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clean purge_dups

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chhylp123
2021-04-03 16:26:58 -04:00
parent 46e899bbae
commit ebfc04d253
6 changed files with 478 additions and 120 deletions
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CommandLines.cpp
+2 -1
View File
@@ -141,7 +141,8 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->number_of_round = 3;
asm_opt->adapterLen = 0;
asm_opt->clean_round = 4;
asm_opt->small_pop_bubble_size = 100000;
///asm_opt->small_pop_bubble_size = 100000;
asm_opt->small_pop_bubble_size = 0;
asm_opt->large_pop_bubble_size = 10000000;
asm_opt->min_drop_rate = 0.2;
asm_opt->max_drop_rate = 0.8;
Overlaps.cpp
+368 -93
View File
@@ -11841,26 +11841,18 @@ trans_chain* t_ch, long long het_cov_thres)
}
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, trans_chain* t_ch)
void set_r_het_flag(ma_ug_t *ug, asg_t *sg, ma_sub_t* coverage_cut, ma_hit_t_alloc* sources, R_to_U* ruIndex, trans_chain* t_ch)
{
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(asm_opt.hom_global_coverage_set)
{
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;
dip_thre_max = asm_opt.hom_global_coverage;
}
else
{
dip_thre_max = asm_opt.hom_global_coverage;
dip_thre_max = ((double)asm_opt.hom_global_coverage)/((double)HOM_PEAK_RATE);
}
dip_thre_max *= 0.75;
@@ -12142,7 +12134,6 @@ bub_label_t* b_mask_t)
ma_ug_destroy(ug);
kv_destroy(new_rtg_edges.a);
output_unitig_graph(sg, coverage_cut, output_file_name, sources, ruIndex, max_hang, min_ovlp);
output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t);
output_trio_unitig_graph(sg, coverage_cut, output_file_name, MOTHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
@@ -12316,7 +12307,6 @@ bub_label_t* b_mask_t)
ma_ug_destroy(ug);
kv_destroy(new_rtg_edges.a);
output_unitig_graph(sg, coverage_cut, output_file_name, sources, ruIndex, max_hang, min_ovlp);
output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang, min_ovlp, 0, b_mask_t);
output_trio_unitig_graph(sg, coverage_cut, output_file_name, MOTHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
@@ -14038,7 +14028,7 @@ 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**/1);
asg_pop_bubble_primary_trio(ug, NULL, trio_flag, DROP, cov, 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);
@@ -14117,14 +14107,12 @@ 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;
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**/1);
asg_pop_bubble_primary_trio(ug, NULL, (uint32_t)-1, DROP, cov, 1);
///untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, (uint32_t)-1, DROP, cov);
///is_first = 0;
if(just_bubble_pop == 0)
{
cut_trio_tip_primary(g, ug, tipsLen, (uint32_t)-1, 0, read_g, reverse_sources, ruIndex, 2);
@@ -14824,18 +14812,13 @@ kvec_asg_arc_t_warp* new_rtg_edges, bub_label_t* b_mask_t)
coverage_cut, max_hang, min_ovlp, asm_opt.purge_level_trio>0?1:0);
if(cov->t_ch)
{
set_r_het_flag(*ug, read_g, coverage_cut, sources, reverse_sources, ruIndex,
new_rtg_edges, max_hang, min_ovlp, cov->t_ch);
set_r_het_flag(*ug, read_g, coverage_cut, sources, ruIndex, 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,
1, 1, cov, 0);
if(asm_opt.recover_atg_cov_min == -1024)
{
asm_opt.recover_atg_cov_max = asm_opt.hom_global_coverage/HOM_PEAK_RATE;
asm_opt.recover_atg_cov_min = asm_opt.recover_atg_cov_max * 0.85;
///asm_opt.recover_atg_cov_max = asm_opt.recover_atg_cov_max * 1.2;
asm_opt.recover_atg_cov_max = INT32_MAX;
}
if(asm_opt.recover_atg_cov_max != INT32_MAX)
@@ -15430,6 +15413,22 @@ static void asg_bub_backtrack_primary_cov(ma_ug_t *ug, uint32_t v0, buf_t *b, ha
if(t_ch)
{
/*******************************for debug************************************/
// uint8_t* debug_het = NULL; CALLOC(debug_het, R_INF.total_reads);
// for (i = 0; i < b->b.n; ++i)
// {
// if((b->b.a[i]>>1) == (b->S.a[0]>>1)) continue;
// p = &(ug->u.a[b->b.a[i]>>1]);
// if(p->n == 0) continue;
// for (k = 0; k < p->n; k++)
// {
// t_ch->is_r_het[p->a[k]>>33] |= P_HET;
// debug_het[p->a[k]>>33] |= 1;
// }
// }
/*******************************for debug************************************/
if(get_real_length(ug->g, v0, NULL) == 2 && get_real_length(ug->g, b->S.a[0]^1, NULL) == 2)
{
long long tmp, max_stop_nodeLen, max_stop_baseLen, bch_occ[2];
@@ -15461,6 +15460,9 @@ static void asg_bub_backtrack_primary_cov(ma_ug_t *ug, uint32_t v0, buf_t *b, ha
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;
/*******************************for debug************************************/
// debug_het[(ori == 1?((p->a[p->n-k-1])>>33):(p->a[k]>>33))] |= 2;
/*******************************for debug************************************/
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;
@@ -15480,6 +15482,9 @@ static void asg_bub_backtrack_primary_cov(ma_ug_t *ug, uint32_t v0, buf_t *b, ha
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;
/*******************************for debug************************************/
// debug_het[(ori == 1?((p->a[p->n-k-1])>>33):(p->a[k]>>33))] |= 2;
/*******************************for debug************************************/
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;
@@ -15529,6 +15534,9 @@ static void asg_bub_backtrack_primary_cov(ma_ug_t *ug, uint32_t v0, buf_t *b, ha
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;
/*******************************for debug************************************/
// debug_het[(ori == 1?((p->a[p->n-k-1])>>33):(p->a[k]>>33))] |= 2;
/*******************************for debug************************************/
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;
@@ -15549,6 +15557,9 @@ static void asg_bub_backtrack_primary_cov(ma_ug_t *ug, uint32_t v0, buf_t *b, ha
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;
/*******************************for debug************************************/
// debug_het[(ori == 1?((p->a[p->n-k-1])>>33):(p->a[k]>>33))] |= 2;
/*******************************for debug************************************/
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;
@@ -15676,7 +15687,20 @@ static void asg_bub_backtrack_primary_cov(ma_ug_t *ug, uint32_t v0, buf_t *b, ha
}
}
/*******************************for debug************************************/
// for (i = 0; i < R_INF.total_reads; i++)
// {
// if(debug_het[i] != 0 && debug_het[i] != 3)
// {
// fprintf(stderr, "ERROR-debug_het[i]: %u, s-utg%.6ul, e-utg%.6ul\n",
// debug_het[i], (v>>1)+1, (b->S.a[0]>>1)+1);
// }
// }
// CALLOC(debug_het, R_INF.total_reads);
// free(debug_het);
// fprintf(stderr, "-init_chain_num: %u, t_ch->chain_num: %u, beg-utg%.6ul, end-utg%.6ul\n",
// init_chain_num, (uint32_t)t_ch->chain_num, (v0>>1)+1, (b->S.a[0]>>1)+1);
// uint32_t *x = NULL, *y = NULL;
@@ -21922,7 +21946,8 @@ int write_ruIndex(R_to_U* ruIndex, char* read_file_name)
fwrite(&ruIndex->len, sizeof(ruIndex->len), 1, fp);
fwrite(ruIndex->index, sizeof(ruIndex->index[0]), ruIndex->len, fp);
fwrite(R_INF.trio_flag, sizeof(R_INF.trio_flag[0]), ruIndex->len, fp);
fwrite(ruIndex->is_het, 1, ruIndex->len, fp);
free(index_name);
fflush(fp);
fclose(fp);
@@ -21947,6 +21972,9 @@ int load_ruIndex(R_to_U* ruIndex, char* read_file_name)
R_INF.trio_flag = (uint8_t*)malloc(sizeof(uint8_t)*(ruIndex)->len);
f_flag += fread(R_INF.trio_flag, sizeof(R_INF.trio_flag[0]), (ruIndex)->len, fp);
CALLOC(ruIndex->is_het, ruIndex->len);
f_flag += fread(ruIndex->is_het, 1, ruIndex->len, fp);
free(index_name);
fflush(fp);
fclose(fp);
@@ -22633,8 +22661,7 @@ uint32_t collect_p_trans)
coverage_cut, max_hang, min_ovlp, (asm_opt.purge_level_primary>0||i_cov)?1:0);
if(cov->t_ch)
{
set_r_het_flag(*ug, read_g, coverage_cut, sources, reverse_sources, ruIndex,
new_rtg_edges, max_hang, min_ovlp, cov->t_ch);
set_r_het_flag(*ug, read_g, coverage_cut, sources, ruIndex, cov->t_ch);
}
adjust_utg_advance(read_g, (*ug), reverse_sources, ruIndex, b_mask_t);
@@ -22674,25 +22701,19 @@ uint32_t collect_p_trans)
rescue_contained_reads_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang,
min_ovlp, 10, 0, 1, NULL, NULL, b_mask_t);
renew_utg(ug, read_g, new_rtg_edges);
if(asm_opt.purge_level_primary > 0)
{
just_contain = 0;
if(asm_opt.purge_level_primary == 1) just_contain = 1;
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,
just_contain, 0, cov, 0);
delete_useless_nodes(ug);
renew_utg(ug, read_g, new_rtg_edges);
}
// if(asm_opt.purge_level_primary > 0)
// {
// just_contain = 0;
// if(asm_opt.purge_level_primary == 1) just_contain = 1;
// 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,
// just_contain, 0, cov, 0);
// delete_useless_nodes(ug);
// renew_utg(ug, read_g, new_rtg_edges);
// }
}
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,
1, cov, 0);
}
n_vtx = read_g->n_seq;
for (v = 0; v < n_vtx; v++)
@@ -22729,7 +22750,6 @@ uint32_t collect_p_trans)
{
asm_opt.recover_atg_cov_max = asm_opt.hom_global_coverage/HOM_PEAK_RATE;
asm_opt.recover_atg_cov_min = asm_opt.recover_atg_cov_max * 0.85;
///asm_opt.recover_atg_cov_max = asm_opt.recover_atg_cov_max * 1.2;
asm_opt.recover_atg_cov_max = INT32_MAX;
}
@@ -22782,12 +22802,14 @@ R_to_U* ruIndex, int max_hang, int min_ovlp)
nsg->seq[v].c = PRIMARY_LABLE;
EvaluateLen(ug->u, v) = ug->u.a[v].n;
}
asg_pop_bubble_primary_trio(ug, &bubble_dist, (uint32_t)-1, DROP, NULL, 0);
cut_trio_tip_primary(ug->g, ug, tipsLen, (uint32_t)-1, 0, sg, reverse_sources, ruIndex, 2);
asg_pop_bubble_primary_trio(ug, &bubble_dist, (uint32_t)-1, DROP, NULL, 0);
cut_trio_tip_primary(ug->g, ug, tipsLen, (uint32_t)-1, 0, sg, reverse_sources, ruIndex, 2);
delete_useless_nodes(&ug);
renew_utg(&ug, sg, &new_rtg_edges);
if(bubble_dist > 0)
{
asg_pop_bubble_primary_trio(ug, &bubble_dist, (uint32_t)-1, DROP, NULL, 0);
delete_useless_nodes(&ug);
renew_utg(&ug, sg, &new_rtg_edges);
}
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp);
@@ -23270,8 +23292,8 @@ void pre_clean(ma_hit_t_alloc* sources, ma_sub_t* coverage_cut, asg_t *sg, uint3
void init_R_to_U(R_to_U* x, uint64_t len)
{
x->len = len;
x->index = (uint32_t*)malloc(sizeof(uint32_t)*(x->len));
memset(x->index, -1, sizeof(uint32_t)*(x->len));
CALLOC(x->index, x->len);
x->is_het = NULL;
}
void destory_R_to_U(R_to_U* x)
@@ -26729,7 +26751,7 @@ int max_hang, int min_ovlp, bubble_type* bub, long long gap_fuzz)
}
void rescue_bubble_by_chain(asg_t *sg, ma_sub_t *coverage_cut, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
uint8_t *rescue_bubble_by_chain(asg_t *sg, ma_sub_t *coverage_cut, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
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, uint32_t chainLenThres, long long gap_fuzz,
bub_label_t* b_mask_t)
@@ -26756,19 +26778,16 @@ bub_label_t* b_mask_t)
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);
ma_ug_destroy(ug); ug = NULL; ug = ma_ug_gen_primary(sg, PRIMARY_LABLE);
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, 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);
if(ha_opt_triobin(&asm_opt))
{
@@ -26777,12 +26796,14 @@ bub_label_t* b_mask_t)
rescue_missing_hap_ovlp(ug, sg, sources, coverage_cut, max_hang, min_ovlp, &bub, gap_fuzz);
}
uint8_t *het_flag = cov->t_ch->is_r_het;
cov->t_ch->is_r_het = NULL;
destory_bubbles(&bub);
destory_hap_cov_t(&cov);
ma_ug_destroy(ug);
kv_destroy(new_rtg_edges.a);
ma_ug_destroy(copy_ug); copy_ug = NULL;
return het_flag;
}
void update_unitig(long long step, long long init, ma_utg_t* nsu, asg_t *r_g,
@@ -28627,6 +28648,273 @@ ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex, int m
}
}
void clean_sg_by_utg(asg_t *sg, ma_ug_t *ug)
{
uint32_t i, v, n_vx, w, k, m, nv, vx, wx;
asg_arc_t *av = NULL;
ma_utg_t *u = NULL;
n_vx = sg->n_seq<<1;
for (v = 0; v < n_vx; v++)
{
nv = asg_arc_n(sg, v);
av = asg_arc_a(sg, v);
for (m = 0; m < nv; m++) av[m].del = (!!1);
}
for (i = 0; i < ug->g->n_seq; ++i)
{
if(ug->g->seq[i].del) continue;
u = &(ug->u.a[i]);
if(ug->g->seq[i].c == ALTER_LABLE)
{
for (k = 0; k < u->n; k++)
{
asg_seq_del(sg, u->a[k]>>33);
}
}
else
{
for (k = 0; (k + 1) < u->n; k++)
{
v = u->a[k]>>32; w = u->a[k+1]>>32;
asg_arc_del(sg, v, w, 0);
asg_arc_del(sg, w^1, v^1, 0);
}
v = i<<1;
nv = asg_arc_n(ug->g, v); av = asg_arc_a(ug->g, v);
for (k = 0; k < nv; k++)
{
if(av[k].del) continue;
w = av[k].v;
vx = (v&1?((ug->u.a[v>>1].a[0]>>32)^1):(ug->u.a[v>>1].a[ug->u.a[v>>1].n-1]>>32));
wx = (w&1?((ug->u.a[w>>1].a[ug->u.a[w>>1].n-1]>>32)^1):(ug->u.a[w>>1].a[0]>>32));
asg_arc_del(sg, vx, wx, 0); asg_arc_del(sg, wx^1, vx^1, 0);
}
v = (i<<1)+1;
nv = asg_arc_n(ug->g, v); av = asg_arc_a(ug->g, v);
for (k = 0; k < nv; k++)
{
if(av[k].del) continue;
w = av[k].v;
vx = (v&1?((ug->u.a[v>>1].a[0]>>32)^1):(ug->u.a[v>>1].a[ug->u.a[v>>1].n-1]>>32));
wx = (w&1?((ug->u.a[w>>1].a[ug->u.a[w>>1].n-1]>>32)^1):(ug->u.a[w>>1].a[0]>>32));
asg_arc_del(sg, vx, wx, 0); asg_arc_del(sg, wx^1, vx^1, 0);
}
}
}
/*******************************for debug************************************/
// ma_ug_t *dbg = ma_ug_gen(sg);
// for (i = 0; i < ug->g->n_seq; ++i)
// {
// if(ug->g->seq[i].del) continue;
// if(ug->g->seq[i].c == ALTER_LABLE)
// {
// asg_seq_del(ug->g, i);
// }
// }
// for (i = 0; i < dbg->g->n_seq; ++i)
// {
// dbg->g->seq[v].c = PRIMARY_LABLE;
// EvaluateLen(dbg->u, v) = dbg->u.a[v].n;
// }
// cmp_untig_graph(dbg, ug);
/*******************************for debug************************************/
}
void flat_bubbles(asg_t *sg, uint8_t* r_het)
{
ma_ug_t *ug = NULL;
ug = ma_ug_gen(sg);
ma_utg_t *u = NULL;
uint32_t n_vtx = ug->g->n_seq<<1, v, convex, i, k, ori, is_het_b, is_het_s, n_pop = 0, pass_b, pass_s;
long long nodeLen, baseLen, max_stop_nodeLen, max_stop_baseLen;
buf_t b; memset(&b, 0, sizeof(buf_t)); b.a = (binfo_t*)calloc(n_vtx, sizeof(binfo_t));
uint8_t* bs_flag = (uint8_t*)calloc(n_vtx, 1);
uint64_t tLen = get_bub_pop_max_dist_advance(ug->g, &b), path, hom_occ, het_occ;
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;
}
n_pop = 1; ///round = 0;
while(n_pop > 0)
{
for (v = n_pop = 0; v < n_vtx; ++v)
{
if(ug->g->seq[v>>1].del) continue;
if(asg_arc_n(ug->g, v) < 2) continue;
if(get_real_length(ug->g, v, NULL) < 2) continue;
if(bs_flag[v] == 1) continue;
if(bs_flag[v] == 0) bs_flag[v] = 1;
if(asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, NULL, NULL, NULL, 0))
{
//note b.b include end, does not include beg
for (i = path = 0; i < b.b.n; i++)
{
if((b.b.a[i]>>1) == (v>>1) || (b.b.a[i]>>1) == (b.S.a[0]>>1))
{
continue;
}
path += ug->u.a[b.b.a[i]>>1].n;
}
bs_flag[v] = 2; bs_flag[b.S.a[0]^1] = 2;
is_het_b = is_het_s = pass_b = pass_s = 0;
//beg is v, end is b.S.a[0]
b.b.n = 0;
get_unitig(ug->g, NULL, v^1, &convex, &nodeLen, &baseLen, &max_stop_nodeLen,
&max_stop_baseLen, 1, &b);
for (i = hom_occ = het_occ = 0; i < b.b.n; i++)
{
u = &(ug->u.a[b.b.a[i]>>1]);
ori = b.b.a[i]&1;
for (k = 0; k < u->n; k++)
{
if(r_het[(ori == 1?(u->a[u->n-k-1]>>33):(u->a[k]>>33))] == N_HET)
{
hom_occ++;
}
else
{
het_occ++;
}
if(het_occ > ((het_occ+hom_occ)*0.85))
{
is_het_b = (het_occ+hom_occ);
}
if((het_occ+hom_occ) == MAX((path+1),5))
{
if(het_occ > ((het_occ+hom_occ)*0.7))
{
pass_b = 1;
}
}
}
}
if(pass_b == 0) continue;
b.b.n = 0;
get_unitig(ug->g, NULL, b.S.a[0], &convex, &nodeLen, &baseLen, &max_stop_nodeLen,
&max_stop_baseLen, 1, &b);
for (i = hom_occ = het_occ= 0; i < b.b.n; i++)
{
u = &(ug->u.a[b.b.a[i]>>1]);
ori = b.b.a[i]&1;
for (k = 0; k < u->n; k++)
{
if(r_het[(ori == 1?(u->a[u->n-k-1]>>33):(u->a[k]>>33))] == N_HET)
{
hom_occ++;
}
else
{
het_occ++;
}
if(het_occ > ((het_occ+hom_occ)*0.85))
{
is_het_s = (het_occ+hom_occ);
}
if((het_occ+hom_occ) == MAX((path+1),5))
{
if(het_occ > ((het_occ+hom_occ)*0.7))
{
pass_s = 1;
}
}
}
}
if(pass_s == 0) continue;
if(is_het_b > path && is_het_s > path && (is_het_b+is_het_s)>(path<<2))
{
asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 1, NULL, NULL, NULL, 0);
n_pop++;
// if(ug->g->seq[2031].c == ALTER_LABLE)
// {
// fprintf(stderr, "######round: %u, s-utg%.6ul, e-utg%.6ul\n",
// round, (v>>1)+1, (b.S.a[0]>>1)+1);
// }
}
}
}
///round++;
}
/*******************************for debug************************************/
// kvec_t(uint64_t) occ_sort; kv_init(occ_sort);
// for (v = n_pop = 0; v < ug->g->n_seq; ++v)
// {
// if(ug->g->seq[v].del) continue;
// if(ug->g->seq[v].c != ALTER_LABLE) continue;
// u = &(ug->u.a[v]);
// kv_push(uint64_t, occ_sort, (uint64_t)((uint32_t)(-1) - (uint32_t)(u->n)) << 32 | (v));
// }
// radix_sort_arch64(occ_sort.a, occ_sort.a + occ_sort.n);
// for (i = 0; i < occ_sort.n; ++i)
// {
// fprintf(stderr, "-utg%.6ul, n=%u\n", ((uint32_t)occ_sort.a[i])+1,
// (uint32_t)(-1) - (uint32_t)(occ_sort.a[i]>>32));
// }
// kv_destroy(occ_sort);
/*******************************for debug************************************/
clean_sg_by_utg(sg, ug);
free(b.a); free(b.S.a); free(b.T.a); free(b.b.a); free(b.e.a);
ma_ug_destroy(ug); free(bs_flag);
}
char *get_outfile_name(char* output_file_name)
{
char *buf = NULL;
CALLOC(buf, strlen(output_file_name) + 25);
if(ha_opt_triobin(&asm_opt) && ha_opt_hic(&asm_opt))
{
sprintf(buf, "%s.hic.bench", output_file_name);
}
else if(ha_opt_triobin(&asm_opt))
{
sprintf(buf, "%s.dip", output_file_name);
}
else if(ha_opt_hic(&asm_opt))
{
sprintf(buf, "%s.hic", output_file_name);
}
else if(asm_opt.flag & HA_F_PARTITION)
{
sprintf(buf, "%s.bp", output_file_name);
}
else
{
sprintf(buf, "%s", output_file_name);
}
return buf;
}
void clean_graph(
int min_dp, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources,
long long n_read, uint64_t* readLen, long long mini_overlap_length,
@@ -28635,6 +28923,7 @@ float min_ovlp_drop_ratio, float max_ovlp_drop_ratio, char* output_file_name,
long long bubble_dist, int read_graph, R_to_U* ruIndex, asg_t **sg_ptr,
ma_sub_t **coverage_cut_ptr, int debug_g)
{
char *o_file = NULL;
ma_sub_t *coverage_cut = *coverage_cut_ptr;
asg_t *sg = *sg_ptr;
bub_label_t b_mask_t;
@@ -28819,7 +29108,10 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
// rescue_no_coverage_aggressive(sg, sources, reverse_sources, &coverage_cut, ruIndex, max_hang_length,
// mini_overlap_length, bubble_dist, 10);
rescue_bubble_by_chain(sg, coverage_cut, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3,
set_hom_global_coverage(&asm_opt, sg, coverage_cut, sources, reverse_sources, ruIndex,
max_hang_length, mini_overlap_length);
ruIndex->is_het = rescue_bubble_by_chain(sg, coverage_cut, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3,
ruIndex, 0.05, 0.9, max_hang_length, mini_overlap_length, 10, gap_fuzz, &b_mask_t);
if (asm_opt.flag & HA_F_VERBOSE_GFA)
@@ -28828,71 +29120,54 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
write_debug_graph(sg, sources, coverage_cut, output_file_name, n_read, reverse_sources, ruIndex);
debug_gfa:;
/*******************************for debug***************************************/
set_hom_global_coverage(&asm_opt, sg, coverage_cut, sources, reverse_sources, ruIndex,
max_hang_length, mini_overlap_length);
}
// set_hom_global_coverage(&asm_opt, sg, coverage_cut, sources, reverse_sources, ruIndex,
// max_hang_length, mini_overlap_length);
o_file = get_outfile_name(output_file_name);
output_unitig_graph(sg, coverage_cut, o_file, sources, ruIndex, max_hang_length, mini_overlap_length);
flat_bubbles(sg, ruIndex->is_het); free(ruIndex->is_het); ruIndex->is_het = NULL;
output_contig_graph_primary_pre(sg, coverage_cut, o_file, sources, reverse_sources,
asm_opt.small_pop_bubble_size, asm_opt.max_short_tip, ruIndex, max_hang_length, mini_overlap_length);
if (ha_opt_triobin(&asm_opt) && ha_opt_hic(&asm_opt))
{
char *buf = (char*)calloc(strlen(output_file_name) + 25, 1);
sprintf(buf, "%s.hic.bench", output_file_name);
benchmark_hic_graph(sg, coverage_cut, buf, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3,
benchmark_hic_graph(sg, coverage_cut, o_file, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3,
ruIndex, 0.05, 0.9, max_hang_length, mini_overlap_length, &b_mask_t);
free(buf);
}
else if (ha_opt_triobin(&asm_opt))
{
char *buf = (char*)calloc(strlen(output_file_name) + 25, 1);
sprintf(buf, "%s.dip", output_file_name);
output_unitig_graph(sg, coverage_cut, buf, sources, ruIndex, max_hang_length, mini_overlap_length);
free(buf);
output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources,
{
output_trio_unitig_graph(sg, coverage_cut, o_file, FATHER, sources,
reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang_length, mini_overlap_length, 0, &b_mask_t);
output_trio_unitig_graph(sg, coverage_cut, output_file_name, MOTHER, sources,
output_trio_unitig_graph(sg, coverage_cut, o_file, MOTHER, sources,
reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex,
0.05, 0.9, max_hang_length, mini_overlap_length, 0, &b_mask_t);
}
else if(ha_opt_hic(&asm_opt))
{
char *buf = (char*)calloc(strlen(output_file_name) + 25, 1);
sprintf(buf, "%s.hic", output_file_name);
output_hic_graph(sg, coverage_cut, buf, sources, reverse_sources, (asm_opt.max_short_tip*2),
output_hic_graph(sg, coverage_cut, o_file, sources, reverse_sources, (asm_opt.max_short_tip*2),
0.15, 3, ruIndex, 0.05, 0.9, max_hang_length, mini_overlap_length, &b_mask_t);
free(buf);
}
else if(asm_opt.flag & HA_F_PARTITION)
{
char *buf = (char*)calloc(strlen(output_file_name) + 25, 1);
sprintf(buf, "%s.bp", output_file_name);
output_bp_graph(sg, coverage_cut, buf, sources, reverse_sources, (asm_opt.max_short_tip*2),
output_bp_graph(sg, coverage_cut, o_file, sources, reverse_sources, (asm_opt.max_short_tip*2),
0.15, 3, ruIndex, 0.05, 0.9, max_hang_length, mini_overlap_length, &b_mask_t);
free(buf);
}
else
{
output_unitig_graph(sg, coverage_cut, output_file_name, sources, ruIndex, max_hang_length, mini_overlap_length);
if(VERBOSE >= 1)
{
output_read_graph(sg, coverage_cut, output_file_name, n_read);
}
output_contig_graph_primary_pre(sg, coverage_cut, output_file_name, sources, reverse_sources,
asm_opt.small_pop_bubble_size, asm_opt.max_short_tip, ruIndex, max_hang_length, mini_overlap_length);
output_contig_graph_primary(sg, coverage_cut, output_file_name, sources, reverse_sources,
output_contig_graph_primary(sg, coverage_cut, o_file, sources, reverse_sources,
(asm_opt.max_short_tip*2), 0.15, 3, ruIndex, 0.05, 0.9, max_hang_length, mini_overlap_length, &b_mask_t);
output_contig_graph_alternative(sg, coverage_cut, output_file_name, sources, ruIndex, max_hang_length, mini_overlap_length);
output_contig_graph_alternative(sg, coverage_cut, o_file, sources, ruIndex, max_hang_length, mini_overlap_length);
}
*coverage_cut_ptr = coverage_cut;
*sg_ptr = sg;
destory_bub_label_t(&b_mask_t);
free(o_file);
fprintf(stderr, "Inconsistency threshold for low-quality regions in BED files: %u%%\n", asm_opt.bed_inconsist_rate);
}
Overlaps.h
+4 -2
View File
@@ -289,10 +289,11 @@ static inline asg_arc_t *asg_arc_pushp(asg_t *g)
// set asg_arc_t::del for v->w
static inline void asg_arc_del(asg_t *g, uint32_t v, uint32_t w, int del)
{
uint32_t i, nv = asg_arc_n(g, v);
uint32_t i, nv = asg_arc_n(g, v)/**, found = 0**/;
asg_arc_t *av = asg_arc_a(g, v);
for (i = 0; i < nv; ++i)
if (av[i].v == w) av[i].del = !!del;
if (av[i].v == w) av[i].del = !!del/**, found = 1**/;
/**if(found == 0) fprintf(stderr, "ERROR\n");**/
}
// set asg_arc_t::del and asg_seq_t::del to 1 for sequence s and all its associated arcs
@@ -470,6 +471,7 @@ uint64_t* source_index, long long listLen);
typedef struct {
uint64_t len;
uint32_t* index;
uint8_t* is_het;
} R_to_U;
void init_R_to_U(R_to_U* x, uint64_t len);
Purge_Dups.cpp
+18 -24
View File
@@ -44,12 +44,6 @@ typedef struct {
uint64_t i;
}kvec_hap_candidates;
#define SELF_EXIST 0
#define REVE_EXIST 1
#define DELETE 2
#define MIXED 3
#define FLIP 4
typedef struct {
uint64_t* vote_counting;
@@ -801,10 +795,7 @@ long long* n_y_beg, long long* n_y_end)
}
#define X2Y 0
#define Y2X 1
#define XCY 2
#define YCX 3
uint32_t classify_hap_overlap(long long xBeg, long long xEnd, long long xLen,
long long yBeg, long long yEnd, long long yLen, long long* r_xBeg, long long* r_xEnd,
long long* r_yBeg, long long* r_yEnd)
@@ -3391,11 +3382,24 @@ double filter_rate)
}
else
{
kv_pushp(hap_overlaps, all_ovlp->x[tn].a, &y);
set_reverse_hap_overlap(y, x, types);
x->status = DELETE;
}
}
}
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;
}
}
void filter_hap_overlaps_by_length(hap_overlaps_list* all_ovlp, uint32_t minLen)
@@ -5468,12 +5472,8 @@ uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans)
///if(debug_enable) print_all_purge_ovlp(ug, &all_ovlp);
filter_hap_overlaps_by_length(&all_ovlp, purege_minLen);
if(collect_p_trans)
{
pt_solve(&all_ovlp, cov->t_ch, ug, read_g, 0.8, R_INF.trio_flag);
goto end_coverage;
}
if(asm_opt.polyploidy <= 2) pt_solve(&all_ovlp, cov->t_ch, ug, read_g, 0.8, R_INF.trio_flag);
if(collect_p_trans) goto end_coverage;
pg = init_p_g_t(ug, cov, read_g);
///normalize_hap_overlaps(&all_ovlp, &back_all_ovlp);
@@ -5509,12 +5509,6 @@ uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans)
r = get_hap_arch(&(all_ovlp.x[uId].a.a[i]), ug->u.a[all_ovlp.x[uId].a.a[i].xUid].len,
ug->u.a[all_ovlp.x[uId].a.a[i].yUid].len, max_hang, asm_opt.max_hang_rate, min_ovlp, &t);
// if(all_ovlp.x[uId].a.a[i].xUid == 118 && all_ovlp.x[uId].a.a[i].yUid == 82)
// {
// fprintf(stderr, "r: %d\n", r);
// print_hap_paf(ug, &(all_ovlp.x[uId].a.a[i]));
// }
if(r < 0) continue;
p = asg_arc_pushp(pg->pg_h_lev);
*p = t;
Purge_Dups.h
+12
View File
@@ -13,6 +13,17 @@
#define REAL_ALTER_THRES 0.1
#define CHAIN_FILTER_RATE 0.7
#define SELF_EXIST 0
#define REVE_EXIST 1
#define DELETE 2
#define MIXED 3
#define FLIP 4
#define X2Y 0
#define Y2X 1
#define XCY 2
#define YCX 3
typedef struct {
uint8_t rev;
uint8_t type;
@@ -53,5 +64,6 @@ ma_sub_t *coverage_cut, int max_hang, int min_ovlp, uint32_t is_collect_trans);
void destory_hap_cov_t(hap_cov_t **x);
void chain_trans_ovlp(hap_cov_t *cov, ma_ug_t *ug, asg_t *read_sg, buf_t* xReads, uint32_t targetBaseLen, uint32_t* xEnd);
int get_specific_hap_overlap(kvec_hap_overlaps* x, uint32_t qn, uint32_t tn);
void set_reverse_hap_overlap(hap_overlaps* dest, hap_overlaps* source, uint32_t* types);
#endif
partig.cpp
+74
View File
@@ -691,6 +691,78 @@ void set_trio_flag(ma_ug_t *ug, asg_t *read_g, uint32_t uID, uint8_t* trio_flag,
// }
}
void filter_ovlp(ma_ug_t *ug, asg_t *read_g, uint32_t uID, hap_overlaps_list* ha, pt_match_t *ma,
int8_t *s)
{
pt_match1_t *o = pt_a(*ma, uID);
uint32_t n = pt_n(*ma, uID), k, qn, tn;
hap_overlaps *p = NULL;
int index;
for (k = 0; k < n; ++k)
{
qn = o[k].sid[0]; tn = o[k].sid[1]; p = NULL;
if((s[qn]*s[tn])!=-1) continue;
index = get_specific_hap_overlap(&(ha->x[qn]), qn, tn);
if(index != -1 && ha->x[qn].a.a[index].score == (long long)o[k].w)
{
p = &(ha->x[qn].a.a[index]);
}
else
{
index = get_specific_hap_overlap(&(ha->x[tn]), tn, qn);
if(index != -1 && ha->x[tn].a.a[index].score == (long long)o[k].w)
{
p = &(ha->x[tn].a.a[index]);
}
}
if(!p) fprintf(stderr, "ERROR\n");
p->status = FLIP;
}
}
void clean_ovlp(ma_ug_t *ug, asg_t *read_g, hap_overlaps_list* ha, pt_g_t *pg, int8_t* s)
{
uint32_t v, i, k, qn, tn, types[4];
types[X2Y] = Y2X; types[Y2X] = X2Y; types[XCY] = YCX; types[YCX] = XCY;
int index;
hap_overlaps *x = NULL, *y = NULL;
for (i = 0; i < pg->e->n_seq; ++i)
{
filter_ovlp(ug, read_g, i, ha, pg->e, s);
}
for (v = 0; v < ha->num; v++)
{
for (i = 0; i < ha->x[v].a.n; i++)
{
qn = ha->x[v].a.a[i].xUid;
tn = ha->x[v].a.a[i].yUid;
x = &(ha->x[v].a.a[i]);
if(x->status != FLIP) continue;
index = get_specific_hap_overlap(&(ha->x[tn]), tn, qn);
if(index != -1)
{
y = &(ha->x[tn].a.a[index]);
set_reverse_hap_overlap(y, x, types);
y->status = FLIP;
}
if(index == -1) fprintf(stderr, "ERROR\n");
}
}
for (v = 0; v < ha->num; v++)
{
for (i = k = 0; i < ha->x[v].a.n; i++)
{
if(ha->x[v].a.a[i].status != FLIP) continue;
ha->x[v].a.a[k] = ha->x[v].a.a[i];
k++;
}
ha->x[v].a.n = k;
}
}
void pt_solve(hap_overlaps_list* ovlp, trans_chain* t_ch, ma_ug_t *ug, asg_t *read_g, double f_rate, uint8_t* trio_flag)
{
pt_svopt_t opt;
@@ -726,6 +798,8 @@ void pt_solve(hap_overlaps_list* ovlp, trans_chain* t_ch, ma_ug_t *ug, asg_t *re
pg->info.a[i].m[0] = z[0], pg->info.a[i].m[1] = z[1];
}
clean_ovlp(ug, read_g, ovlp, pg, s);
free(buf);
free(s);
destory_pt_g_t(&pg);