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hic bubble

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chhylp123
2020-12-29 09:15:44 -05:00
parent 5d506e82c9
commit c545fd84c7
4 changed files with 169 additions and 98 deletions
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hic.cpp
+133 -22
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@@ -114,6 +114,7 @@ typedef struct {
kvec_t(uint32_t) list;
kvec_t(uint32_t) num;
kvec_t(uint64_t) pathLen;
uint64_t f_bub, b_bub;
} bubble_type;
typedef struct {
@@ -165,6 +166,11 @@ typedef struct {
kvec_t(pe_hit) a;
} kvec_pe_hit;
typedef struct {
kvec_t(hc_edge) a;
}kvec_hc_edge;
#define pe_hit_an1_key(x) ((x).s)
KRADIX_SORT_INIT(pe_hit_an1, pe_hit, pe_hit_an1_key, 8)
#define pe_hit_an2_key(x) ((x).e)
@@ -229,6 +235,8 @@ typedef struct {
reads_t R1, R2;
ha_ug_index* ug_index;
void build_bub_graph(ma_ug_t* ug, bubble_type* bub);
void init_ha_ug_index_opt(ha_ug_index* idx, ma_ug_t *ug, int k, pldat_t* p)
{
uint64_t i, n;
@@ -1416,12 +1424,12 @@ inline void get_bubbles(bubble_type* bub, uint64_t id, uint32_t* beg, uint32_t*
if(pathBase) (*pathBase) = bub->pathLen.a[id];
}
void identify_bubbles(ma_ug_t* ug, bubble_type* bub)
void identify_bubbles(ma_ug_t* ug, bubble_type* bub, hc_links* link)
{
asg_cleanup(ug->g);
if (!ug->g->is_symm) asg_symm(ug->g);
memset(bub, 0, sizeof(bubble_type));
uint32_t v, n_vtx = ug->g->n_seq * 2, tLen, i, mode = (((uint32_t)-1)<<2);
uint32_t v, n_vtx = ug->g->n_seq * 2, tLen, i, k, mode = (((uint32_t)-1)<<2);
uint64_t pathLen;
bub->ug = ug;
CALLOC(bub->index, n_vtx);
@@ -1511,15 +1519,24 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub)
if(bub->index[(beg>>1)] != (bub->num.n + 1)) bub->index[(beg>>1)] = (uint32_t)-1;
if(bub->index[(sink>>1)] != (bub->num.n + 1)) bub->index[(sink>>1)] = (uint32_t)-1;
///bub->index[(beg>>1)] = bub->index[(sink>>1)] = (uint32_t)-1;
}
for (i = 0; i < ug->g->n_seq; i++)
{
if(bub->index[i] == bub->num.n + 1) bub->index[i] = bub->num.n;
if(bub->index[i] > bub->num.n)
{
for (k = 0; k < link->a.a[i].f.n; k++)
{
if(link->a.a[i].f.a[k].del || link->a.a[i].f.a[k].dis != RC_1) continue;
bub->index[i] = bub->num.n;
///fprintf(stderr, "utg%.6ul\n", (int)(i+1));
break;
}
}
}
///free(bub->index); bub->index = NULL;
build_bub_graph(ug, bub);
}
@@ -1922,12 +1939,13 @@ void pop_pdq(pdq* q, uint64_t* min_v, uint64_t* min_dis)
}
void get_shortest_path(uint32_t src, pdq* pq, asg_t *sg)
void get_shortest_path(uint32_t src, pdq* pq, asg_t *sg, uint32_t* pre)
{
uint64_t v, u, i, nv, w;
asg_arc_t *av = NULL;
reset_pdq(pq);
pq->dis.a[src] = 0;
if(pre) pre[src] = (uint32_t)-1;
push_pdq(pq, src, 0);
while (pdq_cnt(*pq) > 0)
{
@@ -1947,6 +1965,7 @@ void get_shortest_path(uint32_t src, pdq* pq, asg_t *sg)
{
pq->dis.a[u] = pq->dis.a[v] + w;
push_pdq(pq, u, pq->dis.a[u]);
if(pre) pre[u] = v;
}
}
}
@@ -1969,7 +1988,7 @@ void all_pair_shortest_path(const ha_ug_index* idx, hc_links* link, MT* M)
if (sg->seq[v>>1].del) continue;
t = &(link->a.a[v>>1]);
if (t->e.n == 0) continue;
get_shortest_path(v, &pq, sg);
get_shortest_path(v, &pq, sg, NULL);
for (k = 0; k < pq.dis.n; k++)
{
if(pq.dis.a[k] == (uint64_t)-1) continue;
@@ -2477,7 +2496,7 @@ uint32_t v, uint32_t beg, uint32_t sink)
void set_reverse_links(uint32_t* bub, uint32_t n, kvec_t_u32_warp* reach, uint32_t root, hc_links* link)
{
uint64_t i, k, d = 0;
uint64_t i, k, d = RC_0;
uint32_t v;
for (i = 0; i < n; i++)
{
@@ -2498,11 +2517,13 @@ void set_reverse_links(uint32_t* bub, uint32_t n, kvec_t_u32_warp* reach, uint32
void collect_hc_reverse_links(hc_links* link, ma_ug_t* ug, bubble_type* bub)
{
uint64_t i, j, k, d = 0, m, pre;
uint64_t i, j, k, d = RC_0, m, pre;
uint32_t beg, sink, n, v, *a = NULL;
kvec_t_u32_warp stack, result;
hc_edge *e = NULL;
kv_init(stack.a); kv_init(result.a);
///clean all reverse overlaps within bubbles
///might be wrong
for (i = 0; i < bub->num.n-1; i++)
{
get_bubbles(bub, i, &beg, &sink, &a, &n, NULL);
@@ -2565,6 +2586,7 @@ void collect_hc_reverse_links(hc_links* link, ma_ug_t* ug, bubble_type* bub)
}
kv_destroy(stack.a); kv_destroy(result.a);
for (i = 0; i < link->a.n; i++)
{
for (k = m = 0; k < link->a.a[i].f.n; k++)
@@ -2581,7 +2603,7 @@ void collect_hc_reverse_links(hc_links* link, ma_ug_t* ug, bubble_type* bub)
if(link->a.a[i].f.a[k].del) continue;
if(link->a.a[i].f.a[k].uID == pre)
{
if(link->a.a[i].f.a[k].dis == 0) link->a.a[i].f.a[m-1].dis = 0;
if(link->a.a[i].f.a[k].dis == RC_0) link->a.a[i].f.a[m-1].dis = RC_0;
continue;
}
@@ -2594,9 +2616,6 @@ void collect_hc_reverse_links(hc_links* link, ma_ug_t* ug, bubble_type* bub)
}
// hc_edge *e = NULL;
// for (i = 0; i < link->a.n; i++)
// {
@@ -4198,7 +4217,80 @@ void weight_edges(ha_ug_index* idx, kvec_pe_hit* hits, hc_links* link, bubble_ty
}
}
void init_hic_p(ha_ug_index* idx, kvec_pe_hit* hits, hc_links* link, bubble_type* bub)
void build_bub_graph(ma_ug_t* ug, bubble_type* bub)
{
asg_t *sg = ug->g;
pdq pq;
init_pdq(&pq, sg->n_seq<<1);
uint32_t n_vtx = sg->n_seq<<1, v;
uint32_t *pre = NULL; MALLOC(pre, n_vtx);
uint64_t *flag = NULL; CALLOC(flag, sg->n_seq);
uint64_t k, b_id_0, b_id_1;
uint32_t beg, sink, n, *a, pre_id, adjecent;
for (k = 0; k < bub->num.n-1; k++)
{
get_bubbles(bub, k, &beg, &sink, &a, &n, NULL);
pre_id = beg>>1;
if(bub->index[pre_id] > bub->num.n)
{
flag[pre_id] |= 1;
flag[pre_id] |= (uint64_t)((uint64_t)pre_id<<33);
}
pre_id = sink>>1;
if(bub->index[pre_id] > bub->num.n)
{
flag[pre_id] |= 2;
flag[pre_id] |= (uint64_t)((uint64_t)pre_id<<2);
}
}
for (v = 0; v < n_vtx; ++v)
{
if(sg->seq[v>>1].del) continue;
if(flag[v>>1] == 0) continue;
if((flag[v>>1] & 1) && (flag[v>>1] & 2))
{
fprintf(stderr, "+utg%.6ul -> utg%.6ul\n",
(int)((flag[v>>1]>>33)+1), (int)((flag[v>>1]>>2)+1));
continue;
}
get_shortest_path(v, &pq, sg, pre);
for (k = 0; k < pq.dis.n; k++)
{
if(pq.dis.a[k] == (uint64_t)-1) continue;
if((flag[k>>1]&3) == 0) continue;
if(k == v) continue;
pre_id = pre[k];
adjecent = 0;
while (pre_id != v)
{
if(flag[pre_id>>1] > 0)
{
adjecent = 1;
break;
}
pre_id = pre[pre_id];
}
if(adjecent == 0)
{
b_id_0 = flag[k>>1] & 1? flag[k>>1]>>33 : flag[k>>1]>>2;
b_id_1 = flag[v>>1] & 1? flag[v>>1]>>33 : flag[v>>1]>>2;
if((flag[k>>1] & 3) == 3) fprintf(stderr, "ERROR1\n");
if((flag[v>>1] & 3) == 3) fprintf(stderr, "ERROR2\n");
fprintf(stderr, "-utg%.6ul -> utg%.6ul\n", (int)(b_id_0+1), (int)(b_id_1+1));
}
}
}
free(pre);
free(flag);
destory_pdq(&pq);
}
void init_hic_p(ha_ug_index* idx, kvec_pe_hit* hits, hc_links* link, bubble_type* bub, kvec_hc_edge* back_hc_edge)
{
uint64_t k, i, m, beg, end, t_d, r_idx, f_idx, b_size, med = (uint64_t)-1, uID;
uint32_t b_beg, b_end, n, *a, b_cnt;
@@ -4265,8 +4357,6 @@ void init_hic_p(ha_ug_index* idx, kvec_pe_hit* hits, hc_links* link, bubble_type
{
if((buf.a[k]&1) == 0) r_idx = k;
if((buf.a[k]&1) == 1) f_idx = k;
///fprintf(stderr, "%lu\t%lu\n", buf.a[k]>>1, buf.a[k]&1);
}
buf.n = MIN(r_idx, f_idx);
@@ -4372,19 +4462,29 @@ void init_hic_p(ha_ug_index* idx, kvec_pe_hit* hits, hc_links* link, bubble_type
fprintf(stderr, "idx->a: %f, idx->b: %f, idx->frac: %f, med: %lu\n",
(double)idx->a, (double)idx->b, (double)idx->frac, med);
back_hc_edge->a.n = 0;
hc_edge *e = NULL;
for (i = 0; i < link->a.n; i++)
{
for (k = 0; k < link->a.a[i].f.n; k++)
{
if(link->a.a[i].f.a[k].del) continue;
if(link->a.a[i].f.a[k].dis != 0) continue;
if(link->a.a[i].f.a[k].dis != RC_0) continue;
uID = link->a.a[i].f.a[k].uID;
e = get_hc_edge(link, i, uID, 0);
if(e) e->del = 1;
if(e)
{
kv_push(hc_edge, back_hc_edge->a, *e);
e->del = 1;
}
e = get_hc_edge(link, uID, i, 0);
if(e) e->del = 1;
if(e)
{
kv_push(hc_edge, back_hc_edge->a, *e);
e->del = 1;
}
}
}
@@ -5355,6 +5455,8 @@ int hic_short_align(const char *fn1, const char *fn2, ha_ug_index* idx)
double index_time = yak_realtime();
sldat_t sl;
gzFile fp1, fp2;
kvec_hc_edge back_hc_edge;
kv_init(back_hc_edge.a);
if ((fp1 = gzopen(fn1, "r")) == 0) return 0;
if ((fp2 = gzopen(fn2, "r")) == 0) return 0;
sl.ks1 = kseq_init(fp1);
@@ -5368,7 +5470,7 @@ int hic_short_align(const char *fn1, const char *fn2, ha_ug_index* idx)
fprintf(stderr, "u.n: %d, uID_bits: %lu, pos_bits: %lu\n", (uint32_t)idx->ug->u.n, idx->uID_bits, idx->pos_bits);
bubble_type bub;
identify_bubbles(idx->ug, &bub);
identify_bubbles(idx->ug, &bub, idx->link);
///print_bubbles(idx->ug, &bub, sl.hits.a.n?&sl.hits:NULL, idx->link, idx);
if(!load_hc_hits(&sl.hits, asm_opt.output_file_name))
@@ -5394,7 +5496,7 @@ int hic_short_align(const char *fn1, const char *fn2, ha_ug_index* idx)
///debug_hc_links(idx, idx->link, &sl, &bub, fn1);
init_hic_p((ha_ug_index*)sl.idx, &sl.hits, idx->link, &bub);
init_hic_p((ha_ug_index*)sl.idx, &sl.hits, idx->link, &bub, &back_hc_edge);
H_partition hap;
init_contig_partition(&hap, idx, &bub);
@@ -5404,8 +5506,17 @@ int hic_short_align(const char *fn1, const char *fn2, ha_ug_index* idx)
///print_hc_links(idx->link, 0, &hap);
///print_contig_partition(&hap, "final");
destory_contig_partition(&hap);
// uint32_t i;
// for (i = 0; i < idx->ug->g->n_seq; i++)
// {
// fprintf(stderr, "utg%.6ul, index: %u\n", (int)(i+1), bub.index[i]);
// }
destory_contig_partition(&hap);
kv_destroy(back_hc_edge.a);
return 1;
/*******************************for debug************************************/