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more accurate purging

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chhylp123
2021-03-26 18:07:30 -04:00
parent d89a630ff3
commit 24a19d7976
4 changed files with 446 additions and 138 deletions
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Overlaps.cpp
+145 -89
View File
@@ -11717,15 +11717,20 @@ kvec_asg_arc_t_warp* new_rtg_edges, int max_hang, int min_ovlp)
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, 0);
int tmp_cov = asm_opt.hom_global_coverage;
asm_opt.hom_global_coverage = -1;
int is_set = ((asm_opt.hom_global_coverage != -1)? 1 : 0);
purge_dups(ug, sg, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges,
if(is_set == 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)*0.70;
asm_opt.hom_global_coverage = tmp_cov;
///fprintf(stderr, "dip_thre_max: %lu\n", dip_thre_max);
dip_thre_max = ((double)asm_opt.hom_global_coverage)/((double)HOM_PEAK_RATE);
}
else
{
dip_thre_max = asm_opt.hom_global_coverage;
}
dip_thre_max *= 0.70;
for (i = 0; i < ug->g->n_seq; i++)
{
dip_thres = dip_thre_max;
@@ -11749,6 +11754,96 @@ kvec_asg_arc_t_warp* new_rtg_edges, int max_hang, int min_ovlp)
///fprintf(stderr, "[M::%s] diploid coverage threshold: %lu\n", __func__, dip_thres);
}
void update_hc_links_by_trans_chain(trans_chain* t_ch)
{
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++)
{
x_occ = y_occ = 0;
get_chain_trans(t_ch, i, &x, &x_occ, &y, &y_occ);
for (k = x_k = 0; k < x_occ; k++)
{
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++)
{
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;
}
}
}
/*******************************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************************************/
}
void check_utg_het(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)
{
///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++)
{
if(IF_HOM(i, bub))
{
cov->t_ch->is_het[i] = 0;
}
else
{
cov->t_ch->is_het[i] = 1;
}
}
destory_bubbles(&bub);
}
trans_chain* init_trans_chain(ma_ug_t *ug, uint64_t r_num)
{
@@ -11988,16 +12083,18 @@ bub_label_t* b_mask_t)
hap_cov_t *cov = init_hap_cov_t(ug, sg, sources, ruIndex, reverse_sources, coverage_cut, max_hang, min_ovlp, 1);
hap_cov_t *cov = NULL;
asg_t *copy_sg = copy_read_graph(sg);
ma_ug_t *copy_ug = copy_untig_graph(ug);
///asm_opt.purge_overlap_len = asm_opt.purge_overlap_len_hic;
///asm_opt.purge_simi_thres = asm_opt.purge_simi_rate_hic;
adjust_utg_by_primary(&copy_ug, copy_sg, TRIO_THRES, sources, reverse_sources, coverage_cut,
tipsLen, tip_drop_ratio, stops_threshold, ruIndex, chimeric_rate, drop_ratio,
max_hang, min_ovlp, &new_rtg_edges, cov, b_mask_t, 1);
max_hang, min_ovlp, &new_rtg_edges, &cov, b_mask_t, 1);
ma_ug_destroy(copy_ug);
asg_destroy(copy_sg);
ma_ug_print_bed(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges,
max_hang, min_ovlp, asm_opt.hic_inconsist_rate, NULL, NULL, cov);
@@ -14515,7 +14612,10 @@ 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;
hap_cov_t *cov = init_hap_cov_t(*ug, read_g, sources, ruIndex, reverse_sources, coverage_cut, max_hang, min_ovlp, 0);
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);
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,
@@ -14555,8 +14655,12 @@ 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(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);
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);
@@ -14567,6 +14671,7 @@ kvec_asg_arc_t_warp* new_rtg_edges, bub_label_t* b_mask_t)
renew_utg(ug, read_g, new_rtg_edges);
if (!(asm_opt.flag & HA_F_BAN_POST_JOIN))
{
rescue_missing_overlaps_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang,
@@ -22299,86 +22404,23 @@ ma_hit_t_alloc* sources, R_to_U* ruIndex, trans_chain* t_ch)
ma_ug_destroy(atg);
}
void update_hc_links_by_trans_chain(trans_chain* t_ch)
{
///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++)
{
x_occ = y_occ = 0;
get_chain_trans(t_ch, i, &x, &x_occ, &y, &y_occ);
for (k = x_k = 0; k < x_occ; k++)
{
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++)
{
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;
}
}
}
/*******************************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************************************/
}
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 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, hap_cov_t *i_cov, bub_label_t* b_mask_t,
kvec_asg_arc_t_warp* new_rtg_edges, hap_cov_t **i_cov, bub_label_t* b_mask_t,
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;
if(i_cov == NULL) cov = init_hap_cov_t(*ug, read_g, sources, ruIndex, reverse_sources, coverage_cut, max_hang, min_ovlp, 0);
else cov = i_cov;
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,
coverage_cut, max_hang, min_ovlp, asm_opt.purge_level_primary>0?1:0);
///print_utg_coverage(*ug, coverage_cut, 440, sources);
///exit(0);
// drop_semi_circle((*ug), nsg, read_g, reverse_sources, ruIndex);
// asg_cleanup(nsg);
adjust_utg_advance(read_g, (*ug), reverse_sources, ruIndex, b_mask_t);
nsg = (*ug)->g;
@@ -22394,7 +22436,12 @@ uint32_t collect_p_trans)
delete_useless_nodes(ug);
renew_utg(ug, read_g, new_rtg_edges);
if(i_cov) update_hc_links_by_trans_chain(cov->t_ch);
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;
if(asm_opt.purge_level_primary > 0)
@@ -22490,16 +22537,25 @@ uint32_t collect_p_trans)
recover_utg_by_coverage(ug, read_g, coverage_cut, sources, ruIndex, cov->t_ch);
if(i_cov)
{
update_hc_links_by_trans_chain(cov->t_ch);
if(collect_p_trans)
if(asm_opt.purge_level_primary > 0)
{
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,
0, 0, cov, collect_p_trans);
if(collect_p_trans)
{
// 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,
// 0, 0, cov, collect_p_trans);
}
}
update_hc_links_by_trans_chain(cov->t_ch);
(*i_cov) = cov;
}
else
{
destory_hap_cov_t(&cov);
}
else destory_hap_cov_t(&cov);
ma_ug_destroy(cov_ug);
}
@@ -26514,12 +26570,12 @@ bub_label_t* b_mask_t)
ma_ug_t *ug = NULL;
ug = ma_ug_gen_primary(sg, PRIMARY_LABLE);
hap_cov_t *cov = init_hap_cov_t(ug, sg, sources, ruIndex, reverse_sources, coverage_cut, max_hang, min_ovlp, 1);
hap_cov_t *cov = NULL;
asg_t *copy_sg = copy_read_graph(sg);
ma_ug_t *copy_ug = copy_untig_graph(ug);
adjust_utg_by_primary(&copy_ug, copy_sg, TRIO_THRES, sources, reverse_sources, coverage_cut,
tipsLen, tip_drop_ratio, stops_threshold, ruIndex, chimeric_rate, drop_ratio,
max_hang, min_ovlp, &new_rtg_edges, cov, b_mask_t, 0);
max_hang, min_ovlp, &new_rtg_edges, &cov, b_mask_t, 0);
ma_ug_destroy(copy_ug); copy_ug = NULL;
asg_destroy(copy_sg); copy_sg = NULL;
Overlaps.h
+1 -1
View File
@@ -1104,7 +1104,7 @@ 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 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, hap_cov_t *i_cov, bub_label_t* b_mask_t, uint32_t collect_p_trans);
kvec_asg_arc_t_warp* new_rtg_edges, hap_cov_t **i_cov, bub_label_t* b_mask_t, uint32_t collect_p_trans);
ma_ug_t* copy_untig_graph(ma_ug_t *src);
ma_ug_t* output_trio_unitig_graph(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name,
uint8_t flag, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
Purge_Dups.cpp
+289 -38
View File
@@ -114,14 +114,20 @@ typedef struct {
uint32_t baseBeg, baseEnd;
uint32_t nodeBeg, nodeEnd;
uint32_t h_lev_idx;
uint32_t b_ug_id;
uint32_t b_ug_id, c_ug_id;
}p_node_t;
typedef struct {
uint32_t beg;
uint32_t occ;
}p_g_in_t;
typedef struct {
ma_ug_t *ug;
kvec_t(p_node_t) pg_het_node;
asg_t *pg_het;
asg_t *pg_h_lev;
kvec_t(p_g_in_t) pg_h_lev_idx;
}p_g_t;
void print_peak_line(int c, int x, int exceed, int64_t cnt)
@@ -3269,6 +3275,151 @@ ma_ug_t *ug, asg_t *read_g, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex)
}
}
void get_p_nodes(p_g_t *pg, p_node_t **x, uint32_t *x_occ, uint32_t id)
{
if(x) (*x) = pg->pg_het_node.a + pg->pg_h_lev_idx.a[id].beg;
if(x_occ) (*x_occ) = pg->pg_h_lev_idx.a[id].occ;
}
void normalize_hap_overlaps_advance_by_p_g_t(hap_overlaps_list* all_ovlp, hap_overlaps_list* back_all_ovlp,
ma_ug_t *ug, asg_t *read_g, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex, p_g_t *pg, hap_cov_t *cov,
double filter_rate)
{
hap_overlaps *x = NULL, *y = NULL;
uint32_t v, i, uId, qn, tn;
uint32_t types[4];
types[X2Y] = Y2X; types[Y2X] = X2Y; types[XCY] = YCX; types[YCX] = XCY;
int index;
uint32_t k, qs, qe, ts, te, occ, as, ae, ovlp, hetLen, homLen;
p_node_t *a = NULL;
/*******************************for debug************************************/
// for (v = 0; v < cov->t_ch->u_num; v++)
// {
// fprintf(stderr, "utg%.6ul-is_het=%u\n", v+1, cov->t_ch->is_het[v]);
// }
/*******************************for debug************************************/
for (v = 0; v < all_ovlp->num; v++)
{
uId = v;
for (i = 0; i < all_ovlp->x[uId].a.n; i++)
{
/*****************qn*****************/
qn = all_ovlp->x[uId].a.a[i].xUid;
qs = all_ovlp->x[uId].a.a[i].x_beg_pos;
qe = all_ovlp->x[uId].a.a[i].x_end_pos - 1;
get_p_nodes(pg, &a, &occ, qn);
for (k = 0, hetLen = 0, homLen = 0; k < occ; k++)
{
as = a[k].baseBeg;
ae = a[k].baseEnd;
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)
{
homLen += ovlp;
}
else
{
hetLen += ovlp;
}
}
if(hetLen <= ((hetLen + homLen) * filter_rate))
{
all_ovlp->x[uId].a.a[i].status = DELETE;
continue;
}
/*****************qn*****************/
/*****************tn*****************/
tn = all_ovlp->x[uId].a.a[i].yUid;
ts = all_ovlp->x[uId].a.a[i].y_beg_pos;
te = all_ovlp->x[uId].a.a[i].y_end_pos - 1;
get_p_nodes(pg, &a, &occ, tn);
for (k = 0, hetLen = 0, homLen = 0; k < occ; k++)
{
as = a[k].baseBeg;
ae = a[k].baseEnd;
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)
{
homLen += ovlp;
}
else
{
hetLen += ovlp;
}
}
if(hetLen <= ((hetLen + homLen) * filter_rate))
{
all_ovlp->x[uId].a.a[i].status = DELETE;
continue;
}
/*****************tn*****************/
}
}
for (v = 0; v < all_ovlp->num; v++)
{
uId = v;
k = 0;
for (i = 0; i < all_ovlp->x[uId].a.n; i++)
{
if(all_ovlp->x[uId].a.a[i].status == DELETE) continue;
all_ovlp->x[uId].a.a[k] = all_ovlp->x[uId].a.a[i];
k++;
}
all_ovlp->x[uId].a.n = k;
}
for (v = 0; v < all_ovlp->num; v++)
{
uId = v;
for (i = 0; i < all_ovlp->x[uId].a.n; i++)
{
qn = all_ovlp->x[uId].a.a[i].xUid;
tn = all_ovlp->x[uId].a.a[i].yUid;
x = &(all_ovlp->x[uId].a.a[i]);
index = get_specific_hap_overlap(&(all_ovlp->x[tn]), tn, qn);
if(index != -1)
{
y = &(all_ovlp->x[tn].a.a[index]);
if(x->rev == y->rev && types[x->type]==y->type) continue;
if(x->score >= y->score)
{
kv_push(hap_overlaps, back_all_ovlp->x[tn].a, (*y));
set_reverse_hap_overlap(y, x, types);
}
else
{
kv_push(hap_overlaps, back_all_ovlp->x[qn].a, (*x));
set_reverse_hap_overlap(x, y, types);
}
}
else
{
kv_pushp(hap_overlaps, all_ovlp->x[tn].a, &y);
set_reverse_hap_overlap(y, x, types);
}
}
}
}
void filter_hap_overlaps_by_length(hap_overlaps_list* all_ovlp, uint32_t minLen)
{
if(minLen == 0) return;
@@ -4863,7 +5014,7 @@ int max_hang, int min_ovlp, float drop_ratio)
}
void purge_dups(ma_ug_t *ug, asg_t *read_g, ma_sub_t* coverage_cut, ma_hit_t_alloc* sources,
void purge_dups_back(ma_ug_t *ug, asg_t *read_g, 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* edge, float density,
uint32_t purege_minLen, int max_hang, int min_ovlp, float drop_ratio, uint32_t just_contain,
uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans)
@@ -5036,18 +5187,82 @@ 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)
{
fprintf(stderr, "----------[M::%s]----------\n", __func__);
uint32_t i, offset, v, sid, eid, spos, epos, puid, occ;
p_node_t *t = NULL;
ma_utg_t *u = NULL;
p_node_t *a = NULL;
for (v = 0; v < pg->ug->u.n; v++)
{
///fprintf(stderr, "\nu->n: %u, uid: %u\n", (uint32_t)(pg->ug->u.a[v].n), v);
get_p_nodes(pg, &a, &occ, v);
for (i = 0; i < occ; i++)
{
if(a[i].c_ug_id != v) fprintf(stderr, "sbsbsbsbsb\n");
///fprintf(stderr, "sid: %u, eid: %u\n", a[i].nodeBeg, a[i].nodeEnd);
}
}
for (v = 0, puid = (uint32_t)-1; v < pg->pg_het_node.n; v++)
{
t = &(pg->pg_het_node.a[v]);
sid = t->nodeBeg;
eid = t->nodeEnd;
spos = t->baseBeg;
epos = t->baseEnd;
// 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;
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);
for (i = offset = 0; i < u->n; i++)
{
if(i == sid)
{
if(spos != offset)
{
fprintf(stderr, "ERROR-1\n");
}
}
if(i == eid)
{
if(epos != (offset+read_g->seq[u->a[i]>>33].len - 1))
{
fprintf(stderr, "ERROR-2, real end: %u\n",
(uint32_t)(offset+read_g->seq[u->a[i]>>33].len - 1));
}
}
offset += (uint32_t)u->a[i];
}
}
}
p_g_t *init_p_g_t(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;
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);
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++)
{
@@ -5069,6 +5284,8 @@ p_g_t *init_p_g_t(ma_ug_t *ug, hap_cov_t *cov, asg_t *read_g)
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)
{
l_uid = k_uId = (uint32_t)-1;
@@ -5077,15 +5294,17 @@ p_g_t *init_p_g_t(ma_ug_t *ug, hap_cov_t *cov, asg_t *read_g)
if (k == u->n || k_uId != l_uid)
{
///fprintf(stderr, "l: %u, k: %u, u->n: %u, l_uid: %u\n", l, k, (uint32_t)u->n, l_uid);
if(l_uid != (uint32_t)-1)
{
kv_pushp(p_node_t, pg->pg_het_node, &t);
t->c_ug_id = uId;
t->b_ug_id = l_uid;
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(pg->pg_het_node.n > 1)
if(pg->pg_het_node.n > 1 && pg->pg_het_node.n >= (g_beg_idx + 2))
{
z = &(pg->pg_het_node.a[pg->pg_het_node.n - 2]);
if(t->b_ug_id == z->b_ug_id)
@@ -5093,9 +5312,10 @@ p_g_t *init_p_g_t(ma_ug_t *ug, hap_cov_t *cov, asg_t *read_g)
z->baseEnd = t->baseEnd;
z->nodeEnd = t->nodeEnd;
t = z;
pg->pg_het_node.n--;
}
pg->pg_het_node.n--;
}
///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);
}
l = k;
@@ -5103,20 +5323,59 @@ p_g_t *init_p_g_t(ma_ug_t *ug, hap_cov_t *cov, asg_t *read_g)
}
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, read_g);
return pg;
}
void purge_dups_advance(ma_ug_t *ug, asg_t *read_g, ma_sub_t* coverage_cut, ma_hit_t_alloc* sources,
void destory_p_g_t(p_g_t **pg)
{
if(pg && (*pg))
{
kv_destroy((*pg)->pg_het_node);
kv_destroy((*pg)->pg_h_lev_idx);
asg_destroy((*pg)->pg_het);
asg_destroy((*pg)->pg_h_lev);
free((*pg));
(*pg) = NULL;
}
}
void purge_dups(ma_ug_t *ug, asg_t *read_g, 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* edge, float density,
uint32_t purege_minLen, int max_hang, int min_ovlp, float drop_ratio, uint32_t just_contain,
uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans)
{
asg_t *purge_g = NULL;
purge_g = asg_init();
p_g_t *pg = NULL;
asg_t* nsg = ug->g;
uint32_t v, rId, uId, i, offset;
ma_utg_t* reads = NULL;
@@ -5149,12 +5408,6 @@ uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans)
for (v = 0; v < nsg->n_seq; v++)
{
uId = v;
if(nsg->seq[uId].del || nsg->seq[uId].c == ALTER_LABLE)
{
asg_seq_set(purge_g, uId, 0, 1);
purge_g->seq[uId].c = ALTER_LABLE;
continue;
}
reads = &(ug->u.a[uId]);
for (i = 0, offset = 0; i < reads->n; i++)
{
@@ -5167,9 +5420,6 @@ uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans)
offset += (uint32_t)reads->a[i];
}
asg_seq_set(purge_g, uId, offset, 0);
purge_g->seq[uId].c = PRIMARY_LABLE;
}
@@ -5196,30 +5446,34 @@ uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans)
if(just_coverage) goto end_coverage;
kt_for(asm_opt.thread_num, hap_alignment_advance_worker, &hap_buf, nsg->n_seq);
///if(debug_enable) print_all_purge_ovlp(ug, &all_ovlp);
filter_hap_overlaps_by_length(&all_ovlp, purege_minLen);
pg = init_p_g_t(ug, cov, read_g);
///normalize_hap_overlaps(&all_ovlp, &back_all_ovlp);
normalize_hap_overlaps_advance(&all_ovlp, &back_all_ovlp, ug, read_g, reverse_sources, ruIndex);
normalize_hap_overlaps_advance_by_p_g_t(&all_ovlp, &back_all_ovlp, ug, read_g, reverse_sources,
ruIndex, pg, cov, 0.8);
///normalize_hap_overlaps_advance(&all_ovlp, &back_all_ovlp, ug, read_g, reverse_sources, ruIndex);
///debug_hap_overlaps(&all_ovlp, &back_all_ovlp);
remove_contained_haplotig(&all_ovlp, ug, nsg, purge_g, cov);
remove_contained_haplotig(&all_ovlp, ug, nsg, pg->pg_h_lev, cov);
if(just_contain == 0)
{
for (v = 0; v < all_ovlp.num; v++)
{
uId = v;
if(purge_g->seq[uId].del || purge_g->seq[uId].c == ALTER_LABLE) continue;
if(pg->pg_h_lev->seq[uId].del || pg->pg_h_lev->seq[uId].c == ALTER_LABLE) continue;
for (i = 0; i < all_ovlp.x[uId].a.n; i++)
{
if(all_ovlp.x[uId].a.a[i].status == DELETE) continue;
///if(all_ovlp.x[uId].a.a[i].type == )
if(purge_g->seq[all_ovlp.x[uId].a.a[i].xUid].c == ALTER_LABLE||
purge_g->seq[all_ovlp.x[uId].a.a[i].xUid].del||
purge_g->seq[all_ovlp.x[uId].a.a[i].yUid].c == ALTER_LABLE||
purge_g->seq[all_ovlp.x[uId].a.a[i].yUid].del)
if(pg->pg_h_lev->seq[all_ovlp.x[uId].a.a[i].xUid].c == ALTER_LABLE||
pg->pg_h_lev->seq[all_ovlp.x[uId].a.a[i].xUid].del||
pg->pg_h_lev->seq[all_ovlp.x[uId].a.a[i].yUid].c == ALTER_LABLE||
pg->pg_h_lev->seq[all_ovlp.x[uId].a.a[i].yUid].del)
{
continue;
}
@@ -5237,20 +5491,20 @@ uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans)
// }
if(r < 0) continue;
p = asg_arc_pushp(purge_g);
p = asg_arc_pushp(pg->pg_h_lev);
*p = t;
}
}
asg_cleanup(purge_g);
asg_symm(purge_g);
asg_cleanup(pg->pg_h_lev);
asg_symm(pg->pg_h_lev);
///may need to do transitive reduction
clean_purge_graph(purge_g, drop_ratio, 1);
clean_purge_graph(pg->pg_h_lev, drop_ratio, 1);
// if(debug_enable) print_purge_gfa(ug, purge_g);
// if(debug_enable) print_all_purge_ovlp(ug, &all_ovlp);
link_unitigs(purge_g, ug, &all_ovlp, ruIndex, reverse_sources, coverage_cut, read_g, position_index,
link_unitigs(pg->pg_h_lev, ug, &all_ovlp, ruIndex, reverse_sources, coverage_cut, read_g, position_index,
&(hap_buf.buf[0].u_buffer), &(hap_buf.buf[0].u_buffer_tailIndex), &(hap_buf.buf[0].u_buffer_prevIndex),
max_hang, min_ovlp, edge, hap_buf.buf[0].visit, cov);
}
@@ -5258,28 +5512,25 @@ uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans)
for (v = 0; v < all_ovlp.num; v++)
{
uId = v;
if(purge_g->seq[uId].c == ALTER_LABLE)
if(pg->pg_h_lev->seq[uId].c == ALTER_LABLE)
{
ug->g->seq[uId].c = ALTER_LABLE;
}
}
end_coverage:
uint32_t is_Unitig;
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;
}
asg_cleanup(nsg);
destory_hap_overlaps_list(&all_ovlp);
destory_hap_overlaps_list(&back_all_ovlp);
asg_destroy(purge_g);
if(cov) memset(position_index, -1, sizeof(uint64_t)*read_g->n_seq);
else free(position_index);
destory_hap_alignment_struct_pip(&hap_buf);
destory_p_g_t(&pg);
}
hic.cpp
+11 -10
View File
@@ -2678,17 +2678,17 @@ 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]>>2) == 0)
if((bub->index[i]>>2) == 0)
{
bub->index[i] = (uint32_t)-1;
bub->index[i] = (uint32_t)-1; ///hom
}
else
{
if((bub->index[i]>>2) == 1)
if((bub->index[i]>>2) == 1)
{
bub->index[i] = P_het(*bub); ///potential het
}
else
else
{
bub->index[i] = M_het(*bub); ///must het
}
@@ -2705,11 +2705,11 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *het_flag)
n_occ += ug->u.a[a[v]>>1].n;
}
if((pathLen*2) >= ug->g->seq[beg>>1].len && (pathLen*2) >= ug->g->seq[sink>>1].len)
{
bub->index[(beg>>1)] = (uint32_t)-1;
bub->index[(sink>>1)] = (uint32_t)-1;
}
// if((pathLen*2) >= ug->g->seq[beg>>1].len && (pathLen*2) >= ug->g->seq[sink>>1].len)
// {
// bub->index[(beg>>1)] = (uint32_t)-1;
// bub->index[(sink>>1)] = (uint32_t)-1;
// }
if(n_occ > 3)
{
@@ -2749,7 +2749,7 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *het_flag)
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] == 1)
if(het_flag && het_flag[i])
{
bub->index[i] = P_het(*bub);
}
@@ -2769,6 +2769,7 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *het_flag)
}
bub->b_g = NULL;
bub->b_ug = NULL;
build_bub_graph(ug, bub);
}