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https://github.com/chhylp123/hifiasm.git
synced 2026-09-15 12:47:57 +08:00
new somatic variant popping
This commit is contained in:
chhylp123
215
Overlaps.cpp
215
Overlaps.cpp
@@ -11587,14 +11587,7 @@ uint32_t tn, kv_u_trans_hit_t* ktb, uint32_t bn)
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}
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}
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typedef struct {///[cBeg, cEnd)
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uint32_t u_i, r_i, len, s_pos_cur, s_pre_v, s_pre_w, p_v, p_idx, p_uId, cBeg, cEnd;
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///buf_t* x;
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uint32_t *a, an;
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ma_ug_t *ug;
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asg_t *read_sg;
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trans_chain* t_ch;
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} u_trans_hit_idx;
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void reset_u_trans_hit_idx(u_trans_hit_idx *t, uint32_t* i_x_a, uint32_t i_x_n, ma_ug_t *i_ug,
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asg_t *i_read_sg, trans_chain* i_t_ch, uint32_t i_cBeg, uint32_t i_cEnd)
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@@ -17889,37 +17882,6 @@ hap_cov_t *cov, uint32_t is_update_chain, uint32_t keep_d)
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}
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}
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/****************************may have bugs********************************/
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/**
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if(((m + cur_m) + (np + cur_np)) < (t->m + t->np))
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{
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to_replace = 1;
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}
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else if(((m + cur_m) + (np + cur_np)) == (t->m + t->np))
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{
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if(c + cur_c > t->c)
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{
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to_replace = 1;
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}
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else if(c + cur_c == t->c)
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{
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if(nc + cur_nc > t->nc)
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{
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to_replace = 1;
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}
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else if(nc + cur_nc == t->nc)
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{
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if(d + l > t->d)
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{
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to_replace = 1;
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}
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}
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}
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}
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**/
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if(to_replace)
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{
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t->p = v;
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@@ -29942,6 +29904,178 @@ void flat_bubbles(asg_t *sg, uint8_t* r_het)
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ma_ug_destroy(ug); free(bs_flag);
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}
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uint64_t get_primary_path_len(asg_t *sg, ma_ug_t *ug, uint32_t v0, buf_t *b)
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{
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uint32_t v, u, k;
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uint64_t len;
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ma_utg_t *p = NULL;
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v = b->S.a[0];
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len = 0;
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while (1)
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{
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u = b->a[v].p; // u->v
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if(u == v0) break;
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p = &(ug->u.a[u>>1]);
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for (k = 0; k < p->n; k++)
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{
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len += sg->seq[p->a[k]>>33].len;
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}
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v = u;
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}
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return len;
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}
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void flat_bubbles_advance(asg_t *sg, ma_hit_t_alloc* sources, R_to_U* ruIndex, uint64_t het_thres)
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{
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fprintf(stderr, "het_thres-%lu\n", het_thres);
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ma_ug_t *ug = NULL;
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ug = ma_ug_gen(sg);
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ma_utg_t *u = NULL;
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ma_hit_t *h;
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uint32_t n_vtx = ug->g->n_seq<<1, v, i, k, m, rId, tn, is_Unitig, n_pop = 0;
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uint64_t C_bases, R_bases;
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buf_t b; memset(&b, 0, sizeof(buf_t)); b.a = (binfo_t*)calloc(n_vtx, sizeof(binfo_t));
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uint8_t* bs_flag = (uint8_t*)calloc(n_vtx, 1);
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uint8_t* r_flag = (uint8_t*)calloc(sg->n_seq, sizeof(uint8_t));
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uint64_t tLen = get_bub_pop_max_dist_advance(ug->g, &b);
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for (v = 0; v < ug->g->n_seq; ++v)
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{
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if(ug->g->seq[v].del) continue;
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ug->g->seq[v].c = PRIMARY_LABLE;
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EvaluateLen(ug->u, v) = ug->u.a[v].n;
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}
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n_pop = 1; ///round = 0;
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while(n_pop > 0)
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{
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for (v = n_pop = 0; v < n_vtx; ++v)
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{
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if(ug->g->seq[v>>1].del) continue;
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if(asg_arc_n(ug->g, v) < 2) continue;
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if(get_real_length(ug->g, v, NULL) < 2) continue;
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if(bs_flag[v] == 1) continue;
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if(bs_flag[v] == 0) bs_flag[v] = 1;
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if(asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 0, NULL, NULL, NULL, 0, 0))
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{
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bs_flag[v] = 2; bs_flag[b.S.a[0]^1] = 2;
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//note b.b include end, does not include beg
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for (i = 0; i < b.b.n; i++)
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{
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u = &(ug->u.a[b.b.a[i]>>1]);
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for (k = 0; k < u->n; k++) r_flag[u->a[k]>>33] = 1;
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}
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u = &(ug->u.a[v>>1]);
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for (k = 0; k < u->n; k++) r_flag[u->a[k]>>33] = 1;
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u = &(ug->u.a[b.S.a[0]>>1]);
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for (k = 0; k < u->n; k++) r_flag[u->a[k]>>33] = 1;
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C_bases = 0;
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for (i = 0; i < b.b.n; i++)
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{
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if((b.b.a[i]>>1) == (v>>1) || (b.b.a[i]>>1) == (b.S.a[0]>>1)) continue;
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u = &(ug->u.a[b.b.a[i]>>1]);
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for (k = 0; k < u->n; k++)
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{
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rId = u->a[k]>>33;
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// R_bases += sg->seq[rId].len;
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for (m = 0; m < (uint64_t)(sources[rId].length); m++)
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{
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h = &(sources[rId].buffer[m]);
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///if(h->el != 1) continue;
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tn = Get_tn((*h));
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if(sg->seq[tn].del == 1)
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{
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///get the id of read that contains it
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get_R_to_U(ruIndex, tn, &tn, &is_Unitig);
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if(tn == (uint32_t)-1 || is_Unitig == 1 || sg->seq[tn].del == 1) continue;
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}
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if(sg->seq[tn].del == 1) continue;
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if(r_flag[tn] == 0) continue;
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C_bases += (Get_qe((*h)) - Get_qs((*h)));
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}
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}
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}
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R_bases = get_primary_path_len(sg, ug, v, &b);
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if((C_bases/R_bases) <= het_thres)
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{
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fprintf(stderr, "s-utg%.6ul\te-utg%.6ul\tC_bases:%lu\tR_bases:%lu\n", (v>>1)+1, (b.S.a[0]>>1)+1, C_bases, R_bases);
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asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 1, NULL, NULL, NULL, 0, 0);
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n_pop++;
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}
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for (i = 0; i < b.b.n; i++)
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{
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u = &(ug->u.a[b.b.a[i]>>1]);
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for (k = 0; k < u->n; k++) r_flag[u->a[k]>>33] = 0;
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}
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u = &(ug->u.a[v>>1]);
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for (k = 0; k < u->n; k++) r_flag[u->a[k]>>33] = 0;
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u = &(ug->u.a[b.S.a[0]>>1]);
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for (k = 0; k < u->n; k++) r_flag[u->a[k]>>33] = 0;
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}
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}
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///round++;
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}
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/*******************************for debug************************************/
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// kvec_t(uint64_t) occ_sort; kv_init(occ_sort);
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// for (v = n_pop = 0; v < ug->g->n_seq; ++v)
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// {
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// if(ug->g->seq[v].del) continue;
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// if(ug->g->seq[v].c != ALTER_LABLE) continue;
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// u = &(ug->u.a[v]);
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// kv_push(uint64_t, occ_sort, (uint64_t)((uint32_t)(-1) - (uint32_t)(u->n)) << 32 | (v));
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// }
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// radix_sort_arch64(occ_sort.a, occ_sort.a + occ_sort.n);
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// for (i = 0; i < occ_sort.n; ++i)
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// {
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// fprintf(stderr, "-utg%.6ul, n=%u\n", ((uint32_t)occ_sort.a[i])+1,
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// (uint32_t)(-1) - (uint32_t)(occ_sort.a[i]>>32));
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// }
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// kv_destroy(occ_sort);
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/*******************************for debug************************************/
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clean_sg_by_utg(sg, ug);
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free(b.a); free(b.S.a); free(b.T.a); free(b.b.a); free(b.e.a);
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ma_ug_destroy(ug); free(bs_flag); free(r_flag);
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}
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void flat_soma_v(asg_t *sg, ma_hit_t_alloc* sources, R_to_U* ruIndex)
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{
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uint64_t dip_thre_max;
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if(asm_opt.hom_global_coverage_set)
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{
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dip_thre_max = asm_opt.hom_global_coverage;
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}
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else
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{
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dip_thre_max = ((double)asm_opt.hom_global_coverage)/((double)HOM_PEAK_RATE);
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}
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flat_bubbles_advance(sg, sources, ruIndex, (((double)(dip_thre_max)*1.15)/asm_opt.polyploidy));
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}
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char *get_outfile_name(char* output_file_name)
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{
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char *buf = NULL;
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@@ -30162,7 +30296,8 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
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ruIndex, 0.05, 0.9, max_hang_length, mini_overlap_length, 10, gap_fuzz, &b_mask_t);
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output_unitig_graph(sg, coverage_cut, o_file, sources, ruIndex, max_hang_length, mini_overlap_length);
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flat_bubbles(sg, ruIndex->is_het); free(ruIndex->is_het); ruIndex->is_het = NULL;
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// flat_bubbles(sg, ruIndex->is_het); free(ruIndex->is_het); ruIndex->is_het = NULL;
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flat_soma_v(sg, sources, ruIndex); free(ruIndex->is_het); ruIndex->is_het = NULL;
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output_contig_graph_primary_pre(sg, coverage_cut, o_file, sources, reverse_sources,
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asm_opt.small_pop_bubble_size, asm_opt.max_short_tip, ruIndex, max_hang_length, mini_overlap_length);
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