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save bfore multiple overlaps

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chhylp123
2020-08-23 08:46:33 -04:00
parent 90d3cb69b9
commit 03cf0d475c
15 changed files with 1120 additions and 131 deletions
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Overlaps.cpp
+134 -50
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@@ -2107,6 +2107,37 @@ static inline int asg_is_single_edge(const asg_t *g, uint32_t v, uint32_t start_
return nv;
}
void debug_info_of_specfic_node(const char* name, asg_t *g, char* command)
{
fprintf(stderr, "\n\n\n");
uint32_t v, n_vtx = g->n_seq * 2, queryLen = strlen(name), flag = 0;
for (v = 0; v < n_vtx; ++v)
{
if(queryLen == Get_NAME_LENGTH(R_INF, (v>>1)) && memcmp(name, Get_NAME(R_INF, (v>>1)), Get_NAME_LENGTH(R_INF, (v>>1))) == 0)
{
if(flag == 0) fprintf(stderr, "\nafter %s\n", command);
fprintf(stderr, "****************graph ref_read: %.*s, dir: %u****************\n",
(int)Get_NAME_LENGTH(R_INF, (v>>1)), Get_NAME(R_INF, (v>>1)), v&1);
if(g->seq[v>>1].del)
{
fprintf(stderr, "read has already been deleted.\n");
return;
}
asg_arc_t *av = asg_arc_a(g, v);
uint32_t i, nv = asg_arc_n(g, v);
for (i = 0; i < nv; ++i)
{
fprintf(stderr, "target: %.*s, el: %u, strong: %u, ol: %u, del: %u\n",
(int)Get_NAME_LENGTH(R_INF, (av[i].v>>1)),
Get_NAME(R_INF, (av[i].v>>1)),
av[i].el, av[i].strong, av[i].ol, av[i].del);
}
flag = 1;
}
}
}
asg_t *ma_sg_gen(const ma_hit_t_alloc* sources, long long n_read, const ma_sub_t *coverage_cut,
int max_hang, int min_ovlp)
@@ -8206,13 +8237,96 @@ int asg_arc_del_short_diploi_by_suspect_edge(asg_t *g, int max_ext)
return n_cut;
}
int if_potential_false_node(ma_hit_t_alloc* paf, uint64_t rLen, ma_sub_t* max_left, ma_sub_t* max_right, int if_set)
{
max_left->s = max_right->s = rLen;
max_left->e = max_right->e = 0;
long long j;
uint32_t qs, qe;
for (j = 0; j < paf->length; j++)
{
if(paf->buffer[j].del) continue;
if(paf->buffer[j].el != 1) continue;
qs = Get_qs(paf->buffer[j]);
qe = Get_qe(paf->buffer[j]);
///overlaps from left side
if(qs == 0)
{
if(qs < max_left->s) max_left->s = qs;
if(qe > max_left->e) max_left->e = qe;
}
///overlaps from right side
if(qe == rLen)
{
if(qs < max_right->s) max_right->s = qs;
if(qe > max_right->e) max_right->e = qe;
}
///note: if (qs == 0 && qe == rLen)
///this overlap would be added to both b_left and b_right
///that is what we want
}
if (max_left->e > max_right->s) return 0;
long long new_left_e, new_right_s;
new_left_e = max_left->e;
new_right_s = max_right->s;
for (j = 0; j < paf->length; j++)
{
if(paf->buffer[j].del) continue;
if(paf->buffer[j].el != 1) continue;
qs = Get_qs(paf->buffer[j]);
qe = Get_qe(paf->buffer[j]);
///check contained overlaps
if(qs != 0 && qe != rLen)
{
///[qs, qe), [max_left.s, max_left.e)
if(qs < max_left->e && qe > max_left->e)
{
///if(qe > max_left->e) max_left->e = qe;
if(qe > max_left->e && qe > new_left_e) new_left_e = qe;
}
///[qs, qe), [max_right.s, max_right.e)
if(qs < max_right->s && qe > max_right->s)
{
///if(qs < max_right->s) max_right->s = qs;
if(qs < max_right->s && qs < new_right_s) new_right_s = qs;
}
if(if_set)
{
max_left->e = new_left_e;
max_right->s = new_right_s;
}
}
}
max_left->e = new_left_e;
max_right->s = new_right_s;
if (max_left->e > max_right->s) return 0;
return 1;
}
//reomve edge between two chromesomes
//this node must be a single read
int asg_arc_del_false_node(asg_t *g, int max_ext)
int asg_arc_del_false_node(asg_t *g, ma_hit_t_alloc* sources, int max_ext)
{
double startTime = Get_T();
kvec_t(uint64_t) b;
memset(&b, 0, sizeof(b));
ma_sub_t max_left, max_right;
uint32_t v, n_vtx = g->n_seq * 2;
long long n_cut = 0;
@@ -8242,6 +8356,11 @@ int asg_arc_del_false_node(asg_t *g, int max_ext)
continue;
}
if(if_potential_false_node(&(sources[v>>1]), g->seq[v>>1].len, &max_left, &max_right, 1)==0)
{
continue;
}
asg_arc_t *av = asg_arc_a(g, v);
kv_push(uint64_t, b, (uint64_t)((uint64_t)av[0].ol << 32 | (av - g->arc)));
}
@@ -9582,35 +9701,6 @@ void clean_weak_ma_hit_t(ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_source
void debug_info_of_specfic_node(const char* name, asg_t *g, char* command)
{
fprintf(stderr, "\n\n\n");
uint32_t v, n_vtx = g->n_seq * 2, queryLen = strlen(name);
for (v = 0; v < n_vtx; ++v)
{
if(queryLen == Get_NAME_LENGTH(R_INF, (v>>1)) && memcmp(name, Get_NAME(R_INF, (v>>1)), Get_NAME_LENGTH(R_INF, (v>>1))) == 0)
{
fprintf(stderr, "\nafter %s\n****************graph ref_read: %.*s, dir: %u****************\n",
command, (int)Get_NAME_LENGTH(R_INF, (v>>1)), Get_NAME(R_INF, (v>>1)), v&1);
if(g->seq[v>>1].del)
{
fprintf(stderr, "read has already been deleted.\n");
return;
}
asg_arc_t *av = asg_arc_a(g, v);
uint32_t i, nv = asg_arc_n(g, v);
for (i = 0; i < nv; ++i)
{
fprintf(stderr, "target: %.*s, el: %u, strong: %u, ol: %u, del: %u\n",
(int)Get_NAME_LENGTH(R_INF, (av[i].v>>1)),
Get_NAME(R_INF, (av[i].v>>1)),
av[i].el, av[i].strong, av[i].ol, av[i].del);
}
return;
}
}
}
void debug_info_of_specfic_read(const char* name, ma_hit_t_alloc* sources,
ma_hit_t_alloc* reverse_sources, int id, const char* command)
@@ -9636,8 +9726,8 @@ ma_hit_t_alloc* reverse_sources, int id, const char* command)
{
fprintf(stderr, "\n\n\nafter %s\n", command);
fprintf(stderr, "****************ma_hit_t (%lld)ref_read: %.*s****************\n",
i, (int)Get_NAME_LENGTH(R_INF, i), Get_NAME(R_INF, i));
fprintf(stderr, "****************ma_hit_t (%lld)ref_read: %.*s, len: %lu****************\n",
i, (int)Get_NAME_LENGTH(R_INF, i), Get_NAME(R_INF, i), Get_READ_LENGTH(R_INF, i));
fprintf(stderr, "sources Len: %d, is_fully_corrected: %d\n",
@@ -12954,12 +13044,12 @@ float drop_ratio)
#define T_ROUND 2
asg_t *g = ug->g;
int round = T_ROUND;
redo:
asg_pop_bubble_primary_trio(ug, bubble_dist, (uint32_t)-1, DROP);
untig_asg_arc_simple_large_bubbles_trio(ug, read_g, reverse_sources, 2, ruIndex, (uint32_t)-1, DROP);
if(just_bubble_pop == 0)
{
cut_trio_tip_primary(g, ug, tipsLen, (uint32_t)-1, 0, read_g, reverse_sources, ruIndex,
@@ -13013,7 +13103,7 @@ float drop_ratio)
{
if(round != T_ROUND)
{
unitig_arc_del_short_diploid_by_length(ug->g, drop_ratio);
unitig_arc_del_short_diploid_by_length(ug->g, drop_ratio);
}
round--;
goto redo;
@@ -22764,7 +22854,7 @@ kvec_asg_arc_t_warp* new_rtg_edges)
delete_useless_nodes(ug);
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,
@@ -26792,9 +26882,6 @@ int max_hang, int min_ovlp)
}
}
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,
@@ -26815,7 +26902,6 @@ 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))
{
@@ -26840,11 +26926,10 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
///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);
///debug_info_of_specfic_read("m54329U_190827_173812/166332272/ccs", sources, reverse_sources, -1, "clean");
sg = ma_sg_gen(sources, n_read, coverage_cut, max_hang_length, mini_overlap_length);
asg_arc_del_trans(sg, gap_fuzz);
asm_opt.coverage = get_coverage(sources, coverage_cut, n_read);
if(VERBOSE >= 1)
@@ -26856,9 +26941,8 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
}
asg_cut_tip(sg, asm_opt.max_short_tip);
///debug_info_of_specfic_node("m64062_190803_042216/15205346/ccs", sg, "inner_1");
///drop_inexact_edegs_at_bubbles(sg, bubble_dist);
///debug_info_of_specfic_node("m54329U_190827_173812/166332272/ccs", sg, "beg");
if(clean_round > 0)
{
@@ -26896,7 +26980,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
asg_arc_identify_simple_bubbles_multi(sg, 1);
//reomve edge between two chromesomes
//this node must be a single read
asg_arc_del_false_node(sg, asm_opt.max_short_tip);
asg_arc_del_false_node(sg, sources, asm_opt.max_short_tip);
asg_cut_tip(sg, asm_opt.max_short_tip);
/****************************may have bugs********************************/
/****************************may have bugs********************************/
@@ -27044,10 +27128,7 @@ long long bubble_dist, int read_graph, int write)
init_R_to_U(&ruIndex, n_read);
asg_t *sg = NULL;
ma_sub_t* coverage_cut = NULL;
// debug_info_of_specfic_read("m64011_190329_072846/80545633/ccs", sources, reverse_sources, -1, "clean");
///actually min_thres = asm_opt.max_short_tip + 1 there are asm_opt.max_short_tip reads
min_thres = asm_opt.max_short_tip + 1;
@@ -27073,6 +27154,9 @@ long long bubble_dist, int read_graph, int write)
&R_INF, output_file_name);
}
///debug_info_of_specfic_read("m64062_190803_042216/15205346/ccs", sources, reverse_sources, -1, "beg");
if (!(asm_opt.flag & HA_F_BAN_ASSEMBLY))
{
try_rescue_overlaps(sources, reverse_sources, n_read, 4);