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bug fix for bubble scanning

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chhylp123
2021-04-23 20:40:43 -04:00
parent a5b29b00bd
commit 7b07e355b7
8 changed files with 183 additions and 97 deletions
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Overlaps.cpp
+40 -53
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@@ -12736,7 +12736,7 @@ bub_label_t* b_mask_t)
///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, 1/**0**/);
print_utg(copy_ug, copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang,
min_ovlp, &new_rtg_edges);
@@ -13466,14 +13466,12 @@ bub_label_t* b_mask_t)
hap_cov_t *cov = NULL;
asg_t *copy_sg = copy_read_graph(sg);
ma_ug_t *copy_ug = copy_untig_graph(ug);
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, 1);
max_hang, min_ovlp, &new_rtg_edges, &cov, b_mask_t, 1, 1);
print_utg(copy_ug, copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang,
min_ovlp, &new_rtg_edges);
ma_ug_destroy(copy_ug);
asg_destroy(copy_sg);
@@ -15318,7 +15316,6 @@ int just_bubble_pop, float drop_ratio, hap_cov_t *cov)
{
pre_cons = get_graph_statistic(g);
asg_pop_bubble_primary_trio(ug, NULL, (uint32_t)-1, DROP, cov, 1);
if(just_bubble_pop == 0)
{
///need consider tangles
@@ -16088,7 +16085,7 @@ kvec_asg_arc_t_warp* new_rtg_edges, bub_label_t* b_mask_t)
{
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, 0,
cov, 0);
cov, 0, 0);
///delete_useless_nodes(ug);
delete_useless_trio_nodes(ug, read_g, coverage_cut, sources, ruIndex);
}
@@ -16388,6 +16385,7 @@ void dfs_trans_chain_bub(asg_t *g, hap_cov_t *cov, uint32_t v, uint32_t beg, uin
{
b->b.n--;
cur = b->b.a[b->b.n];
if(flag[cur>>1] == 0 && (cur>>1) != (v>>1)) continue;
flag[cur>>1] = 0;
ncur = asg_arc_n(g, cur);
@@ -16396,6 +16394,7 @@ void dfs_trans_chain_bub(asg_t *g, hap_cov_t *cov, uint32_t v, uint32_t beg, uin
{
if(acur[i].del) continue;
if((acur[i].v>>1) == beg || (acur[i].v>>1) == sink) continue;
if(flag[acur[i].v>>1] == 0) continue;
kv_push(uint32_t, b->b, acur[i].v);
}
}
@@ -16406,6 +16405,7 @@ void dfs_trans_chain_bub(asg_t *g, hap_cov_t *cov, uint32_t v, uint32_t beg, uin
{
b->b.n--;
cur = b->b.a[b->b.n];
if(flag[cur>>1] == 0 && (cur>>1) != (v>>1)) continue;
flag[cur>>1] = 0;
ncur = asg_arc_n(g, cur);
@@ -16414,6 +16414,7 @@ void dfs_trans_chain_bub(asg_t *g, hap_cov_t *cov, uint32_t v, uint32_t beg, uin
{
if(acur[i].del) continue;
if((acur[i].v>>1) == beg || (acur[i].v>>1) == sink) continue;
if(flag[acur[i].v>>1] == 0) continue;
kv_push(uint32_t, b->b, acur[i].v);
}
}
@@ -16641,14 +16642,14 @@ void chain_origin_trans_uid_c_bubble(uint32_t query, buf_t *target, buf_t *idx,
// in a resolved bubble, mark unused vertices and arcs as "reduced"
static void asg_bub_backtrack_primary_cov(ma_ug_t *ug, uint32_t v0, buf_t *b, hap_cov_t *cov, uint32_t is_update_chain)
{
uint32_t i, k, k_i, v, u, uLen = 0, uCov = 0, uId, rId, ori;
uint32_t i, k, k_i, v, u, uLen = 0, uCov = 0, uId, rId, ori;
ma_utg_t* p = NULL;
trans_chain* t_ch = (is_update_chain?cov->t_ch:NULL);
///b->S.a[0] is the sink of this bubble
///assert(b->S.n == 1);
///first remove all nodes in this bubble
for (i = 0; i < b->b.n; ++i)
///assert(b->S.n == 1);
///first remove all nodes in this bubble
for (i = 0; i < b->b.n; ++i)
{
uId = b->b.a[i]>>1;
if(uId == (b->S.a[0]>>1)) continue;
@@ -16664,10 +16665,10 @@ static void asg_bub_backtrack_primary_cov(ma_ug_t *ug, uint32_t v0, buf_t *b, ha
///v is the sink of this bubble
v = b->S.a[0];
///recover node
do {
u = b->a[v].p; // u->v
v = b->S.a[0];
///recover node
do {
u = b->a[v].p; // u->v
if(v != b->S.a[0])
{
uId = v>>1;
@@ -16680,16 +16681,16 @@ static void asg_bub_backtrack_primary_cov(ma_ug_t *ug, uint32_t v0, buf_t *b, ha
uLen += cov->read_g->seq[rId].len;
}
}
v = u;
} while (v != v0);
v = u;
} while (v != v0);
uCov = (uLen == 0? 0 : uCov / uLen);
///v is the sink of this bubble
v = b->S.a[0];
///recover node
do {
u = b->a[v].p; // u->v
v = b->S.a[0];
///recover node
do {
u = b->a[v].p; // u->v
if(v != b->S.a[0])
{
uId = v>>1;
@@ -16701,8 +16702,8 @@ static void asg_bub_backtrack_primary_cov(ma_ug_t *ug, uint32_t v0, buf_t *b, ha
cov->cov[rId] += (uCov * cov->read_g->seq[rId].len);
}
}
v = u;
} while (v != v0);
v = u;
} while (v != v0);
if(t_ch)
@@ -16763,7 +16764,6 @@ static void asg_bub_backtrack_primary_cov(ma_ug_t *ug, uint32_t v0, buf_t *b, ha
}
}
topologicalSortUtil(ug->g, cov, v0, b->S.a[0]);
///if(cov->t_ch->topo_res.n != b->b.n - 1) fprintf(stderr, "ERROR-4\n");
if(cov->t_ch->topo_res.n == 0) return;
@@ -16773,8 +16773,10 @@ static void asg_bub_backtrack_primary_cov(ma_ug_t *ug, uint32_t v0, buf_t *b, ha
if(uId == (b->S.a[0]>>1)) continue;
dfs_trans_chain_bub(ug->g, cov, uId, v0>>1, b->S.a[0]>>1);
if(cov->t_ch->b_buf_0.b.n == 0) continue;
chain_origin_trans_uid_c_bubble(cov->t_ch->topo_res.a[i], &(t_ch->b_buf_0), b, ug, cov);
/***********************x***********************/
uId = cov->t_ch->topo_res.a[i]>>1;
p = &(ug->u.a[uId]);
@@ -17528,7 +17530,6 @@ hap_cov_t *cov, uint32_t is_update_chain, uint32_t keep_d)
/****************************may have bugs********************************/
///if(keep_d != 0) debug_asg_bub_pop1_primary_trio(g, utg, v0, max_dist, b, positive_flag, negative_flag, 1);
/****************************may have bugs********************************/
if(cov && utg) asg_bub_backtrack_primary_cov(utg, v0, b, cov, is_update_chain);
if(is_pop) asg_bub_backtrack_primary(g, v0, b);
if(path_base_len || path_nodes) asg_bub_backtrack_primary_length(g, utg, v0, b, path_base_len, path_nodes);
@@ -23678,7 +23679,7 @@ 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)
uint32_t collect_p_trans, uint32_t collect_p_trans_f)
{
asg_t* nsg = (*ug)->g;
uint32_t v, n_vtx = nsg->n_seq, k, rId, just_contain;
@@ -23686,9 +23687,8 @@ uint32_t collect_p_trans)
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||i_cov)?1:0);
if(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);
nsg = (*ug)->g;
n_vtx = nsg->n_seq;
for (v = 0; v < n_vtx; ++v)
@@ -23698,14 +23698,11 @@ uint32_t collect_p_trans)
EvaluateLen((*ug)->u, v) = (*ug)->u.a[v].n;
}
clean_primary_untig_graph(*ug, read_g, sources, reverse_sources, coverage_cut, tipsLen, tip_drop_ratio,
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(i_cov && collect_p_trans == 0) goto skip_purge;
if(asm_opt.purge_level_primary > 0)
{
///print_debug_gfa(read_g, *ug, coverage_cut, "debug_purge", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);
@@ -23713,7 +23710,7 @@ uint32_t collect_p_trans)
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, !!(cov->t_ch&&collect_p_trans));
just_contain, 0, cov, !!(cov->t_ch&&collect_p_trans), collect_p_trans_f);
delete_useless_nodes(ug);
renew_utg(ug, read_g, new_rtg_edges);
}
@@ -23855,26 +23852,21 @@ R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ov
kvec_asg_arc_t_warp new_rtg_edges;
kv_init(new_rtg_edges.a);
adjust_utg_by_primary(&ug, 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, NULL, b_mask_t, 0);
max_hang, min_ovlp, &new_rtg_edges, NULL, b_mask_t, 0, 0);
if(asm_opt.b_low_cov > 0)
{
break_ug_contig(&ug, sg, &R_INF, coverage_cut, sources, ruIndex, &new_rtg_edges, max_hang, min_ovlp,
&asm_opt.b_low_cov, NULL, asm_opt.m_rate);
}
if(asm_opt.b_high_cov > 0)
{
break_ug_contig(&ug, sg, &R_INF, coverage_cut, sources, ruIndex, &new_rtg_edges, max_hang, min_ovlp,
NULL, &asm_opt.b_high_cov, asm_opt.m_rate);
}
ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, 0);
fprintf(stderr, "Writing primary contig GFA to disk... \n");
@@ -27096,8 +27088,8 @@ void reset_bub(bubble_type* bub, ma_ug_t *ug, trans_chain* back_ug_chain, kvec_a
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, back_ug_chain->is_r_het, NULL);
update_bubble_chain(ug, bub, 0, 1);
resolve_bubble_chain_tangle(ug, bub);
// update_bubble_chain(ug, bub, 0, 1);
// resolve_bubble_chain_tangle(ug, bub);
// 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);
}
@@ -27396,16 +27388,20 @@ bub_label_t* b_mask_t)
ma_ug_t *ug = NULL;
ug = ma_ug_gen_primary(sg, PRIMARY_LABLE);
// FILE* output_file = fopen("straw-debug.noseq.gfa", "w");
// ma_ug_print_simple(ug, &R_INF, sg, coverage_cut, sources, ruIndex, "utg", output_file);
// fclose(output_file);
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, 0);
ma_ug_destroy(copy_ug); copy_ug = NULL;
asg_destroy(copy_sg); copy_sg = NULL;
uint32_t beg_idx, occ;
bubble_type bub;
memset(&bub, 0, sizeof(bubble_type));
@@ -29276,7 +29272,7 @@ ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex, int m
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, NULL,
opt->purge_simi_thres, opt->purge_overlap_len, max_hang, min_ovlp, 0, 0, 1, cov, 0);
opt->purge_simi_thres, opt->purge_overlap_len, max_hang, min_ovlp, 0, 0, 1, cov, 0, 0);
destory_hap_cov_t(&cov);
ma_ug_destroy(ug);
@@ -29562,7 +29558,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
init_bub_label_t(&b_mask_t, MIN(10, asm_opt.thread_num), sg->n_seq);
goto debug_gfa;
}
///just for debug
renew_graph_init(sources, reverse_sources, sg, coverage_cut, ruIndex, n_read);
@@ -29571,7 +29566,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
///normalize_ma_hit_t_single_side(sources, n_read);
normalize_ma_hit_t_single_side_advance(sources, n_read);
normalize_ma_hit_t_single_side_advance(reverse_sources, n_read);
if (ha_opt_triobin(&asm_opt))
{
drop_edges_by_trio(sources, n_read);
@@ -29580,7 +29574,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
{
memset(R_INF.trio_flag, AMBIGU, R_INF.total_reads*sizeof(uint8_t));
}
///print_binned_reads(sources, n_read, coverage_cut);
clean_weak_ma_hit_t(sources, reverse_sources, n_read);
@@ -29592,7 +29585,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
ma_hit_cut(sources, n_read, readLen, mini_overlap_length, &coverage_cut);
///print_binned_reads(sources, n_read, coverage_cut);
ma_hit_flt(sources, n_read, coverage_cut, max_hang_length, mini_overlap_length);
///fix_binned_reads(sources, n_read, coverage_cut);
///just need to deal with trio here
ma_hit_contained_advance(sources, n_read, coverage_cut, ruIndex, max_hang_length, mini_overlap_length);
@@ -29601,7 +29593,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
///debug_info_of_specfic_node((char*)"m64043_200504_050026/93784180/ccs", sg, ruIndex, (char*)"sbsbsb");
init_bub_label_t(&b_mask_t, MIN(10, asm_opt.thread_num), sg->n_seq);
asg_arc_del_trans(sg, gap_fuzz);
asm_opt.coverage = get_coverage(sources, coverage_cut, n_read);
@@ -29617,7 +29608,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
asg_cut_tip(sg, asm_opt.max_short_tip);
///debug_info_of_specfic_node("m64043_200505_112554/8849050/ccs", sg, "inner_1");
///drop_inexact_edegs_at_bubbles(sg, bubble_dist);
if(clean_round > 0)
{
@@ -29696,7 +29686,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
asg_cut_tip(sg, asm_opt.max_short_tip);
}
}
if(VERBOSE >= 1)
{
fprintf(stderr, "\n\n**********final clean**********\n");
@@ -29715,7 +29704,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
asg_arc_del_orthology_multiple_way(sg, reverse_sources, 0.4, asm_opt.max_short_tip, ruIndex);
asg_cut_tip(sg, asm_opt.max_short_tip);
@@ -29725,7 +29713,6 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
asg_cut_tip(sg, asm_opt.max_short_tip);
asg_arc_del_simple_circle_untig(sources, coverage_cut, sg, 100, 0);
///note: don't apply asg_arc_del_too_short_overlaps() after this function!!!!
rescue_contained_reads_aggressive(NULL, sg, sources, coverage_cut, ruIndex, max_hang_length,
mini_overlap_length, 10, 1, 0, NULL, NULL, &b_mask_t);
@@ -29738,13 +29725,13 @@ 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);
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);
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;