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chhylp123
2021-09-10 17:17:44 -04:00
parent 17b5cb21d3
commit 809ca18dda
18 changed files with 1569 additions and 1031 deletions
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248
horder.cpp
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@@ -2178,9 +2178,9 @@ uint64_t rs, uint64_t re, uint64_t limit_s, uint64_t limit_e, int unique_only)
return cnt;
}
void detect_lowNs(kvec_pe_hit *hit, uint64_t sHit, uint64_t eHit, kvec_t_u64_warp *b,
h_cov_t *Np, uint64_t len, uint64_t cutoff_s, uint64_t cutoff_e, h_covs *res,
h_covs *cov_buf, h_covs *b_points, uint64_t local_bound, int unique_only)
int detect_lowNs(kvec_pe_hit *hit, uint64_t sHit, uint64_t eHit, kvec_t_u64_warp *b,
h_cov_t *Np, uint64_t len, uint64_t cutoff_s, uint64_t cutoff_e, uint64_t force_cutoff, uint64_t force_cutoff_cov,
h_covs *res, h_covs *cov_buf, h_covs *b_points, uint64_t local_bound, int unique_only)
{
uint64_t cov_hic, cov_utg, cov_ava, i, p0s, p0e, p1s, p1e, span_s, span_e, cutoff, bs, be, occ = 0;
uint64_t sPos, ePos, min_cutoff;
@@ -2219,6 +2219,18 @@ h_covs *cov_buf, h_covs *b_points, uint64_t local_bound, int unique_only)
radix_sort_ho64(b->a.a, b->a.a+b->a.n);
cov_utg = get_hic_cov_interval(b->a.a, b->a.n, 1, NULL, NULL, NULL);
cov_ava = (cov_utg? cov_hic/cov_utg:0);
if(force_cutoff != (uint64_t)-1 || force_cutoff_cov != (uint64_t)-1)
{
min_cutoff = get_sub_cov(hit, sHit, eHit, len, Np->s, Np->e, sPos, ePos, unique_only);
if((force_cutoff != (uint64_t)-1 && min_cutoff <= (cov_ava/force_cutoff)) ||
(force_cutoff_cov != (uint64_t)-1 && min_cutoff <= force_cutoff_cov))
{
kv_pushp(h_cov_t, *b_points, &p);
p->s = get_hit_suid(*hit, sHit); p->e = Np->dp; p->dp = 0;
return 1;
}
}
///if cov_ava == 0, do nothing or break?
/*******************************for debug************************************/
// fprintf(stderr, "\n[M::%s::] utg%.6lul, ulen: %lu, # hic hits: %lu, map cov: %lu, utg cov: %lu, average: %lu\n",
@@ -2269,24 +2281,29 @@ h_covs *cov_buf, h_covs *b_points, uint64_t local_bound, int unique_only)
{
kv_pushp(h_cov_t, *b_points, &p);
p->s = get_hit_suid(*hit, sHit); p->e = Np->dp; p->dp = 0;
return 1;
/*******************************for debug************************************/
// fprintf(stderr, "consensus_break-rid: %lu\n", p->e);
/*******************************for debug************************************/
}
}
return 0;
}
uint64_t break_scaffold(horder_t *h, uint64_t cutoff_s, uint64_t cutoff_e, uint64_t local_bound, int unique_only)
uint64_t break_scaffold(horder_t *h, uint64_t cutoff_s, uint64_t cutoff_e, uint64_t force_cutoff, uint64_t force_cutoff_cov,
uint64_t local_bound, int unique_only, h_covs *r_b_points)
{
uint64_t k, l, i, ulen;
kvec_t_u64_warp b; kv_init(b.a);
h_covs cov_buf; kv_init(cov_buf);
h_covs res; kv_init(res);
h_covs b_points; kv_init(b_points);
h_covs *b_points = NULL;
if(r_b_points) b_points = r_b_points;
else CALLOC(b_points, 1);
b_points->n = 0;
h_covs Ns; kv_init(Ns);
ma_ug_t *ug = h->ug;
kvec_pe_hit *hits = &(h->u_hits);
b_points.n = 0;
for (k = 1, l = 0; k <= hits->a.n; ++k)
{
if (k == hits->a.n || (get_hit_suid(*hits, k) != get_hit_suid(*hits, l)))
@@ -2302,8 +2319,10 @@ uint64_t break_scaffold(horder_t *h, uint64_t cutoff_s, uint64_t cutoff_e, uint6
{
for (i = 0; i < Ns.n; i++)
{
detect_lowNs(hits, l, k, &b, &(Ns.a[i]), ulen, cutoff_s, cutoff_e,
&res, &cov_buf, &b_points, local_bound, unique_only);
if(detect_lowNs(hits, l, k, &b, &(Ns.a[i]), ulen, cutoff_s, cutoff_e, force_cutoff,
force_cutoff_cov, &res, &cov_buf, b_points, local_bound, unique_only) && r_b_points){
b_points->a[b_points->n-1].dp = i;
}
}
}
}
@@ -2311,15 +2330,68 @@ uint64_t break_scaffold(horder_t *h, uint64_t cutoff_s, uint64_t cutoff_e, uint6
}
}
break_utg_horder(h, &b_points);
if(!r_b_points){
break_utg_horder(h, b_points);
kv_destroy(*b_points);
}
kv_destroy(b.a);
kv_destroy(cov_buf);
kv_destroy(res);
kv_destroy(b_points);
kv_destroy(Ns);
return b_points.n;
return b_points->n;
}
uint64_t break_scaffold_mean(horder_t *h, uint64_t cutoff_s, uint64_t cutoff_e, uint64_t force_cutoff, uint64_t force_cutoff_cov,
uint64_t local_bound, int unique_only, h_covs *r_b_points)
{
uint64_t k, l, i, ulen;
kvec_t_u64_warp b; kv_init(b.a);
h_covs cov_buf; kv_init(cov_buf);
h_covs res; kv_init(res);
h_covs *b_points = NULL;
if(r_b_points) b_points = r_b_points;
else CALLOC(b_points, 1);
b_points->n = 0;
h_covs Ns; kv_init(Ns);
ma_ug_t *ug = h->ug;
kvec_pe_hit *hits = &(h->u_hits);
for (k = 1, l = 0; k <= hits->a.n; ++k)
{
if (k == hits->a.n || (get_hit_suid(*hits, k) != get_hit_suid(*hits, l)))
{
ulen = ug->u.a[get_hit_suid(*hits, l)].len;
Ns.n = 0;
// if(ulen >= BREAK_THRES)
{
get_Ns(&(ug->u.a[get_hit_suid(*hits, l)]), &Ns);
if(Ns.n)
{
for (i = 0; i < Ns.n; i++)
{
if(detect_lowNs(hits, l, k, &b, &(Ns.a[i]), ulen, cutoff_s, cutoff_e, force_cutoff,
force_cutoff_cov, &res, &cov_buf, b_points, local_bound, unique_only) && r_b_points){
b_points->a[b_points->n-1].dp = i;
}
}
}
}
l = k;
}
}
if(!r_b_points){
break_utg_horder(h, b_points);
kv_destroy(*b_points);
}
kv_destroy(b.a);
kv_destroy(cov_buf);
kv_destroy(res);
kv_destroy(Ns);
return b_points->n;
}
@@ -2729,7 +2801,7 @@ void update_scg(horder_t *h, trans_col_t *t_idx)
h->sg.g->seq[i].ez[0] = ug->u.a[i].len>>1;
h->sg.g->seq[i].ez[1] = ug->u.a[i].len - (ug->u.a[i].len>>1);
}
idx = build_interval_idx(hits, ug);
idx = build_interval_idx(hits, ug);///idx is used to get density
for (i = 0, e.n = 0; i < hits->a.n; i++)
{
@@ -3397,10 +3469,12 @@ uint32_t get_sl_occ(sc_lay_t *sl)
void refine_layout(horder_t *h, sc_lay_t *sl, uint8_t *vis)
{
uint32_t k, m/**, max_utg, max_sc**/;
uint32_t k/**m, max_utg, max_sc**/;
lay_t *p = NULL;
uint8_t *sgv = NULL; MALLOC(sgv, sl->n);
double *w = NULL; MALLOC(w, sl->n);
/**
uint32_t *idx = NULL; MALLOC(idx, h->sg.g->n_seq);
memset(idx, -1, sizeof(uint32_t)*h->sg.g->n_seq);
@@ -3412,8 +3486,6 @@ void refine_layout(horder_t *h, sc_lay_t *sl, uint8_t *vis)
idx[p->a[m]>>1] = k;
}
}
/**
while (get_max_anchor(h, sl, vis, w, sgv, idx, &max_utg, &max_sc))
{
@@ -3422,6 +3494,7 @@ void refine_layout(horder_t *h, sc_lay_t *sl, uint8_t *vis)
vis[max_utg<<1] = vis[(max_utg<<1)+1] = 1;
idx[max_utg] = max_sc;
}
free(idx);
**/
for (k = 0; k < h->sg.g->n_seq; k++)
@@ -3434,8 +3507,7 @@ void refine_layout(horder_t *h, sc_lay_t *sl, uint8_t *vis)
vis[(k<<1)] = vis[(k<<1)+1] = 1;
}
free(w); free(idx); free(sgv);
free(w); free(sgv);
}
@@ -3591,7 +3663,7 @@ void update_avoids(horder_t *h, sc_lay_t *sl)
h->avoid.n = m;
}
void update_ug_by_layout(horder_t *h, sc_lay_t *sl)
void update_ug_by_layout(horder_t *h, sc_lay_t *sl, ma_ug_t* i_ug)
{
uint32_t i;
lay_t *p = NULL;
@@ -3603,7 +3675,7 @@ void update_ug_by_layout(horder_t *h, sc_lay_t *sl)
{
p = &(sl->a[i]);
kv_pushp(ma_utg_t, sug->u, &pu);
generate_scaffold(pu, p, h->ug, h->r_g);
generate_scaffold(pu, p, i_ug?i_ug:h->ug, h->r_g);
}
ma_ug_destroy(h->ug);
h->ug = sug;
@@ -3677,7 +3749,14 @@ void get_long_switch_scaffolds(horder_t *h, sc_lay_t *sl, osg_t *lg)
kv_destroy(idx);
}
void layout_scg(horder_t *h, double nw_thres, uint32_t occ_thres)
void destory_sc_lay_t(sc_lay_t *sl)
{
uint32_t i;
for (i = 0; i < sl->n; i++) kv_destroy(sl->a[i]);
kv_destroy(*sl);
}
void layout_scg(horder_t *h, double nw_thres, uint32_t occ_thres, sc_lay_t *r_sl)
{
uint32_t k;
osg_arc_t *p = NULL, *lp = NULL;
@@ -3708,17 +3787,23 @@ void layout_scg(horder_t *h, double nw_thres, uint32_t occ_thres)
get_backbone_layout(h, &sl, lg, vis);
get_long_switch_scaffolds(h, &sl, lg);
// get_long_switch_scaffolds(h, &sl, lg);
refine_layout(h, &sl, vis);
// print_N50_layout(h->ug, &sl);
update_ug_by_layout(h, &sl);
update_ug_by_layout(h, &sl, NULL);
print_N50(h->ug);
kv_destroy(sl);
if(r_sl){
r_sl->a = sl.a; sl.a = NULL;
r_sl->m = sl.m; sl.m = 0;
r_sl->n = sl.n; sl.n = 0;
}
destory_sc_lay_t(&sl);
osg_destroy(lg);
free(vis);
}
@@ -3729,7 +3814,7 @@ void renew_scaffold(horder_t *h)
while (1)
{
update_u_hits(&(h->u_hits), &(h->r_hits), h->ug, h->r_g);
if(!break_scaffold(h, 5, 15, 2500000, 1)) break;
if(!break_scaffold(h, 5, 15, (uint64_t)-1, (uint64_t)-1, 2500000, 1, NULL)) break;
print_N50(h->ug);
}
fprintf(stderr, "[M::%s::%.3f] \n", __func__, yak_realtime()-index_time);
@@ -3789,7 +3874,7 @@ void scaffold_hap(horder_t *h, ug_opt_t *opt, trans_col_t *t_idx, uint32_t round
{
update_u_hits(&(h->u_hits), &(h->r_hits), h->ug, h->r_g);
update_scg(h, t_idx);
layout_scg(h, 1.001, 19);
layout_scg(h, 1.001, 19, NULL);
renew_scaffold(h);
}
@@ -3832,7 +3917,7 @@ void scaffold_ug(horder_t *h, ma_ug_t *ug, ug_opt_t *opt, uint32_t round, char *
fprintf(stderr, "[M::%s::]**i->%u**\n", __func__, i);
update_scg(h, NULL);
fprintf(stderr, "[M::%s::]***i->%u***\n", __func__, i);
layout_scg(h, 1.001, 19);
layout_scg(h, 1.001, 19, NULL);
fprintf(stderr, "[M::%s::]****i->%u****\n", __func__, i);
renew_scaffold(h);
fprintf(stderr, "[M::%s::]*****i->%u*****\n", __func__, i);
@@ -3887,7 +3972,7 @@ asg_t *i_rg, ma_ug_t* i_ug, bubble_type* bub, kv_u_trans_t *ref, ug_opt_t *opt,
{
update_u_hits(&(h->u_hits), &(h->r_hits), h->ug, h->r_g);
update_scg(h, t_idx);
layout_scg(h, 1.001, 19);
layout_scg(h, 1.001, 19, NULL);
renew_scaffold(h);
}
@@ -3902,6 +3987,113 @@ asg_t *i_rg, ma_ug_t* i_ug, bubble_type* bub, kv_u_trans_t *ref, ug_opt_t *opt,
return h;
}
void cpy_u_hits(kvec_pe_hit *u_hits, kvec_pe_hit *i_hits, uint32_t u_n)
{
uint64_t i;
memset(u_hits, 0, sizeof(kvec_pe_hit));
u_hits->pos_mode = i_hits->pos_mode;
u_hits->uID_bits = i_hits->uID_bits;
u_hits->a.n = u_hits->a.m = i_hits->a.n;
MALLOC(u_hits->a.a, u_hits->a.n);
memcpy(u_hits->a.a, i_hits->a.a, u_hits->a.n*sizeof(pe_hit));
for (i = 0; i < u_hits->a.n; i++) u_hits->a.a[i].id = 1;
idx_hits(u_hits, u_n);
}
void update_sc_lay(sc_lay_t *sl, h_covs *b)
{
uint64_t k, l, i, pidx, cidx;
lay_t *s = NULL;
lay_t *p = NULL;
for (k = 1, l = 0; k <= b->n; ++k)
{
if (k == b->n || (b->a[k].s != b->a[l].s))
{
s = &(sl->a[b->a[l].s]);
for (i = l, pidx = 0; i < k; i++){
cidx = b->a[i].dp;
kv_pushp(lay_t, *sl, &p);
kv_init(*p);
p->n = p->m = (cidx - pidx + 1)<<1;
MALLOC(p->a, p->n);
mempcpy(p->a, s->a + (pidx<<1), sizeof(*(p->a))*p->n);
pidx = cidx + 1;
}
if(pidx >= (s->n>>1)) fprintf(stderr, "ERROR-update\n");
cidx = (s->n>>1)-1;
kv_pushp(lay_t, *sl, &p);
kv_init(*p);
p->n = p->m = (cidx - pidx + 1)<<1;
MALLOC(p->a, p->n);
mempcpy(p->a, s->a + (pidx<<1), sizeof(*(p->a))*p->n);
free(s->a); s->n = s->m = 0;
l = k;
}
}
for (i = k = 0; i < sl->n; i++){
if(!sl->a[i].a) continue;
sl->a[k] = sl->a[i];
sl->a[i].a = NULL; sl->a[i].n = sl->a[i].m = 0;
if(sl->a[k].n == 2){
sl->a[k].a[0] >>= 1; sl->a[k].a[0] <<= 1;
sl->a[k].a[1] >>= 1; sl->a[k].a[1] <<= 1; sl->a[k].a[1]++;
}
k++;
}
sl->n = k;
}
void renew_scaffold_utg(horder_t *h, sc_lay_t *sl, ma_ug_t* i_ug)
{
double index_time = yak_realtime();
h_covs b; kv_init(b);
while (1)
{
update_u_hits(&(h->u_hits), &(h->r_hits), h->ug, h->r_g);
if(!break_scaffold(h, 5, 15, 15, 25, 2500000, 1, &b)) break;
update_sc_lay(sl, &b);
update_ug_by_layout(h, sl, i_ug);
print_N50(h->ug);
}
fprintf(stderr, "[M::%s::%.3f] \n", __func__, yak_realtime()-index_time);
kv_destroy(b);
}
spg_t *scf_g(sc_lay_t *sl, ma_ug_t* ug)
{
spg_t *scg = NULL; CALLOC(scg, 1); scg->ug = ug;
uint64_t i, k;
lay_t *p = NULL;
for (i = 0; i < sl->n; i++){
p = &(sl->a[i]);
kv_push(uint64_t, scg->idx, (uint64_t)scg->dst.n << 32 | (p->n>>1));
for (k = 0; k < p->n; k+=2) kv_push(uint32_t, scg->dst, p->a[k]);
}
return scg;
}
spg_t *horder_utg(kvec_pe_hit *i_hits, uint64_t i_hits_uid_bits, uint64_t i_hits_pos_mode,
asg_t *i_rg, ma_ug_t* i_ug, bubble_type* bub, ug_opt_t *opt)
{
horder_t *h = NULL; CALLOC(h, 1);
sc_lay_t sl; kv_init(sl);
get_r_hits(i_hits, &(h->r_hits), i_rg, i_ug, bub, i_hits_uid_bits, i_hits_pos_mode);
h->r_g = copy_read_graph(i_rg);
horder_clean_sg_by_utg(h->r_g, i_ug);
h->ug = copy_untig_graph(i_ug); asg_destroy(h->ug->g); h->ug->g = NULL;
cpy_u_hits(&(h->u_hits), i_hits, h->ug->u.n);
update_scg(h, NULL);
layout_scg(h, ((double)1)/((double)0.75), 19, &sl);
renew_scaffold_utg(h, &sl, i_ug);
spg_t *scg = scf_g(&sl, i_ug);
destory_sc_lay_t(&sl);
destory_horder_t(&h);
return scg;
}
void ha_aware_order(kvec_pe_hit *r_hits, asg_t *rg, ma_ug_t *ug_fa, ma_ug_t *ug_mo, kv_u_trans_t *ref,