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chhylp123
2021-04-01 21:02:57 -04:00
parent 0605aa1961
commit 46e899bbae
11 changed files with 1494 additions and 401 deletions
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hic.cpp
+225 -13
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@@ -19,7 +19,7 @@ KDQ_INIT(uint64_t)
#define OFFSET_RATE 0.000000001
#define OFFSET_SECOND_RATE 0.0000000001
#define SCALL 10000
#define OFFSET_RATE_MAX_W 20.8286263517*SCALL
#define OFFSET_RATE_MAX_W 6.90675477865*SCALL
#define OFFSET_RATE_MIN_W 4.0000003e-10*SCALL
#define HIC_COUNTER_BITS 12
@@ -4143,8 +4143,8 @@ void print_hc_links(hc_links* link, int dir, H_partition* hap)
}
}
fprintf(stderr, "self-utg%.6dl\tFW:%f\tRW:%f\tRT:%f\n**************************************************\n",
(int)(i+1), f_w, r_w, (f_w+r_w) != 0? r_w/(f_w+r_w):0);
// fprintf(stderr, "self-utg%.6dl\tFW:%f\tRW:%f\tRT:%f\n**************************************************\n",
// (int)(i+1), f_w, r_w, (f_w+r_w) != 0? r_w/(f_w+r_w):0);
}
}
@@ -7437,6 +7437,7 @@ void update_bsg(asg_t *bsg, kvec_asg_arc_t_warp* edges)
}
void resolve_bubble_chain_tangle(ma_ug_t* ug, bubble_type* bub)
{
double index_time = yak_realtime();
ma_ug_t *bub_ug = bub->b_ug;
asg_t *bsg = bub->b_g;
uint32_t k, i, v, n_vx, new_bub;
@@ -7605,11 +7606,13 @@ void resolve_bubble_chain_tangle(ma_ug_t* ug, bubble_type* bub)
kv_destroy(res_btg.a); kv_destroy(res_utg.a); kv_destroy(edges.a);
///print_debug_bubble_graph(bub, ug, asm_opt.output_file_name);
fprintf(stderr, "[M::%s::%.3f]\n", __func__, yak_realtime()-index_time);
}
void update_bubble_chain(ma_ug_t* ug, bubble_type* bub, uint32_t is_middle, uint32_t is_end)
{
double index_time = yak_realtime();
if(bub->b_ug) ma_ug_destroy(bub->b_ug);
if(bub->chain_weight.a) kv_destroy(bub->chain_weight);
kvec_t_u32_warp broken;
@@ -7828,7 +7831,7 @@ void update_bubble_chain(ma_ug_t* ug, bubble_type* bub, uint32_t is_middle, uint
}
}
**/
fprintf(stderr, "[M::%s::%.3f]\n", __func__, yak_realtime()-index_time);
}
void set_b_utg_weight_flag(bubble_type* bub, buf_t* b, uint32_t v, uint8_t* vis_flag, uint32_t flag, uint32_t* occ)
@@ -8187,6 +8190,7 @@ int double_check_bub_branch(asg_arc_t *t, ma_ug_t *bs_ug, double *e_w, uint32_t
void clean_bubble_chain_by_HiC(ma_ug_t* ug, hc_links* link, bubble_type* bub)
{
double index_time = yak_realtime();
ma_ug_t *bs_ug = bub->b_ug;
uint32_t v, u, i, m, max_i, nv, rv, n_vx, root, flag_pri = 1, flag_aux = 2, flag_ava = 4, occ;
double w, cutoff = 2/**, max_w_cutoff = MAX(MIN(100*OFFSET_RATE_MIN_W, OFFSET_RATE_MAX_W/100), OFFSET_RATE_MIN_W)**/;
@@ -8383,11 +8387,13 @@ void clean_bubble_chain_by_HiC(ma_ug_t* ug, hc_links* link, bubble_type* bub)
free(vis); free(is_vis); free(is_used); free(dedup); free(b.b.a); free(e_w); free(e_occ);
kv_destroy(stack.a); kv_destroy(result.a); kv_destroy(res_utg.a); kv_destroy(edges.a);
ma_ug_destroy(back_bs_ug);
fprintf(stderr, "[M::%s::%.3f]\n", __func__, yak_realtime()-index_time);
}
void append_boundary_chain(ma_ug_t* ug, hc_links* link, bubble_type* bub)
{
double index_time = yak_realtime();
ma_ug_t *bs_ug = bub->b_ug;
uint32_t v, u, i, k, beg_idx, m, nv, n_vx, flag_pri = 1, flag_aux = 2, flag_ava = 4;
uint32_t root, rId_0, ori_0, root_0, new_bub;
@@ -8538,6 +8544,7 @@ void append_boundary_chain(ma_ug_t* ug, hc_links* link, bubble_type* bub)
// }
// }
/*******************************for debug************************************/
fprintf(stderr, "[M::%s::%.3f]\n", __func__, yak_realtime()-index_time);
}
int cmp_chain_hic_w_weight(const void * a, const void * b)
@@ -9408,12 +9415,12 @@ int get_trans_rate_function(ha_ug_index* idx, kvec_pe_hit* hits, hc_links* link,
return 0;
}
// for (i = 0; i < dis->n; i++)
// {
// if(i > 0 && dis->a[i].beg != dis->a[i-1].end) fprintf(stderr, "ERROR: dis->a[i].beg: %lu, dis->a[i-1].end: %lu\n", dis->a[i].beg, dis->a[i-1].end);
// fprintf(stderr, "beg: %lu, end: %lu, cnt_0: %lu, cnt_1: %lu, error_rate: %f\n",
// dis->a[i].beg, dis->a[i].end, dis->a[i].cnt_0, dis->a[i].cnt_1, (double)(dis->a[i].cnt_1)/(double)(dis->a[i].cnt_1 + dis->a[i].cnt_0));
// }
for (i = 0; i < dis->n; i++)
{
if(i > 0 && dis->a[i].beg != dis->a[i-1].end) fprintf(stderr, "ERROR: dis->a[i].beg: %lu, dis->a[i-1].end: %lu\n", dis->a[i].beg, dis->a[i-1].end);
fprintf(stderr, "beg: %lu, end: %lu, cnt_0: %lu, cnt_1: %lu, error_rate: %f\n",
dis->a[i].beg, dis->a[i].end, dis->a[i].cnt_0, dis->a[i].cnt_1, (double)(dis->a[i].cnt_1)/(double)(dis->a[i].cnt_1 + dis->a[i].cnt_0));
}
LeastSquare_advance(dis, idx, med);
// fprintf(stderr, "idx->a: %f, idx->b: %f, idx->frac: %f, med: %lu\n",
@@ -9441,6 +9448,196 @@ int get_trans_rate_function(ha_ug_index* idx, kvec_pe_hit* hits, hc_links* link,
}
int get_trans_rate_function_advance(ha_ug_index* idx, kvec_pe_hit* hits, hc_links* link, bubble_type* bub, MT* M, H_partition* hap, trans_idx* dis)
{
kvec_t(uint64_t) buf;
kv_init(buf);
uint64_t beg, end, cnt[2];
uint64_t k, i, t_d, r_idx, f_idx, med = (uint64_t)-1;
int beg_status, end_status;
for (i = 0; i < link->a.n; i++)
{
for (k = 0; k < link->a.a[i].e.n; k++)
{
link->a.a[i].e.a[k].dis = (uint64_t)-1;
}
}
fill_utg_distance_multi(idx, link, M, bub);
buf.n = 0;
for (k = 0; k < hits->a.n; ++k)
{
beg = ((hits->a.a[k].s<<1)>>(64 - idx->uID_bits));
end = ((hits->a.a[k].e<<1)>>(64 - idx->uID_bits));
if(IF_HOM(beg, *bub)) continue;
if(IF_HOM(end, *bub)) continue;
t_d = get_hic_distance(&(hits->a.a[k]), link, idx);
if(t_d == (uint64_t)-1) continue;
if(beg == end)
{
t_d = (t_d << 1);
}
else
{
beg_status = get_phase_status(hap, beg);
if(beg_status != 1 && beg_status != -1) continue;
end_status = get_phase_status(hap, end);
if(end_status != 1 && end_status != -1) continue;
if(beg_status != end_status)
{
t_d = (t_d << 1) + 1;
}
else
{
t_d = (t_d << 1);
}
}
kv_push(uint64_t, buf, t_d);
}
///might have bias, we may not use right linkage larger than trans rc linkage
radix_sort_hc64(buf.a, buf.a+buf.n);
for (k = 0, r_idx = f_idx = (uint64_t)-1; k < buf.n; k++)
{
if((buf.a[k]&1) == 0) r_idx = k;
if((buf.a[k]&1) == 1) f_idx = k;
}
buf.n = MIN(r_idx, f_idx);
trans_p_t* p = NULL;
dis->n = 0;
uint64_t bin_size = MIN(2250, buf.n>>8), m;
i = 0;
while (i < buf.n)
{
kv_pushp(trans_p_t, *dis, &p);
p->beg = i;
cnt[0] = cnt[1] = 0;
k = MIN(i+bin_size, buf.n);
for (; i < k; i++)
{
cnt[buf.a[i]&1]++;
}
p->end = i;
p->cnt_0 = cnt[0];
p->cnt_1 = cnt[1];
}
i = m = 0; med = (uint64_t)-1;
while(i < dis->n)
{
if(dis->a[i].cnt_0 > 0 && dis->a[i].cnt_1 > 0)
{
dis->a[m] = dis->a[i];
m++;
i++;
continue;
}
if(med == (uint64_t)-1) med = buf.a[dis->a[i].beg]>>1;
k = i; cnt[0] = cnt[1] = 0;
for (; i < dis->n; i++)
{
cnt[0] += dis->a[i].cnt_0;
cnt[1] += dis->a[i].cnt_1;
if(cnt[0] > 0 && cnt[1] > 0) break;
}
if(i < dis->n)
{
dis->a[m].cnt_0 = cnt[0];
dis->a[m].cnt_1 = cnt[1];
dis->a[m].beg = dis->a[k].beg;
dis->a[m].end = dis->a[i].end;
m++;
i++;
continue;
}
cnt[0] -= dis->a[k].cnt_0;
cnt[1] -= dis->a[k].cnt_1;
while (1)
{
cnt[0] += dis->a[k].cnt_0;
cnt[1] += dis->a[k].cnt_1;
if(cnt[0] > 0 && cnt[1] > 0) break;
if(k == 0)
{
k = (uint64_t)-1;
break;
}
k--;
}
if(k != (uint64_t)-1)
{
dis->a[m].cnt_0 = cnt[0];
dis->a[m].cnt_1 = cnt[1];
dis->a[m].end = dis->a[i-1].end;
continue;
}
m = 0;
break;
}
dis->n = m;
if(dis->n == 0)
{
kv_destroy(buf);
return 0;
}
for (i = 0; i < dis->n; i++)
{
dis->a[i].beg = buf.a[dis->a[i].beg]>>1;
dis->a[i].end = (buf.a[dis->a[i].end-1]>>1);
}
for (i = 0; i < dis->n - 1; i++)
{
dis->a[i].end += ((dis->a[i+1].beg - dis->a[i].end)/2);
dis->a[i+1].beg = dis->a[i].end;
}
for (i = 0; i < dis->n; i++)
{
if(i > 0 && dis->a[i].beg != dis->a[i-1].end) fprintf(stderr, "ERROR: dis->a[i].beg: %lu, dis->a[i-1].end: %lu\n", dis->a[i].beg, dis->a[i-1].end);
fprintf(stderr, "beg: %lu, end: %lu, cnt_0: %lu, cnt_1: %lu, error_rate: %f\n",
dis->a[i].beg, dis->a[i].end, dis->a[i].cnt_0, dis->a[i].cnt_1, (double)(dis->a[i].cnt_1)/(double)(dis->a[i].cnt_1 + dis->a[i].cnt_0));
}
LeastSquare_advance(dis, idx, med);
// fprintf(stderr, "idx->a: %f, idx->b: %f, idx->frac: %f, med: %lu\n",
// (double)idx->a, (double)idx->b, (double)idx->frac, med);
dis->max = dis->a[dis->n-1].end;
kv_destroy(buf);
if(idx->a < 0) idx->a = 0;
if(idx->a == 0)
{
idx->b = MAX((((double)(dis->a[dis->n-1].cnt_1))/((double)(dis->a[dis->n-1].cnt_0 + dis->a[dis->n-1].cnt_1))), idx->b);
}
if(idx->b < 0 && get_trans(idx, dis->max) < 0)
{
idx->b = ((double)(dis->a[dis->n-1].cnt_1))/((double)(dis->a[dis->n-1].cnt_0 + dis->a[dis->n-1].cnt_1));
}
// fprintf(stderr, "idx->a: %f, idx->b: %f, idx->frac: %f, med: %lu\n",
// (double)idx->a, (double)idx->b, (double)idx->frac, med);
return 1;
}
void init_hic_p(ha_ug_index* idx, kvec_pe_hit* hits, hc_links* link, bubble_type* bub,
kvec_hc_edge* back_hc_edge, MT* M, H_partition* hap, uint32_t ignore_dis)
{
@@ -9450,7 +9647,7 @@ kvec_hc_edge* back_hc_edge, MT* M, H_partition* hap, uint32_t ignore_dis)
if(bub->round_id > 0 && ignore_dis == 0)
{
is_comples_weight = get_trans_rate_function(idx, hits, link, bub, M, hap, &dis);
is_comples_weight = get_trans_rate_function_advance(idx, hits, link, bub, M, hap, &dis);
}
@@ -10304,6 +10501,7 @@ void print_contig_partition(H_partition* hap, const char* debug)
void adjust_contig_partition(H_partition* hap, hc_links* link)
{
double index_time = yak_realtime();
uint32_t i, k, *h0, h0_n, *h1, h1_n;
uint32_t h0_status[4], h1_status[4], h0_status_max;
int h0_h, h1_h;
@@ -10404,6 +10602,7 @@ void adjust_contig_partition(H_partition* hap, hc_links* link)
hap->g_p.a[i].weight[1] = get_cluster_weight(hap, link, h1, h1_n);
hap->g_p.a[i].weight_convex = get_cluster_inner_weight(hap, link, h0, h0_n, h1, h1_n);
}
fprintf(stderr, "[M::%s::%.3f]\n", __func__, yak_realtime()-index_time);
}
uint32_t get_weightest_uid(uint32_t* a, uint32_t n, H_partition* hap, uint8_t* hap_label_flag,
@@ -11733,6 +11932,7 @@ int graph_bipartiteness(uint32_t* b_a, uint32_t b_a_n, uint8_t *color, hc_links*
void assign_per_unitig_G_partition(G_partition* g_p, uint64_t hap_n, hc_links* link, bubble_type* bub,
uint32_t bubble_first)
{
double index_time = yak_realtime();
reset_G_partition(g_p, hap_n);
partition_warp* res = NULL;
@@ -11872,7 +12072,7 @@ uint32_t bubble_first)
g_p->index[res->a.a[k]] = (g_p->index[res->a.a[k]] << 1) + 1;
}
}
fprintf(stderr, "[M::%s::%.3f]\n", __func__, yak_realtime()-index_time);
}
typedef struct {
@@ -12093,6 +12293,7 @@ bub_sort_vec* w_stack, uint8_t* vis, uint32_t* set_hap, uint32_t n_utg, uint32_t
void sort_bubble_ele(G_partition* g_p, hc_links* link, bubble_type* bub, uint32_t n_utg)
{
double index_time = yak_realtime();
kvec_t_u64_warp stack; kv_init(stack.a);
bub_sort_vec w_stack; kv_init(w_stack);
uint8_t* vis = NULL; MALLOC(vis, n_utg);
@@ -12106,6 +12307,7 @@ void sort_bubble_ele(G_partition* g_p, hc_links* link, bubble_type* bub, uint32_
}
kv_destroy(stack.a); kv_destroy(w_stack); free(vis); free(set_hap);
fprintf(stderr, "[M::%s::%.3f]\n", __func__, yak_realtime()-index_time);
}
uint32_t init_contig_partition(H_partition* hap, ha_ug_index* idx, bubble_type* bub, hc_links* link)
@@ -13214,22 +13416,32 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
bub.round_id = 0; bub.n_round = 2;
for (bub.round_id = 0; bub.round_id < bub.n_round; bub.round_id++)
{
fprintf(stderr, "0********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
identify_bubbles(idx->ug, &bub, idx->cov->t_ch->is_r_het);
fprintf(stderr, "1********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
if(bub.round_id == 0)
{
fprintf(stderr, "2********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
collect_hc_links(sl.idx, &sl.hits, &link, &bub, &M);
fprintf(stderr, "3********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
collect_hc_reverse_links(&link, idx->ug, &bub);
fprintf(stderr, "4********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
}
init_hic_p((ha_ug_index*)sl.idx, &sl.hits, &link, &bub, &back_hc_edge, &M, &hap, 0);
fprintf(stderr, "5********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
///init_hic_p_new((ha_ug_index*)sl.idx, &sl.hits, idx->link, &bub, &back_hc_edge, &M);
reset_H_partition(&hap, (bub.round_id == 0? 1 : 0));
fprintf(stderr, "6********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
init_contig_partition(&hap, idx, &bub, &link);
fprintf(stderr, "7********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
phasing_improvement(&hap, &(hap.g_p), idx, &bub, &link);
fprintf(stderr, "8********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
label_unitigs(&(hap.g_p), idx->ug);
fprintf(stderr, "9********bub.round_id: %u(::%.3f)********\n", bub.round_id, yak_realtime());
///print_hc_links(idx->link, 0, &hap);
}
///print_hc_links(idx->link, 0, &hap);
print_hc_links(&link, 0, &hap);
cluster_contigs(&bub, idx, &sl.hits, &M, &hap, &link);