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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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hic.cpp
+201 -34
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@@ -2378,7 +2378,7 @@ void dfs_bubble(asg_t *g, kvec_t_u32_warp* stack, kvec_t_u32_warp* result, uint3
uint32_t get_unitig_het_arb(ma_ug_t* ug, uint32_t uid, uint8_t *r_het_flag, kv_u_trans_t *ref, uint32_t m_het_occ,
uint32_t m_het_label, uint32_t p_het_label, uint32_t n_het_label)
{
if(ref && u_trans_n(*ref, uid) > 0) return m_het_label;
if(ref && ref->idx.n > 0 && u_trans_n(*ref, uid) > 0) return m_het_label;
ma_utg_t *u = &(ug->u.a[uid]);
uint32_t k, rId;
uint32_t het_occ, hom_occ;
@@ -2411,7 +2411,6 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *r_het_flag, kv_u_t
uint64_t pathLen;
bub->ug = ug;
bub->b_bub = bub->b_end_bub = bub->tangle_bub = bub->cross_bub = bub->mess_bub = 0;
if(bub->round_id == 0)
{
buf_t b; memset(&b, 0, sizeof(buf_t)); b.a = (binfo_t*)calloc(n_vtx, sizeof(binfo_t));
@@ -2421,10 +2420,8 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *r_het_flag, kv_u_t
bub->b_ug = NULL; kv_init(bub->chain_weight);
bub->b_s_idx.n = ug->g->n_seq;
memset(bub->b_s_idx.a, -1, bub->b_s_idx.n * sizeof(uint64_t));
CALLOC(bub->index, n_vtx);
for (i = 0; i < ug->g->n_seq; i++) ug->g->seq[i].c = 0;
for (v = 0; v < n_vtx; ++v)
{
if(ug->g->seq[v>>1].del) continue;
@@ -2445,7 +2442,6 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *r_het_flag, kv_u_t
}
}
kvec_t_u32_warp stack, result;
kv_init(stack.a); kv_init(result.a);
for (v = 0; v < n_vtx; ++v)
@@ -2498,16 +2494,14 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *r_het_flag, kv_u_t
}
}
}
kv_push(uint32_t, bub->num, bub->list.n);
free(b.a); free(b.S.a); free(b.T.a); free(b.b.a); free(b.e.a);
bub->f_bub = bub->num.n - 1; ///bub->s_bub = bub->num.n - 1;
for (i = 0; i < ug->g->n_seq; i++)
{
bub->index[i] = get_unitig_het_arb(ug, i, r_het_flag, ref, 20, M_het(*bub), P_het(*bub), (uint32_t)-1);
}
for (i = 0; i < ug->g->n_seq; i++)
{
bub->index[i] = get_unitig_het_arb(ug, i, r_het_flag, ref, 20, M_het(*bub), P_het(*bub), (uint32_t)-1);
}
for (i = 0; i < bub->f_bub; i++)
{
get_bubbles(bub, i, &beg, &sink, &a, &n, &pathLen);
@@ -2555,7 +2549,6 @@ void identify_bubbles(ma_ug_t* ug, bubble_type* bub, uint8_t *r_het_flag, kv_u_t
bub->b_s_idx.a[v] |= i;
}
}
for (i = 0; i < ug->g->n_seq; i++)
{
if(bub->index[i] == M_het(*bub)) bub->index[i] = P_het(*bub);
@@ -4923,7 +4916,7 @@ int load_hc_hits(kvec_pe_hit* hits, ma_ug_t* ug, const char *fn)
}
fclose(fp);
// fprintf(stderr, "[M::%s::] ==> Hi-C linkages have been loaded\n", __func__);
fprintf(stderr, "[M::%s::] ==> Hi-C linkages have been loaded\n", __func__);
return 1;
}
@@ -14883,14 +14876,56 @@ inline uint32_t trans_checking_pass(bubble_type* bub, kv_u_trans_t *ref, uint32_
return 1;
}
uint32_t get_u_trans_spec_idx(kv_u_trans_t *ta, uint32_t qn, uint32_t tn, u_trans_t **r_a, uint32_t *occ, uint32_t *idx)
{
if(r_a) (*r_a) = NULL;
if(occ) (*occ) = 0;
if(idx) (*idx) = (uint32_t)-1;
u_trans_t *a = NULL;
uint32_t n, st, i;
a = u_trans_a(*ta, qn);
n = u_trans_n(*ta, qn);
for (st = 0, i = 1; i <= n; ++i)
{
if (i == n || a[i].tn != a[st].tn)
{
if(a[st].tn == tn)
{
if(r_a) (*r_a) = a + st;
if(occ) (*occ) = i - st;
if(idx) (*idx) = st + ((*ta).idx.a[(qn)]>>32);
return 1;
}
st = i;
}
}
return 0;
}
void interpr_hit(ha_ug_index* idx, uint64_t x, uint32_t rLen, uint32_t *uid, uint32_t *beg, uint32_t *end);
int hic_sc_type(ha_ug_index* idx, kvec_pe_hit* hits, uint64_t k)
{
uint32_t s_uid, s_beg, s_end, e_uid, e_beg, e_end, slen, elen, x = 0;
interpr_hit(idx, hits->a.a[k].s, hits->a.a[k].len>>32, &s_uid, &s_beg, &s_end);
s_beg = (s_beg+s_end)>>1; slen = idx->ug->u.a[s_uid].len;
if(s_beg >= (slen>>1)) x+=1;
interpr_hit(idx, hits->a.a[k].e, (uint32_t)hits->a.a[k].len, &e_uid, &e_beg, &e_end);
e_beg = (e_beg+e_end)>>1; elen = idx->ug->u.a[e_uid].len;
if(e_beg >= (elen>>1)) x+=2;
return x;
}
void weight_kv_u_trans(ha_ug_index* idx, kvec_pe_hit* hits, hc_links* link, bubble_type* bub,
kv_u_trans_t *ta, trans_idx* dis)
kv_u_trans_t *ta, trans_idx* dis, int sc_weight)
{
uint64_t k, i, shif = 64 - idx->uID_bits, beg, end, t_d;
u_trans_t *e1 = NULL, *e2 = NULL;
long double weight;
double *sw = NULL;
u_trans_t *p = NULL;
uint32_t is_cc;
uint32_t is_cc, ii1, ii2;
for (i = 0, ta->idx.n = ta->n = 0; i < link->a.n; i++)
{
@@ -14908,6 +14943,11 @@ kv_u_trans_t *ta, trans_idx* dis)
}
}
kt_u_trans_t_idx(ta, idx->ug->g->n_seq);
if(sc_weight) {
k = ta->n*3;
MALLOC(sw, k);
for (i = 0; i < k; i++) sw[i] = 0;
}
for (k = 0; k < hits->a.n; ++k)
@@ -14925,16 +14965,38 @@ kv_u_trans_t *ta, trans_idx* dis)
// if(t_d == (uint64_t)-1 && is_cc == 0) continue;
// if(t_d == (uint64_t)-1 && !dis) continue;
get_u_trans_spec(ta, beg, end, &e1, NULL);
get_u_trans_spec(ta, end, beg, &e2, NULL);
get_u_trans_spec_idx(ta, beg, end, &e1, NULL, &ii1);
get_u_trans_spec_idx(ta, end, beg, &e2, NULL, &ii2);
if(e1 == NULL || e2 == NULL) continue;
weight = 1;
if(dis) weight = get_trans_weight_advance(idx, t_d, dis);
e1->nw -= weight; e1->occ++;
e2->nw -= weight; e2->occ++;
if(sc_weight){
i = hic_sc_type(idx, hits, k);
if(i == 0){
e1->nw -= weight; e2->nw -= weight;
}
else{
i--;
sw[(ii1*3)+i] -= weight;
sw[(ii2*3)+i] -= weight;
}
} else{
e1->nw -= weight; e2->nw -= weight;
}
e1->occ++; e2->occ++;
}
if(sc_weight) {
for (i = 0; i < ta->n; ++i){
if(ta->a[i].nw > sw[(i*3)]) ta->a[i].nw = sw[(i*3)];
if(ta->a[i].nw > sw[(i*3)+1]) ta->a[i].nw = sw[(i*3)+1];
if(ta->a[i].nw > sw[(i*3)+2]) ta->a[i].nw = sw[(i*3)+2];
ta->a[i].nw *= 4/**2**/;
}
free(sw);
}
}
void interpr_hit(ha_ug_index* idx, uint64_t x, uint32_t rLen, uint32_t *uid, uint32_t *beg, uint32_t *end)
@@ -15450,7 +15512,7 @@ ha_ug_index* idx, bubble_type* bub, int8_t *s, mc_gg_status *sa, uint32_t ignore
if(hits->idx.n == 0) idx_hc_links(hits, idx, bub);
weight_kv_u_trans(idx, hits, lk, bub, ta, is_comples_weight == 1? &dis : NULL);
weight_kv_u_trans(idx, hits, lk, bub, ta, is_comples_weight == 1? &dis : NULL, asm_opt.flag&HA_F_USKEW?0:1);
// if(bub->round_id == bub->n_round-1)
// {
// print_debug_hc_links(idx, bub, lk, ta, hits);
@@ -15686,12 +15748,9 @@ void resolve_tangles_hic(ha_ug_index *idx, bubble_type *bub, kvec_pe_hit *hits,
uint64_t shif = 64 - idx->uID_bits, qn, tn;
pe_hit *h_a = NULL;
u_trans_t *p = NULL;
identify_bubbles(idx->ug, bub, idx->t_ch->ir_het, &(idx->t_ch->k_trans));
ta->idx.n = ta->n = 0;
if(hits->idx.n == 0) idx_hc_links(hits, idx, NULL);
for (qn = 0; qn < hits->idx.n; qn++)
{
h_a = hits->a.a + (hits->idx.a[qn]>>32);
@@ -15713,9 +15772,7 @@ void resolve_tangles_hic(ha_ug_index *idx, bubble_type *bub, kvec_pe_hit *hits,
}
}
}
radix_sort_u_trans_m(ta->a, ta->a + ta->n);
for (k = 1, l = 0, m = 0; k <= ta->n; ++k)
{
if (k == ta->n || ta->a[l].qn != ta->a[k].qn || ta->a[l].tn != ta->a[k].tn) //same qn and tn
@@ -15736,23 +15793,21 @@ void resolve_tangles_hic(ha_ug_index *idx, bubble_type *bub, kvec_pe_hit *hits,
}
ta->n = m;
kt_u_trans_t_idx(ta, idx->ug->g->n_seq);
resolve_bubble_chain_by_hic(idx, ta, bub);
ta->idx.n = ta->n = 0;
}
void print_kv_u_trans_t(kv_u_trans_t *ta)
void print_kv_u_trans_t(kv_u_trans_t *ta, ma_ug_t* ug)
{
uint32_t i;
u_trans_t *p = NULL;
for (i = 0; i < ta->n; i++)
{
p = &(ta->a[i]);
fprintf(stderr, "q-utg%.6ul\tqs(%u)\tqe(%u)\tt-utg%.6ul\tts(%u)\tte(%u)\trev(%u)\tw(%f)\tf(%u)\n",
p->qn+1, p->qs, p->qe, p->tn+1, p->ts, p->te, p->rev, p->nw, p->f);
fprintf(stderr, "q-utg%.6ul\tql(%u)\tqs(%u)\tqe(%u)\tt-utg%.6ul\ttl(%u)\tts(%u)\tte(%u)\trev(%u)\tw(%f)\tf(%u)\n",
p->qn+1, ug->u.a[p->qn].len, p->qs, p->qe, p->tn+1, ug->u.a[p->tn].len, p->ts, p->te, p->rev, p->nw, p->f);
}
fprintf(stderr, "[M::%s::] \n", __func__);
}
@@ -16191,6 +16246,61 @@ void renew_idx_para(ha_ug_index* idx, ma_ug_t* ug)
idx->rev_mode = ((uint64_t)1) << 63;
}
uint32_t get_oe_occ(uint32_t qn, uint32_t tn, kvec_pe_hit* hits, ha_ug_index* idx)
{
uint64_t shif = 64 - idx->uID_bits, occ = 0;
pe_hit *h_a = hits->a.a + (hits->idx.a[qn]>>32);
uint32_t h_occ = (uint32_t)(hits->idx.a[qn]), i;
for (i = 0; i < h_occ; i++) {
if(((h_a[i].s<<1)>>shif)==qn && ((h_a[i].e<<1)>>shif)==tn) occ++;
}
return occ;
}
void optimize_u_trans(kv_u_trans_t *ovlp, kvec_pe_hit* hits, ha_ug_index* idx)
{
if(hits->idx.n == 0) idx_hc_links(hits, idx, NULL);
uint64_t i, m, occ;
u_trans_t *x = NULL, *p = NULL;
kv_u_trans_t k_trans;
kv_init(k_trans); kv_init(k_trans.idx);
for (i = 0; i < ovlp->n; i++){
x = &(ovlp->a[i]);
if(x->qn > x->tn) continue;
if(x->f != RC_2 || x->del) continue;
occ = get_oe_occ(x->qn, x->tn, hits, idx) + get_oe_occ(x->tn, x->qn, hits, idx);
kv_pushp(u_trans_t, k_trans, &p);
(*p) = (*x); p->nw = (x->nw*(1-(((double)(occ<<1))/((double)(hits->occ.a[x->qn]+hits->occ.a[x->tn])))));
if(p->nw < 0) fprintf(stderr, "ERROR-nw\n");
if(p->nw == 0) p->nw = x->nw*0.005;
if(p->nw == 0) {
k_trans.n--;
}
else {
kv_pushp(u_trans_t, k_trans, &p);
(*p) = k_trans.a[k_trans.n-2];
p->qn = k_trans.a[k_trans.n-2].tn; p->qs = k_trans.a[k_trans.n-2].ts; p->qe = k_trans.a[k_trans.n-2].te;
p->tn = k_trans.a[k_trans.n-2].qn; p->ts = k_trans.a[k_trans.n-2].qs; p->te = k_trans.a[k_trans.n-2].qe;
}
}
kt_u_trans_t_idx(&k_trans, idx->ug->g->n_seq);
mc_solve(NULL, NULL, &k_trans, idx->ug, idx->read_g, 0.8, R_INF.trio_flag, 1, NULL, 1, NULL, NULL, 1);
for (i = m = 0; i < ovlp->n; i++){
x = &(ovlp->a[i]);
if(x->del) continue;
if(x->f == RC_2){
get_u_trans_spec(&k_trans, x->qn, x->tn, &p, NULL);
if(!p) continue;
}
ovlp->a[m++] = ovlp->a[i];
}
ovlp->n = m;
kt_u_trans_t_idx(ovlp, idx->ug->g->n_seq);
free(hits->idx.a); hits->idx.a = NULL; hits->idx.n = hits->idx.m = 0;
free(hits->occ.a); hits->occ.a = NULL; hits->occ.n = hits->occ.m = 0;
kv_destroy(k_trans); kv_destroy(k_trans.idx);
}
int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_opt_t *opt, kvec_pe_hit **rhits)
{
double index_time = yak_realtime();
@@ -16209,15 +16319,16 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
alignment_worker_pipeline(&sl, fn1, fn2);
write_hc_hits(&sl.hits, idx->ug, asm_opt.output_file_name);
}
sl.hits.uID_bits = idx->uID_bits; sl.hits.pos_mode = idx->pos_mode;
optimize_u_trans(&(idx->t_ch->k_trans), &sl.hits, idx);
filter_kv_u_trans_t(&(idx->t_ch->k_trans), idx->ug, 0.5);
// print_kv_u_trans_t(&(idx->t_ch->k_trans), idx->ug);
// flter_by_cov(idx, &sl.hits, 2);
// update_hits(idx, &sl.hits, idx->t_ch->is_r_het);
///debug_hc_hits_v14(&sl.hits, asm_opt.output_file_name, sl.idx);
////dedup_hits(&(sl.hits), sl.idx);
///write_hc_hits_v14(&sl.hits, asm_opt.output_file_name);
sl.hits.uID_bits = idx->uID_bits; sl.hits.pos_mode = idx->pos_mode;
if(asm_opt.misjoin_len > 0)
{
update_switch_unitig(idx->ug, idx->read_g, &(sl.hits), &(idx->t_ch->k_trans), 10, 20, asm_opt.misjoin_len, 0.15);
@@ -16255,7 +16366,7 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
// update_trans_g(idx, &k_trans, &bub);
/*******************************for debug************************************/
mc_solve(NULL, NULL, &k_trans, idx->ug, idx->read_g, 0.8, R_INF.trio_flag,
(bub.round_id == 0? 1 : 0), s->s, 1, /**&bub**/NULL, &(idx->t_ch->k_trans));
(bub.round_id == 0? 1 : 0), s->s, 1, /**&bub**/NULL, &(idx->t_ch->k_trans), 0);
/*******************************for debug************************************/
label_unitigs_sm(s->s, NULL, idx->ug);
@@ -16321,6 +16432,49 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_o
return 1;
}
spg_t *hic_short_pre_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx, ug_opt_t *opt, kvec_pe_hit **rhits)
{
// double index_time = yak_realtime();
sldat_t sl;
sl.idx = idx;
sl.t_ch = idx->t_ch;
sl.chunk_size = 20000000;
sl.n_thread = asm_opt.thread_num;
sl.total_base = sl.total_pair = 0;
idx->hap_cnt = asm_opt.hap_occ;
kv_init(sl.hits.a); kv_init(sl.hits.idx); kv_init(sl.hits.occ);
if(!load_hc_hits(&sl.hits, idx->ug, asm_opt.output_file_name))
{
alignment_worker_pipeline(&sl, fn1, fn2);
fprintf(stderr, "sb0sb\n");
write_hc_hits(&sl.hits, idx->ug, asm_opt.output_file_name);
fprintf(stderr, "sb1sb\n");
}
sl.hits.uID_bits = idx->uID_bits; sl.hits.pos_mode = idx->pos_mode;
kv_u_trans_t k_trans;
kv_init(k_trans); kv_init(k_trans.idx);
bubble_type bub;
memset(&bub, 0, sizeof(bubble_type));
bub.round_id = 0; bub.n_round = asm_opt.n_weight;
fprintf(stderr, "sb2sb\n");
resolve_tangles_hic(idx, &bub, &sl.hits, &k_trans);
fprintf(stderr, "sb3sb\n");
spg_t *scg = horder_utg(&sl.hits, idx->uID_bits, idx->pos_mode, idx->read_g, idx->ug, &bub, opt);
fprintf(stderr, "sb4sb\n");
if(rhits){
CALLOC(*rhits, 1);
(**rhits) = sl.hits;
sl.hits.a.a = NULL;
sl.hits.idx.a = NULL;
sl.hits.occ.a = NULL;
}
kv_destroy(sl.hits.a); kv_destroy(sl.hits.idx); kv_destroy(sl.hits.occ);
kv_destroy(k_trans); kv_destroy(k_trans.idx);
destory_bubbles(&bub);
return scg;
}
int load_psg_t(psg_t **sg, const char *fn)
{
uint64_t flag = 0;
@@ -16433,7 +16587,7 @@ int hic_short_align_poy(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx,
// }
/*******************************for debug************************************/
}
write_psg_t(s, asm_opt.output_file_name);
if((asm_opt.flag & HA_F_VERBOSE_GFA)) write_psg_t(s, asm_opt.output_file_name);
skip_flipping:
verbose_het_stat(&bub);
@@ -16488,6 +16642,19 @@ void hic_analysis(ma_ug_t *ug, asg_t* read_g, trans_chain* t_ch, ug_opt_t *opt,
destory_hc_pt_index(ug_index);free(ug_index);
}
spg_t *hic_pre_analysis(ma_ug_t *ug, asg_t* read_g, trans_chain* t_ch, ug_opt_t *opt, kvec_pe_hit **rhits)
{
ug_index = NULL;
int exist = (asm_opt.load_index_from_disk?
load_hc_pt_index(&ug_index, ug, asm_opt.output_file_name) : 0);
if(exist == 0) ug_index = build_unitig_index(ug, asm_opt.hic_mer_length, asm_opt.hap_occ, 0, asm_opt.thread_num);
if(exist == 0) write_hc_pt_index(ug_index, asm_opt.output_file_name);
ug_index->ug = ug;
ug_index->read_g = read_g;
ug_index->t_ch = t_ch;
return hic_short_pre_align(asm_opt.hic_reads[0], asm_opt.hic_reads[1], ug_index, opt, rhits);
}
void init_ug_idx(ma_ug_t *ug, uint64_t k, uint64_t up_bound, uint64_t low_bound, uint64_t build_idx)
{