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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
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@@ -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;