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r317

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chhylp123
2021-03-27 02:46:48 -04:00
parent 24a19d7976
commit 0605aa1961
6 changed files with 371 additions and 209 deletions
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CommandLines.h
+1 -1
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@@ -3,7 +3,7 @@
#include <pthread.h>
#define HA_VERSION "0.14.2-r316"
#define HA_VERSION "0.14.2-r317"
#define VERBOSE 0
Overlaps.cpp
+194 -150
View File
@@ -11319,6 +11319,7 @@ void collect_trans_cov(const char* cmd, buf_t* pri, buf_t* aux, ma_ug_t *ug, asg
if(t_ch)
{
t_ch->is_r_het[(ori == 1?(u->a[u->n-k-1]>>33):(u->a[k]>>33))] |= P_HET;
c_uId = get_origin_uid((ori == 1?((u->a[u->n-k-1]^(uint64_t)(0x100000000))>>32):(u->a[k]>>32)),
t_ch);
if(c_uId == (uint32_t)-1 || p_uId == c_uId) continue;
@@ -11344,6 +11345,7 @@ void collect_trans_cov(const char* cmd, buf_t* pri, buf_t* aux, ma_ug_t *ug, asg
if(t_ch)
{
t_ch->is_r_het[(ori == 1?(u->a[u->n-k-1]>>33):(u->a[k]>>33))] |= P_HET;
c_uId = get_origin_uid((ori == 1?((u->a[u->n-k-1]^(uint64_t)(0x100000000))>>32):(u->a[k]>>32)),
t_ch);
if(c_uId == (uint32_t)-1 || p_uId == c_uId) continue;
@@ -11709,9 +11711,9 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, int max_hang, int min_ovlp)
kv_destroy(new_rtg_edges.a);
}
void classify_untigs(ma_ug_t *ug, asg_t *sg, ma_sub_t* coverage_cut,
void classify_untigs_debug(ma_ug_t *ug, asg_t *sg, ma_sub_t* coverage_cut,
ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex,
kvec_asg_arc_t_warp* new_rtg_edges, int max_hang, int min_ovlp)
kvec_asg_arc_t_warp* new_rtg_edges, int max_hang, int min_ovlp, trans_chain* t_ch)
{
uint64_t i, dip_thre_max, dip_thres, n_utg;
uint8_t* primary_flag = (uint8_t*)calloc(sg->n_seq, sizeof(uint8_t));
@@ -11724,12 +11726,13 @@ kvec_asg_arc_t_warp* new_rtg_edges, int max_hang, int min_ovlp)
purge_dups(ug, sg, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges,
asm_opt.purge_simi_thres, asm_opt.purge_overlap_len, max_hang, min_ovlp, 0, 0, 1, cov, 0);
dip_thre_max = ((double)asm_opt.hom_global_coverage)/((double)HOM_PEAK_RATE);
asm_opt.hom_global_coverage = -1;
}
else
{
dip_thre_max = asm_opt.hom_global_coverage;
}
dip_thre_max *= 0.70;
dip_thre_max *= 0.75;
for (i = 0; i < ug->g->n_seq; i++)
{
@@ -11748,100 +11751,182 @@ kvec_asg_arc_t_warp* new_rtg_edges, int max_hang, int min_ovlp)
{
ug->g->seq[i].c = 0;
}
uint32_t flag = get_unitig_het_arb(&ug->u.a[i], t_ch->is_r_het, 2, 1, 0);
if(flag != ug->g->seq[i].c)
{
if(flag == 0 || ug->g->seq[i].c == 0) fprintf(stderr, "Attention\n");
fprintf(stderr, "utg%.6lul, flag: %u, ug->g->seq[i].c: %u\n", i+1, flag, ug->g->seq[i].c);
}
}
free(primary_flag);
destory_hap_cov_t(&cov);
///fprintf(stderr, "[M::%s] diploid coverage threshold: %lu\n", __func__, dip_thres);
fprintf(stderr, "[M::%s] diploid coverage threshold: %lu\n", __func__, dip_thre_max);
exit(0);
}
void update_hc_links_by_trans_chain(trans_chain* t_ch)
void set_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,
trans_chain* t_ch, long long het_cov_thres)
{
if(t_ch == NULL) return;
///fprintf(stderr, "sbsbsbsbsbsb1sbsbsbsbsbsb, l0_chain: %u, chain_num: %u\n", t_ch->l0_chain, t_ch->chain_num);
uint32_t i, k, *x = NULL, x_occ, *y = NULL, y_occ, x_k, y_k;
memset(t_ch->is_het, 0, t_ch->u_num);
for (i = 0; i < t_ch->l0_chain; i++)
ma_utg_t *u = &(ug->u.a[uID]);
uint32_t k, j, rId, tn, is_Unitig;
long long R_bases = 0, C_bases = 0;
long long cov_in_s, cov_in_e, cov_out_s, cov_out_e, cov_in, cov_out, try_cov, cen_cov;
uint32_t nv, i;
asg_arc_t *av = NULL;
ma_hit_t *h;
if(u->m == 0) return;
///set
for (k = 0; k < u->n; k++)
{
x_occ = y_occ = 0;
get_chain_trans(t_ch, i, &x, &x_occ, &y, &y_occ);
rId = u->a[k]>>33;
r_flag[rId] = 1;
}
for (k = x_k = 0; k < x_occ; k++)
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++)
{
if(x[k] == (uint32_t)-1) continue;
x_k++;
}
for (k = y_k = 0; k < y_occ; k++)
{
if(y[k] == (uint32_t)-1) continue;
y_k++;
}
if(x_k == 0 || y_k == 0)
{
for (k = 0; k < x_occ; k++) x[k] = (uint32_t)-1;
for (k = 0; k < y_occ; k++) y[k] = (uint32_t)-1;
}
else
{
for (k = 0; k < x_occ; k++)
u = &(ug->u.a[av[j].v>>1]);
for (k = 0; k < u->n; k++)
{
if(x[k] == (uint32_t)-1) continue;
t_ch->is_het[x[k]>>1] = 1;
}
for (k = 0; k < y_occ; k++)
{
if(y[k] == (uint32_t)-1) continue;
t_ch->is_het[y[k]>>1] = 1;
rId = u->a[k]>>33;
r_flag[rId] = 2;
}
}
}
/*******************************for debug************************************/
// for (i = 0; i < t_ch->l0_chain; i++)
// {
// x_occ = y_occ = 0;
// get_chain_trans(t_ch, i, &x, &x_occ, &y, &y_occ);
// fprintf(stderr, "\n******x******");
// for (k = 0; k < x_occ; k++)
// {
// fprintf(stderr, "utg%.6ul\t%u\n", (x[k]>>1)+1, x[k]&1);
// }
// fprintf(stderr, "******y******");
// for (k = 0; k < y_occ; k++)
// {
// fprintf(stderr, "utg%.6ul\t%u\n", (y[k]>>1)+1, y[k]&1);
// }
// }
// exit(0);
/*******************************for debug************************************/
u = &(ug->u.a[uID]);
for (k = 0; k < u->n; k++)
{
rId = u->a[k]>>33;
cov_in = cov_out = 0;
cov_in_s = cov_in_e = cov_out_s = cov_out_e = 0;
for (j = 0; j < (uint64_t)(sources[rId].length); j++)
{
h = &(sources[rId].buffer[j]);
///if(h->del) continue;
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] == 0) continue;
if(r_flag[tn] == 1)
{
cov_in += (Get_qe((*h)) - Get_qs((*h)));
if(((Get_qs((*h)) <= coverage_cut[rId].s))) cov_in_s++;
if(((Get_qe((*h)) >= coverage_cut[rId].e))) cov_in_e++;
}
if(r_flag[tn] == 2)
{
cov_out += (Get_qe((*h)) - Get_qs((*h)));
if(((Get_qs((*h)) <= coverage_cut[rId].s))) cov_out_s++;
if(((Get_qe((*h)) >= coverage_cut[rId].e))) cov_out_e++;
}
}
if(cov_out_s >= cov_out_e) ///more out overlap from s
{
cen_cov = cov_in_e;
try_cov = cov_in_s + cov_out_s;
}
else ///more out overlap from e
{
cen_cov = cov_in_s;
try_cov = cov_in_e + cov_out_e;
}
if(cov_out <= (cov_in*0.1))
{
C_bases = cov_in + cov_out;
R_bases = (coverage_cut[rId].e - coverage_cut[rId].s);
}
else if((try_cov <= cen_cov*1.1) && (MIN(cov_out_s, cov_out_e)<=((MAX(cov_out_s, cov_out_e))*0.2)))
{
C_bases = cov_in + cov_out;
R_bases = (coverage_cut[rId].e - coverage_cut[rId].s);
}
else
{
C_bases = cen_cov;
R_bases = 1;
}
if((R_bases <= 0) || ((C_bases/R_bases) <= het_cov_thres))
{
t_ch->is_r_het[rId] |= C_HET;
}
}
///reset
for (k = 0; k < u->n; k++)
{
rId = u->a[k]>>33;
r_flag[rId] = 0;
}
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] = 0;
}
}
}
}
void check_utg_het(ma_ug_t *ug, asg_t *sg, ma_sub_t* coverage_cut,
void set_r_het_flag(ma_ug_t *ug, asg_t *sg, ma_sub_t* coverage_cut,
ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex,
kvec_asg_arc_t_warp* new_rtg_edges, int max_hang, int min_ovlp, hap_cov_t *cov)
kvec_asg_arc_t_warp* new_rtg_edges, int max_hang, int min_ovlp, trans_chain* t_ch)
{
///set by cov->t_ch
update_hc_links_by_trans_chain(cov->t_ch);
bubble_type bub;
memset(&bub, 0, sizeof(bubble_type));
///set by coverage
classify_untigs(ug, sg, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges, max_hang, min_ovlp);
///set by bubble
identify_bubbles(ug, &bub, cov->t_ch->is_het);
uint32_t i;
for (i = 0; i < ug->g->n_seq; i++)
uint64_t m, dip_thre_max, dip_thres;
uint8_t* primary_flag = (uint8_t*)calloc(sg->n_seq, sizeof(uint8_t));
int is_set = ((asm_opt.hom_global_coverage != -1)? 1 : 0);
if(is_set == 0)
{
if(IF_HOM(i, bub))
{
cov->t_ch->is_het[i] = 0;
}
else
{
cov->t_ch->is_het[i] = 1;
}
hap_cov_t *cov = init_hap_cov_t(ug, sg, sources, ruIndex, reverse_sources, coverage_cut, max_hang, min_ovlp, 0);
purge_dups(ug, sg, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges,
asm_opt.purge_simi_thres, asm_opt.purge_overlap_len, max_hang, min_ovlp, 0, 0, 1, cov, 0);
dip_thre_max = ((double)asm_opt.hom_global_coverage)/((double)HOM_PEAK_RATE);
destory_hap_cov_t(&cov);
asm_opt.hom_global_coverage = -1;
}
destory_bubbles(&bub);
else
{
dip_thre_max = asm_opt.hom_global_coverage;
}
dip_thre_max *= 0.75;
///fprintf(stderr, "dip_thre_max: %lu\n", dip_thre_max);
for (m = 0; m < ug->g->n_seq; m++)
{
dip_thres = dip_thre_max;
///if(ug->u.a[m].n <= dip_thre_max) dip_thres = dip_thre_max * 1.1;
set_ug_coverage_aggressive(ug, m, sg, coverage_cut, sources, ruIndex, primary_flag, t_ch, dip_thres);
}
free(primary_flag);
}
@@ -11855,7 +11940,7 @@ trans_chain* init_trans_chain(ma_ug_t *ug, uint64_t r_num)
kv_init(x->rescue_hom);
MALLOC(x->u_idx, r_num);
memset(x->u_idx, -1, x->r_num*sizeof(uint32_t));
CALLOC(x->is_het, x->u_num);
CALLOC(x->is_r_het, x->r_num);
memset(&(x->b_buf), 0, sizeof(buf_t));
kv_init(x->topo_buf);
kv_init(x->topo_res);
@@ -11909,7 +11994,7 @@ void destory_trans_chain(trans_chain **x)
kv_destroy((*x)->iDXs);
kv_destroy((*x)->rescue_hom);
free((*x)->u_idx);
free((*x)->is_het);
free((*x)->is_r_het);
uint32_t k;
for (k = 0; k < (*x)->bed.n; k++) kv_destroy((*x)->bed.a[k]);
kv_destroy((*x)->bed);
@@ -12105,8 +12190,7 @@ bub_label_t* b_mask_t)
new_rtg_edges.a.n = 0;
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp);
classify_untigs(ug, sg, coverage_cut, sources, reverse_sources, ruIndex, &new_rtg_edges,
max_hang, min_ovlp);
///classify_untigs(ug, sg, coverage_cut, sources, reverse_sources, ruIndex, &new_rtg_edges, max_hang, min_ovlp);
hic_analysis(ug, sg, cov);
destory_hap_cov_t(&cov);
ma_ug_destroy(ug);
@@ -13834,7 +13918,7 @@ float drop_ratio, uint32_t trio_flag, float trio_drop_rate, hap_cov_t *cov)
redo:
///print_untig((ug), 61955, "i-0:", 0);
asg_pop_bubble_primary_trio(ug, NULL, trio_flag, DROP, cov, is_first?0:1);
asg_pop_bubble_primary_trio(ug, NULL, trio_flag, DROP, cov, /**is_first?0:1**/1);
///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);
@@ -13911,14 +13995,14 @@ int just_bubble_pop, float drop_ratio, hap_cov_t *cov)
#define T_ROUND 2
asg_t *g = ug->g;
int round = T_ROUND;
uint32_t is_first = 1;
///uint32_t is_first = 1;
redo:
///print_graph_statistic(g, "beg");
///print_debug_gfa(read_g, ug, coverage_cut, "debug_trans_ovlp_hg002", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);
asg_pop_bubble_primary_trio(ug, NULL, (uint32_t)-1, DROP, cov, is_first?0:1);
asg_pop_bubble_primary_trio(ug, NULL, (uint32_t)-1, DROP, cov, /**is_first?0:1**/1);
///untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, (uint32_t)-1, DROP, cov);
is_first = 0;
///is_first = 0;
if(just_bubble_pop == 0)
{
@@ -14612,10 +14696,13 @@ kvec_asg_arc_t_warp* new_rtg_edges, bub_label_t* b_mask_t)
{
asg_t* nsg = (*ug)->g;
uint32_t v, n_vtx = nsg->n_seq;
ma_ug_t *cov_ug = NULL;
if(asm_opt.purge_level_trio > 0) cov_ug = copy_untig_graph(*ug);
hap_cov_t *cov = init_hap_cov_t(*ug, read_g, sources, ruIndex, reverse_sources,
coverage_cut, max_hang, min_ovlp, asm_opt.purge_level_trio>0?1:0);
if(asm_opt.purge_level_primary > 0)
{
set_r_het_flag(*ug, read_g, coverage_cut, sources, reverse_sources, ruIndex,
new_rtg_edges, max_hang, min_ovlp, cov->t_ch);
}
purge_dups(*ug, read_g, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges,
asm_opt.purge_simi_thres, asm_opt.purge_overlap_len, max_hang, min_ovlp, drop_ratio,
@@ -14655,12 +14742,6 @@ kvec_asg_arc_t_warp* new_rtg_edges, bub_label_t* b_mask_t)
clean_trio_untig_graph(*ug, read_g, coverage_cut, sources, reverse_sources, tipsLen,
tip_drop_ratio, stops_threshold, ruIndex, NULL, NULL, 0, 0, 0, chimeric_rate, 0, 0, drop_ratio, flag, drop_rate, cov);
if(cov_ug)
{
check_utg_het(cov_ug, read_g, coverage_cut, sources, reverse_sources, ruIndex,
new_rtg_edges, max_hang, min_ovlp, cov);
}
///delete_useless_nodes(ug);
delete_useless_trio_nodes(ug, read_g, coverage_cut, sources, ruIndex);
@@ -15251,6 +15332,7 @@ static void asg_bub_backtrack_primary_cov(ma_ug_t *ug, uint32_t v0, buf_t *b, ha
ori = t_ch->b_buf.b.a[i]&1;
for (k = 0; k < p->n; k++)
{
t_ch->is_r_het[(ori == 1?((p->a[p->n-k-1])>>33):(p->a[k]>>33))] |= P_HET;
c_uId = get_origin_uid((ori == 1?((p->a[p->n-k-1]^(uint64_t)(0x100000000))>>32):(p->a[k]>>32)), t_ch);
if(c_uId == (uint32_t)-1 || p_uId == c_uId) continue;
p_uId = c_uId;
@@ -15269,6 +15351,7 @@ static void asg_bub_backtrack_primary_cov(ma_ug_t *ug, uint32_t v0, buf_t *b, ha
ori = t_ch->b_buf.b.a[i]&1;
for (k = 0; k < p->n; k++)
{
t_ch->is_r_het[(ori == 1?((p->a[p->n-k-1])>>33):(p->a[k]>>33))] |= P_HET;
c_uId = get_origin_uid((ori == 1?((p->a[p->n-k-1]^(uint64_t)(0x100000000))>>32):(p->a[k]>>32)), t_ch);
if(c_uId == (uint32_t)-1 || p_uId == c_uId) continue;
p_uId = c_uId;
@@ -15317,6 +15400,7 @@ static void asg_bub_backtrack_primary_cov(ma_ug_t *ug, uint32_t v0, buf_t *b, ha
ori = cov->t_ch->topo_res.a[i]&1;
for (k = 0, p_uId = (uint32_t)-1; k < p->n; k++)
{
t_ch->is_r_het[(ori == 1?((p->a[p->n-k-1])>>33):(p->a[k]>>33))] |= P_HET;
c_uId = get_origin_uid((ori == 1?((p->a[p->n-k-1]^(uint64_t)(0x100000000))>>32):(p->a[k]>>32)), t_ch);
if(c_uId == (uint32_t)-1 || p_uId == c_uId) continue;
p_uId = c_uId;
@@ -15336,6 +15420,7 @@ static void asg_bub_backtrack_primary_cov(ma_ug_t *ug, uint32_t v0, buf_t *b, ha
ori = t_ch->b_buf.b.a[k_i]&1;
for (k = 0; k < p->n; k++)
{
t_ch->is_r_het[(ori == 1?((p->a[p->n-k-1])>>33):(p->a[k]>>33))] |= P_HET;
c_uId = get_origin_uid((ori == 1?((p->a[p->n-k-1]^(uint64_t)(0x100000000))>>32):(p->a[k]>>32)), t_ch);
if(c_uId == (uint32_t)-1 || p_uId == c_uId) continue;
p_uId = c_uId;
@@ -22181,6 +22266,7 @@ void reset_trans_chain(trans_chain* t_ch, ma_utg_t *u)
if(u->n == 0 || u->m == 0) return;
for (k = 0; k < u->n; k++)
{
t_ch->is_r_het[u->a[k]>>33] = N_HET;
c_uId = get_origin_uid(u->a[k]>>32, t_ch);
if(c_uId == (uint32_t)-1) continue;
c_uId >>= 1;
@@ -22415,12 +22501,14 @@ uint32_t collect_p_trans)
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 = NULL;
ma_ug_t *cov_ug = NULL;
if(asm_opt.purge_level_primary > 0) cov_ug = copy_untig_graph(*ug);
cov = init_hap_cov_t(*ug, read_g, sources, ruIndex, reverse_sources,
hap_cov_t *cov = init_hap_cov_t(*ug, read_g, sources, ruIndex, reverse_sources,
coverage_cut, max_hang, min_ovlp, asm_opt.purge_level_primary>0?1:0);
if(asm_opt.purge_level_primary > 0)
{
set_r_het_flag(*ug, read_g, coverage_cut, sources, reverse_sources, ruIndex,
new_rtg_edges, max_hang, min_ovlp, cov->t_ch);
}
adjust_utg_advance(read_g, (*ug), reverse_sources, ruIndex, b_mask_t);
nsg = (*ug)->g;
@@ -22435,14 +22523,9 @@ uint32_t collect_p_trans)
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_ug)
{
check_utg_het(cov_ug, read_g, coverage_cut, sources, reverse_sources, ruIndex,
new_rtg_edges, max_hang, min_ovlp, cov);
}
if(i_cov) goto skip_purge;
///classify_untigs_debug(*ug, read_g, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges, max_hang, min_ovlp, cov->t_ch);
if(asm_opt.purge_level_primary > 0)
{
@@ -22547,15 +22630,12 @@ uint32_t collect_p_trans)
}
}
update_hc_links_by_trans_chain(cov->t_ch);
(*i_cov) = cov;
}
else
{
destory_hap_cov_t(&cov);
}
ma_ug_destroy(cov_ug);
}
}
@@ -26226,52 +26306,16 @@ R_to_U* ruIndex, int max_hang, int min_ovlp, uint32_t backward_steps, uint32_t b
}
void reset_bub(bubble_type* bub, ma_ug_t *ug, asg_t *sg, ma_ug_t *back_ug, trans_chain* back_ug_chain,
R_to_U* ruIndex, ma_sub_t *coverage_cut, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
int max_hang, int min_ovlp, kvec_asg_arc_t_warp* new_rtg_edges)
void reset_bub(bubble_type* bub, ma_ug_t *ug, trans_chain* back_ug_chain, kvec_asg_arc_t_warp* new_rtg_edges)
{
uint32_t v, k, uId, is_Unitig, occ_het;
ma_utg_t *nsu = NULL;
for (v = 0; v < back_ug->g->n_seq; v++)
{
nsu = &(back_ug->u.a[v]);
if(nsu->m == 0) continue;
if(back_ug->g->seq[v].del) continue;
for (k = 0; k < nsu->n; k++)
{
set_R_to_U(ruIndex, nsu->a[k]>>33, v, 1, &(sg->seq[nsu->a[k]>>33].c));
}
}
uint8_t* ug_het_flag = NULL; CALLOC(ug_het_flag, ug->g->n_seq);
for (v = 0; v < ug->g->n_seq; v++)
{
nsu = &(ug->u.a[v]);
for (k = occ_het = 0; k < nsu->n; k++)
{
get_R_to_U(ruIndex, nsu->a[k]>>33, &uId, &is_Unitig);
if(uId == (uint32_t)-1 || is_Unitig != 1) continue;
if(back_ug_chain->is_het[uId]) occ_het++;
}
if(occ_het > (nsu->n*0.8)) ug_het_flag[v] = 1;
}
for (v = 0; v < ruIndex->len; v++)
{
get_R_to_U(ruIndex, v, &uId, &is_Unitig);
if(is_Unitig == 1) ruIndex->index[v] = (uint32_t)-1;
}
destory_bubbles(bub);
memset(bub, 0, sizeof(bubble_type));
new_rtg_edges->a.n = 0;
classify_untigs(ug, sg, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges, max_hang, min_ovlp);
identify_bubbles(ug, bub, ug_het_flag);
///classify_untigs(ug, sg, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges, max_hang, min_ovlp);
identify_bubbles(ug, bub, back_ug_chain->is_r_het);
update_bubble_chain(ug, bub, 0, 1);
resolve_bubble_chain_tangle(ug, bub);
free(ug_het_flag);
// fprintf(stderr, "bub.f_bub: %lu, bub.b_bub: %lu, bub.b_end_bub: %lu, bub.tangle_bub: %lu, bub.cross_bub: %lu\n",
// bub->f_bub, bub->b_bub, bub->b_end_bub, bub->tangle_bub, bub->cross_bub);
}
@@ -26585,7 +26629,7 @@ bub_label_t* b_mask_t)
bubble_type bub;
memset(&bub, 0, sizeof(bubble_type));
copy_ug = copy_untig_graph(ug);
reset_bub(&bub, ug, sg, copy_ug, cov->t_ch, ruIndex, coverage_cut, sources, reverse_sources, max_hang, min_ovlp, &new_rtg_edges);
reset_bub(&bub, ug, cov->t_ch, &new_rtg_edges);
beg_idx = bub.f_bub; occ = bub.b_bub + bub.b_end_bub + bub.tangle_bub;
rescue_bubbles_by_contained_reads(ug, sg, sources, coverage_cut, ruIndex, max_hang, min_ovlp, chainLenThres, beg_idx, occ, &bub, b_mask_t);
///output_unitig_graph(sg, coverage_cut, (char*)"debug_1.rescue", sources, ruIndex, max_hang, min_ovlp);
@@ -26593,14 +26637,14 @@ bub_label_t* b_mask_t)
ma_ug_destroy(ug); ug = NULL; ug = ma_ug_gen_primary(sg, PRIMARY_LABLE);
reset_bub(&bub, ug, sg, copy_ug, cov->t_ch, ruIndex, coverage_cut, sources, reverse_sources, max_hang, min_ovlp, &new_rtg_edges);
reset_bub(&bub, ug, cov->t_ch, &new_rtg_edges);
beg_idx = bub.f_bub; occ = bub.b_bub + bub.b_end_bub + bub.tangle_bub;
rescue_bubbles_by_missing_ovlp(ug, sg, sources, coverage_cut, ruIndex, max_hang, min_ovlp, chainLenThres, beg_idx, occ, &bub, b_mask_t);
///output_unitig_graph(sg, coverage_cut, (char*)"debug_2.hic", sources, ruIndex, max_hang, min_ovlp);
ma_ug_destroy(ug); ug = NULL; ug = ma_ug_gen_primary(sg, PRIMARY_LABLE);
reset_bub(&bub, ug, sg, copy_ug, cov->t_ch, ruIndex, coverage_cut, sources, reverse_sources, max_hang, min_ovlp, &new_rtg_edges);
reset_bub(&bub, ug, cov->t_ch, &new_rtg_edges);
beg_idx = bub.f_bub; occ = bub.b_bub + bub.b_end_bub + bub.tangle_bub;
rescue_bubbles_by_missing_ovlp_backward(ug, sg, sources, coverage_cut, ruIndex, max_hang, min_ovlp, chainLenThres, beg_idx, occ, &bub, b_mask_t);
///output_unitig_graph(sg, coverage_cut, (char*)"debug_3.hic", sources, ruIndex, max_hang, min_ovlp);
@@ -26608,7 +26652,7 @@ bub_label_t* b_mask_t)
if(ha_opt_triobin(&asm_opt))
{
ma_ug_destroy(ug); ug = NULL; ug = ma_ug_gen_primary(sg, PRIMARY_LABLE);
reset_bub(&bub, ug, sg, copy_ug, cov->t_ch, ruIndex, coverage_cut, sources, reverse_sources, max_hang, min_ovlp, &new_rtg_edges);
reset_bub(&bub, ug, cov->t_ch, &new_rtg_edges);
rescue_missing_hap_ovlp(ug, sg, sources, coverage_cut, max_hang, min_ovlp, &bub, gap_fuzz);
}
Overlaps.h
+4 -1
View File
@@ -1053,13 +1053,16 @@ typedef struct{
kvec_t(uint64_t) enzymes;
} hc_links;
#define N_HET 0
#define C_HET 1
#define P_HET 2
typedef struct{
kvec_t(uint32_t) uIDs;
kvec_t(uint32_t) iDXs;
kvec_t(uint32_t) rescue_hom;
uint32_t* u_idx;
uint8_t* is_het;
uint8_t* is_r_het;
uint32_t r_num, u_num;
uint32_t chain_num;
uint32_t l0_chain, l1_chain;
Purge_Dups.cpp
+139 -16
View File
@@ -114,7 +114,7 @@ typedef struct {
uint32_t baseBeg, baseEnd;
uint32_t nodeBeg, nodeEnd;
uint32_t h_lev_idx;
uint32_t b_ug_id, c_ug_id;
uint32_t h_status, c_ug_id;
}p_node_t;
typedef struct {
@@ -3303,10 +3303,6 @@ double filter_rate)
/*******************************for debug************************************/
for (v = 0; v < all_ovlp->num; v++)
{
uId = v;
@@ -3324,7 +3320,7 @@ double filter_rate)
ovlp = ((MIN(qe, ae) >= MAX(qs, as))? MIN(qe, ae) - MAX(qs, as) + 1 : 0);
if(homLen + hetLen > 0 && ovlp == 0) break;
if(ovlp == 0) continue;
if(cov->t_ch->is_het[a[k].b_ug_id>>1] == 0)
if(a[k].h_status == N_HET)
{
homLen += ovlp;
}
@@ -3354,7 +3350,7 @@ double filter_rate)
ovlp = ((MIN(te, ae) >= MAX(ts, as))? MIN(te, ae) - MAX(ts, as) + 1 : 0);
if(homLen + hetLen > 0 && ovlp == 0) break;
if(ovlp == 0) continue;
if(cov->t_ch->is_het[a[k].b_ug_id>>1] == 0)
if(a[k].h_status == N_HET)
{
homLen += ovlp;
}
@@ -5187,10 +5183,10 @@ uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans)
destory_hap_alignment_struct_pip(&hap_buf);
}
void debug_p_g_t(p_g_t* pg, asg_t *read_g)
void debug_p_g_t(p_g_t* pg, hap_cov_t *cov, asg_t *read_g)
{
fprintf(stderr, "----------[M::%s]----------\n", __func__);
uint32_t i, offset, v, sid, eid, spos, epos, puid, occ;
uint32_t i, offset, v, sid, eid, spos, epos, p_status, p_uid, occ;
p_node_t *t = NULL;
ma_utg_t *u = NULL;
p_node_t *a = NULL;
@@ -5207,7 +5203,7 @@ void debug_p_g_t(p_g_t* pg, asg_t *read_g)
}
for (v = 0, puid = (uint32_t)-1; v < pg->pg_het_node.n; v++)
for (v = 0, p_status = (uint32_t)-1, p_uid = (uint32_t)-1; v < pg->pg_het_node.n; v++)
{
t = &(pg->pg_het_node.a[v]);
sid = t->nodeBeg;
@@ -5217,9 +5213,12 @@ void debug_p_g_t(p_g_t* pg, asg_t *read_g)
// fprintf(stderr, "sid: %u, eid: %u, spos: %u, epos: %u, t->b_ug_id: %u\n",
// sid, eid, spos, epos, (uint32_t)t->b_ug_id);
// fprintf(stderr, "pg->pg_het_node.n: %u\n", (uint32_t)pg->pg_het_node.n);
if(puid == t->b_ug_id) fprintf(stderr, "ERROR-(-1)\n");
if(t->b_ug_id == (uint32_t)-1) fprintf(stderr, "ERROR-(-2)\n");
puid = t->b_ug_id;
if(p_uid == t->c_ug_id && p_status == t->h_status)
{
fprintf(stderr, "ERROR-(-1)\n");
}
p_status = t->h_status;
p_uid = t->c_ug_id;
u = &(pg->ug->u.a[t->c_ug_id]);
///fprintf(stderr, "u->n: %u, sid: %u, eid: %u\n", (uint32_t)u->n, sid, eid);
@@ -5242,14 +5241,45 @@ void debug_p_g_t(p_g_t* pg, asg_t *read_g)
}
}
offset += (uint32_t)u->a[i];
if(i >= sid && i <= eid)
{
if((!!cov->t_ch->is_r_het[u->a[i]>>33]) != t->h_status)
{
fprintf(stderr, "ERROR-(-3): is_r_het: %u, h_status: %u\n", cov->t_ch->is_r_het[u->a[i]>>33], t->h_status);
}
}
}
}
}
p_g_t *init_p_g_t(ma_ug_t *ug, hap_cov_t *cov, asg_t *read_g)
void print_p_g_t_interval(p_g_t* pg, hap_cov_t *cov)
{
fprintf(stderr, "----------[M::%s]----------\n", __func__);
uint32_t i, v, sid, eid;
p_node_t *t = NULL;
ma_utg_t *u = NULL;
for (v = 0; v < pg->pg_het_node.n; v++)
{
t = &(pg->pg_het_node.a[v]);
sid = t->nodeBeg;
eid = t->nodeEnd;
u = &(pg->ug->u.a[t->c_ug_id]);
fprintf(stderr, "\nu->n=%u, sid=%u, eid=%u, h_status=%u\n",
(uint32_t)u->n, sid, eid, t->h_status);
for (i = sid; i <= eid; i++)
{
fprintf(stderr, "id:i:%u------>utg%.6ul\n",
(uint32_t)(u->a[i]>>33), (get_origin_uid(u->a[i]>>32, cov->t_ch)>>1)+1);
}
}
fprintf(stderr, "----------[M::%s]----------\n", __func__);
}
/**
p_g_t *init_p_g_t_back(ma_ug_t *ug, hap_cov_t *cov, asg_t *read_g)
{
uint32_t v, uId, k_uId, l_uid, k, l, offset, l_pos, g_beg_idx, occ, ovlp, tLen, zLen;
p_g_t *pg = NULL; CALLOC(pg, 1);
@@ -5356,6 +5386,99 @@ p_g_t *init_p_g_t(ma_ug_t *ug, hap_cov_t *cov, asg_t *read_g)
return pg;
}
**/
p_g_t *init_p_g_t(ma_ug_t *ug, hap_cov_t *cov, asg_t *read_g)
{
uint32_t v, uId, k, l, offset, l_pos, g_beg_idx, occ, ovlp, tLen, zLen;
p_g_t *pg = NULL; CALLOC(pg, 1);
pg->ug = ug;
asg_t* nsg = pg->ug->g;
ma_utg_t *u = NULL;
p_node_t *t = NULL, *z = NULL;
asg_arc_t *e = NULL;
p_g_in_t *x = NULL;
pg->pg_het = asg_init();
pg->pg_h_lev = asg_init();
kv_init(pg->pg_het_node);
kv_init(pg->pg_h_lev_idx);
for (v = 0; v < nsg->n_seq; v++)
{
uId = v;
if(nsg->seq[uId].del || nsg->seq[uId].c == ALTER_LABLE)
{
asg_seq_set(pg->pg_h_lev, uId, 0, 1);
pg->pg_h_lev->seq[uId].c = ALTER_LABLE;
continue;
}
asg_seq_set(pg->pg_h_lev, uId, ug->u.a[uId].len, 0);
pg->pg_h_lev->seq[uId].c = PRIMARY_LABLE;
}
for (v = 0; v < nsg->n_seq; v++)
{
uId = v;
if(nsg->seq[uId].del || nsg->seq[uId].c == ALTER_LABLE) continue;
u = &(ug->u.a[uId]);
g_beg_idx = pg->pg_het_node.n;
///fprintf(stderr, "\n+v: %u, pg->pg_het_node.n: %u\n", v, (uint32_t)pg->pg_het_node.n);
for (k = 1, l = 0, offset = 0, l_pos = 0; k <= u->n; ++k)
{
///if(k < u->n && cov->t_ch->is_r_het[u->a[k]>>33] == 0) fprintf(stderr, "sbsbs-uId=%u\n", uId);
if (k == u->n || (!!cov->t_ch->is_r_het[u->a[k]>>33]) != (!!cov->t_ch->is_r_het[u->a[l]>>33]))
{
kv_pushp(p_node_t, pg->pg_het_node, &t);
t->c_ug_id = uId;
t->h_status = (!!cov->t_ch->is_r_het[u->a[l]>>33]);
t->baseBeg = l_pos;
t->baseEnd = offset + read_g->seq[u->a[k-1]>>33].len - 1;
t->nodeBeg = l;
t->nodeEnd = k - 1;
///if(t->b_ug_id == (uint32_t)-1) fprintf(stderr, "xxxx\n");
asg_seq_set(pg->pg_het, pg->pg_het_node.n-1, t->baseEnd+1-t->baseBeg, 0);
///fprintf(stderr, "l: %u, k: %u, u->n: %u, t->h_status: %u\n", l, k, u->n, t->h_status);
l = k;
l_pos = offset + (uint32_t)u->a[k-1];
}
offset += (uint32_t)u->a[k-1];
}
occ = pg->pg_het_node.n - g_beg_idx;
kv_pushp(p_g_in_t, pg->pg_h_lev_idx, &x);
x->beg = g_beg_idx; x->occ = occ;
///fprintf(stderr, "-v: %u, pg->pg_het_node.n: %u\n", v, (uint32_t)pg->pg_het_node.n);
if(occ > 1)
{
for (k = g_beg_idx; (k + 1) < pg->pg_het_node.n; ++k)
{
t = &(pg->pg_het_node.a[k]); tLen = t->baseEnd + 1 - t->baseBeg;
z = &(pg->pg_het_node.a[k+1]); zLen = z->baseEnd + 1 - z->baseBeg;
ovlp = ((MIN(t->baseEnd, z->baseEnd) >= MAX(t->baseBeg, z->baseBeg))?
MIN(t->baseEnd, z->baseEnd) - MAX(t->baseBeg, z->baseBeg) + 1 : 0);
e = asg_arc_pushp(pg->pg_het);
e->ol = ovlp;
e->ul = (k<<1); e->ul <<= 32; e->ul += (tLen - ovlp);
e->v = ((k+1)<<1); e->del = 0; e->el = e->no_l_indel = e->strong = 1;
e = asg_arc_pushp(pg->pg_het);
e->ol = ovlp;
e->ul = ((k+1)<<1)+1; e->ul <<= 32; e->ul += (zLen - ovlp);
e->v = (k<<1)+1; e->del = 0; e->el = e->no_l_indel = e->strong = 1;
}
}
}
asg_cleanup(pg->pg_het);
///debug_p_g_t(pg, cov, read_g);
///print_p_g_t_interval(pg, cov);
return pg;
}
void destory_p_g_t(p_g_t **pg)
{
hic.cpp
+31 -40
View File
@@ -2564,8 +2564,31 @@ void dfs_bubble(asg_t *g, kvec_t_u32_warp* stack, kvec_t_u32_warp* result, uint3
}
}
uint32_t get_unitig_het_arb(ma_utg_t* u, uint8_t *r_het_flag, uint32_t m_het_label, uint32_t p_het_label, uint32_t n_het_label)
{
uint32_t k, rId;
uint32_t het_occ, hom_occ;
for (k = 0, het_occ = hom_occ = 0; k < u->n; k++)
{
rId = u->a[k]>>33;
if((r_het_flag[rId] & P_HET)) return m_het_label;
if((r_het_flag[rId] & C_HET) || (r_het_flag[rId] & P_HET))
{
het_occ++;
}
else
{
hom_occ++;
}
}
if((het_occ+hom_occ) == 0) return n_het_label; ///hom
if(het_occ > ((het_occ+hom_occ)*0.8)) return m_het_label; ///must het
if(het_occ >= hom_occ) return p_het_label; ///potential het
return n_het_label; ///hom
}
void update_bub_b_s_idx(bubble_type* bub);
void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *het_flag)
void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *r_het_flag)
{
asg_cleanup(ug->g);
if (!ug->g->is_symm) asg_symm(ug->g);
@@ -2586,16 +2609,7 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *het_flag)
memset(bub->b_s_idx.a, -1, bub->b_s_idx.n * sizeof(uint64_t));
CALLOC(bub->index, n_vtx);
for (i = 0; i < ug->g->n_seq; i++)
{
if(ug->g->seq[i].c > 0)
{
bub->index[i] = (ug->g->seq[i].c << 2);
ug->g->seq[i].c = 0;
}
}
for (i = 0; i < ug->g->n_seq; i++) ug->g->seq[i].c = 0;
for (v = 0; v < n_vtx; ++v)
{
@@ -2636,7 +2650,6 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *het_flag)
if((result.a.n + 3) != b.b.n && (result.a.n + 2) != b.b.n) break;
}
}
if(i == b.b.n)
{
@@ -2675,26 +2688,11 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *het_flag)
kv_push(uint32_t, bub->num, bub->list.n);
free(b.a); free(b.S.a); free(b.T.a); free(b.b.a); free(b.e.a);
bub->f_bub = bub->num.n - 1; ///bub->s_bub = bub->num.n - 1;
for (i = 0; i < ug->g->n_seq; i++)
{
if((bub->index[i]>>2) == 0)
{
bub->index[i] = (uint32_t)-1; ///hom
}
else
{
if((bub->index[i]>>2) == 1)
{
bub->index[i] = P_het(*bub); ///potential het
}
else
{
bub->index[i] = M_het(*bub); ///must het
}
}
}
for (i = 0; i < ug->g->n_seq; i++)
{
bub->index[i] = get_unitig_het_arb(&(ug->u.a[i]), r_het_flag, M_het(*bub), P_het(*bub), (uint32_t)-1);
}
for (i = 0; i < bub->f_bub; i++)
{
@@ -2747,13 +2745,6 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *het_flag)
for (i = 0; i < ug->g->n_seq; i++)
{
if(bub->index[i] == M_het(*bub)) bub->index[i] = P_het(*bub);
if(bub->index[i] > P_het(*bub))
{
if(het_flag && het_flag[i])
{
bub->index[i] = P_het(*bub);
}
}
}
}
else
@@ -13223,7 +13214,7 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
bub.round_id = 0; bub.n_round = 2;
for (bub.round_id = 0; bub.round_id < bub.n_round; bub.round_id++)
{
identify_bubbles(idx->ug, &bub, idx->cov->t_ch->is_het);
identify_bubbles(idx->ug, &bub, idx->cov->t_ch->is_r_het);
if(bub.round_id == 0)
{
collect_hc_links(sl.idx, &sl.hits, &link, &bub, &M);
hic.h
+2 -1
View File
@@ -62,11 +62,12 @@ void get_bubbles(bubble_type* bub, uint64_t id, uint32_t* beg, uint32_t* sink, u
int load_hc_links(hc_links* link, const char *fn);
void write_hc_links(hc_links* link, const char *fn);
void destory_bubbles(bubble_type* bub);
void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *het_flag);
void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *r_het_flag);
void resolve_bubble_chain_tangle(ma_ug_t* ug, bubble_type* bub);
uint32_t connect_bub_occ(bubble_type* bub, uint32_t root_id, uint32_t check_het);
void get_bub_id(bubble_type* bub, uint32_t root, uint64_t* id0, uint64_t* id1, uint32_t check_het);
void update_bubble_chain(ma_ug_t* ug, bubble_type* bub, uint32_t is_middle, uint32_t is_end);
void set_b_utg_weight_flag(bubble_type* bub, buf_t* b, uint32_t v, uint8_t* vis_flag, uint32_t flag, uint32_t* occ);
uint32_t get_unitig_het_arb(ma_utg_t* u, uint8_t *r_het_flag, uint32_t m_het_label, uint32_t p_het_label, uint32_t n_het_label);
#endif