continue;
if(aw[i].v == (b.b.a[b.b.n-1]^1)) continue;
inner_flag = check_different_haps_base(g, ug, read_sg, b.b.a[b.b.n-1]^1, aw[i].v,
inner_flag = /**check_different_haps_base**/check_different_haps(g, ug, read_sg, b.b.a[b.b.n-1]^1, aw[i].v,
reverse_sources, &b_0, &b_1, ruIndex, min_edge_length, 1);
if(inner_flag == NON_PLOID) operation = CUT;
}
@@ -14880,7 +14980,7 @@ R_to_U* ruIndex, uint32_t min_edge_length, float drop_ratio, hap_cov_t *cov, utg
n_reduced++;
operation = TRIM;
flag = check_different_haps_base(g, ug, read_sg, av[v_maxLen_i].v, av[i].v,
flag = /**check_different_haps_base**/check_different_haps(g, ug, read_sg, av[v_maxLen_i].v, av[i].v,
reverse_sources, &b_0, &b_1, ruIndex, min_edge_length, 1);
// #define UNAVAILABLE (uint32_t)-1
// #define PLOID 0
@@ -14987,7 +15087,7 @@ R_to_U* ruIndex, uint32_t min_edge_length, float drop_ratio, uint32_t stops_thre
{
n_reduced++;
operation = TRIM;
flag = check_different_haps_base(g, ug, read_sg, a_convex[convex_i].v, a_convex[i].v,
flag = /**check_different_haps_base**/check_different_haps(g, ug, read_sg, a_convex[convex_i].v, a_convex[i].v,
reverse_sources, &b_0, &b_1, ruIndex, min_edge_length, stops_threshold);
// #define UNAVAILABLE (uint32_t)-1
// #define PLOID 0
@@ -15181,7 +15281,7 @@ hap_cov_t *cov, utg_trans_t *o)
if(return_flag != END_TIPS) continue;
flag = check_different_haps_base(g, ug, read_sg, av[base_maxLen_i].v, av[i].v,
flag = /**check_different_haps_base**/check_different_haps(g, ug, read_sg, av[base_maxLen_i].v, av[i].v,
reverse_sources, &b_0, &b_1, ruIndex, miniedgeLen, 1);
// if((av[i].v>>1) == 255 && (av[base_maxLen_i].v>>1) == 33)
@@ -15507,7 +15607,9 @@ hap_cov_t *cov, utg_trans_t *o)
if(ll>convexLen && max_stop_baseLen>=ll*MAX_STOP_RATE)
{
flag = check_different_haps_base(g, ug, read_sg, a_convex[convex_i].v, a_convex[i].v,
// flag = check_different_haps(g, ug, read_sg, a_convex[convex_i].v, a_convex[i].v,
// reverse_sources, &b_0, &b_1, ruIndex, miniedgeLen, stops_threshold);
flag = /**check_different_haps_base**/check_different_haps(g, ug, read_sg, a_convex[convex_i].v, a_convex[i].v,
reverse_sources, &b_0, &b_1, ruIndex, miniedgeLen, stops_threshold);
// #define UNAVAILABLE (uint32_t)-1
// #define PLOID 0
@@ -15651,7 +15753,7 @@ R_to_U* ruIndex, utg_trans_t *o)
}
if(k != b_0.b.n) break;
if(check_different_haps_base(g, ug, read_sg, wv, aw[i].v, reverse_sources, &b_0, &b_1,
if(/**check_different_haps_base**/check_different_haps(g, ug, read_sg, wv, aw[i].v, reverse_sources, &b_0, &b_1,
ruIndex, miniedgeLen, stops_threshold)==PLOID)
{
break;
@@ -15697,7 +15799,7 @@ R_to_U* ruIndex, utg_trans_t *o)
}
if(k != b_0.b.n) break;
if(check_different_haps_base(g, ug, read_sg, wv, aw[i].v, reverse_sources, &b_0, &b_1,
if(/**check_different_haps_base**/check_different_haps(g, ug, read_sg, wv, aw[i].v, reverse_sources, &b_0, &b_1,
ruIndex, miniedgeLen, stops_threshold)==PLOID)
{
break;
@@ -16651,7 +16753,7 @@ void drop_semi_circle(ma_ug_t *ug, asg_t* nsg, asg_t* read_g, ma_hit_t_alloc* re
}
get_real_length(nsg, convex_f, &convex_f);
if(convex_f != convex_b) continue;
if(check_different_haps_base(nsg, ug, read_g, v^1, av[i].v,
if(/**check_different_haps_base**/check_different_haps(nsg, ug, read_g, v^1, av[i].v,
reverse_sources, &b_0, &b_1, ruIndex, 2, 1) == PLOID)
{
av[i].del = 1;
@@ -20280,7 +20382,7 @@ uint32_t* r_next_uID, R_to_U* ruIndex)
// #define UNAVAILABLE (uint32_t)-1
// #define PLOID 0
// #define NON_PLOID 1
if(returnFlag == 1 && check_different_haps_base(nsg, ug, read_g, beg, next_uID,
if(returnFlag == 1 && /**check_different_haps_base**/check_different_haps(nsg, ug, read_g, beg, next_uID,
reverse_sources, b_0, b_1, ruIndex, minLongUntig-1, 1) == PLOID)
{
///output_tangles(beg, next_uID, u_vecs->a.a, u_vecs->a.n, (char*)("???"));
@@ -23554,7 +23656,7 @@ void unroll_simple_case_advance(ma_ug_t *ug, asg_t* read_g, ma_hit_t_alloc* reve
continue;
}
if(check_different_haps_base(nsg, ug, read_g, beg, end, reverse_sources, &b_0, &b_1,
if(/**check_different_haps_base**/check_different_haps(nsg, ug, read_g, beg, end, reverse_sources, &b_0, &b_1,
ruIndex, 2, 1) == PLOID)
{
continue;