From 1a6f386823805090bbe11870b2eebf7a0a76017b Mon Sep 17 00:00:00 2001 From: chhylp123 Date: Sun, 4 Apr 2021 20:27:19 -0400 Subject: [PATCH] backup trans_chain --- Overlaps.cpp | 13 ------------- Purge_Dups.cpp | 50 ++------------------------------------------------ hic.cpp | 24 ------------------------ 3 files changed, 2 insertions(+), 85 deletions(-) diff --git a/Overlaps.cpp b/Overlaps.cpp index 0456f52..e6c2c28 100644 --- a/Overlaps.cpp +++ b/Overlaps.cpp @@ -12115,32 +12115,24 @@ bub_label_t* b_mask_t) ma_ug_t *copy_ug = copy_untig_graph(ug); ///asm_opt.purge_overlap_len = asm_opt.purge_overlap_len_hic; ///asm_opt.purge_simi_thres = asm_opt.purge_simi_rate_hic; - fprintf(stderr, "sb0sb\n"); adjust_utg_by_primary(©_ug, copy_sg, TRIO_THRES, sources, reverse_sources, coverage_cut, tipsLen, tip_drop_ratio, stops_threshold, ruIndex, chimeric_rate, drop_ratio, max_hang, min_ovlp, &new_rtg_edges, &cov, b_mask_t, 1); - fprintf(stderr, "sb1sb\n"); ma_ug_destroy(copy_ug); asg_destroy(copy_sg); - fprintf(stderr, "sb2sb\n"); ma_ug_print_bed(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, asm_opt.hic_inconsist_rate, NULL, NULL, cov); - fprintf(stderr, "sb3sb\n"); - fprintf(stderr, "sb4sb\n"); new_rtg_edges.a.n = 0; ma_ug_seq(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp); ///classify_untigs(ug, sg, coverage_cut, sources, reverse_sources, ruIndex, &new_rtg_edges, max_hang, min_ovlp); - fprintf(stderr, "sb5sb\n"); hic_analysis(ug, sg, cov); - fprintf(stderr, "sb6sb\n"); - destory_hap_cov_t(&cov); ma_ug_destroy(ug); kv_destroy(new_rtg_edges.a); @@ -28895,11 +28887,6 @@ void flat_bubbles(asg_t *sg, uint8_t* r_het) { asg_bub_pop1_primary_trio(ug->g, NULL, v, tLen, &b, (uint32_t)-1, (uint32_t)-1, 1, NULL, NULL, NULL, 0); n_pop++; - // if(ug->g->seq[2031].c == ALTER_LABLE) - // { - // fprintf(stderr, "######round: %u, s-utg%.6ul, e-utg%.6ul\n", - // round, (v>>1)+1, (b.S.a[0]>>1)+1); - // } } } } diff --git a/Purge_Dups.cpp b/Purge_Dups.cpp index 85c6538..08fb745 100644 --- a/Purge_Dups.cpp +++ b/Purge_Dups.cpp @@ -4326,50 +4326,6 @@ hap_cov_t *cov) } } -/** -void collect_reverse_unitig_pair(hc_links* link, ma_ug_t *ug, hap_overlaps* t) -{ - uint32_t i = 0, k = 0, rId_0, rId_1, pre_0, pre_1, b_0 = t->xUid, b_1 = t->yUid; - uint64_t d = RC_2; - ma_utg_t* u_b_0 = &(ug->u.a[b_0]); - ma_utg_t* u_b_1 = &(ug->u.a[b_1]); - if(u_b_0->n == 0) return; - if(u_b_1->n == 0) return; - - for (i = t->x_beg_id, pre_0 = (uint32_t)-1; i < t->x_end_id; i++) - { - rId_0 = u_b_0->a[i]>>33; - if(link->u_idx[rId_0] == (uint32_t)-1) continue; - if(pre_0 == link->u_idx[rId_0]) continue; - pre_0 = link->u_idx[rId_0]; - - for (k = t->y_beg_id, pre_1 = (uint32_t)-1; k < t->y_end_id; k++) - { - rId_1 = u_b_1->a[k]>>33; - if(link->u_idx[rId_1] == (uint32_t)-1) continue; - if(pre_1 == link->u_idx[rId_1]) continue; - pre_1 = link->u_idx[rId_1]; - push_hc_edge(&(link->a.a[pre_0]), pre_1, 1, 1, &d); - push_hc_edge(&(link->a.a[pre_1]), pre_0, 1, 1, &d); - } - } -} - - -void collect_reverse_unitigs_purge(buf_t* b_0, hc_links* link, ma_ug_t *ug, hap_overlaps_list* all_ovlp) -{ - if(b_0->b.n <= 1) return; - uint32_t k; - int index = 0; - for (k = 0; k < b_0->b.n - 1; k++) - { - index = get_specific_hap_overlap(&(all_ovlp->x[b_0->b.a[k]>>1]), b_0->b.a[k]>>1, b_0->b.a[k+1]>>1); - if(index == -1) continue; - collect_reverse_unitig_pair(link, ug, &(all_ovlp->x[b_0->b.a[k]>>1].a.a[index])); - } -} -**/ - void print_het_ovlp(p_g_t *pg, ma_ug_t *ug, hap_overlaps_list* ha, double filter_rate) { uint32_t v, i, k, n_vtx = pg->pg_h_lev->n_seq * 2, nv, qn, qs, qe, tn, ts, te, as, ae, occ, ovlp, hetLen, homLen; @@ -4530,7 +4486,6 @@ void print_het_ovlp(p_g_t *pg, ma_ug_t *ug, hap_overlaps_list* ha, double filter } } - void link_unitigs(asg_t *purge_g, ma_ug_t *ug, hap_overlaps_list* all_ovlp, R_to_U* ruIndex, ma_hit_t_alloc* reverse_sources, ma_sub_t *coverage_cut, asg_t *read_g, uint64_t* position_index, kvec_asg_arc_t_offset* u_buffer, kvec_t_i32_warp* tailIndex, @@ -5543,9 +5498,9 @@ void collect_purge_trans_cov(ma_ug_t *ug, hap_overlaps_list* ha, trans_chain* t_ { for (i = 0; i < ha->x[v].a.n; i++) { - if(x->yUid < x->xUid) continue; x = &(ha->x[v].a.a[i]); - + if(x->yUid < x->xUid) continue; + q = &(ug->u.a[x->xUid]); s = x->x_beg_id; e = x->x_end_id; o = 0; for (k = s, p_uId = (uint32_t)-1; k < e; k++) { @@ -5755,7 +5710,6 @@ uint32_t just_coverage, hap_cov_t *cov, uint32_t collect_p_trans) destory_hap_overlaps_list(&back_all_ovlp); if(cov) memset(position_index, -1, sizeof(uint64_t)*read_g->n_seq); else free(position_index); - destory_hap_alignment_struct_pip(&hap_buf); destory_p_g_t(&pg); } diff --git a/hic.cpp b/hic.cpp index c7438db..8c70943 100644 --- a/hic.cpp +++ b/hic.cpp @@ -3796,15 +3796,6 @@ void write_hc_links(hc_links* link, const char *fn) fwrite(&link->enzymes.n, sizeof(link->enzymes.n), 1, fp); fwrite(link->enzymes.a, sizeof(uint64_t), link->enzymes.n, fp); - // fwrite(&link->r_num, sizeof(link->r_num), 1, fp); - // fwrite(link->u_idx, sizeof(uint32_t), 1, fp); - - // fwrite(&(link->bed.n), sizeof(link->bed.n), 1, fp); - // for (k = 0; k < link->bed.n; k++) - // { - // fwrite(&(link->bed.a[k].n), sizeof(link->bed.a[k].n), 1, fp); - // fwrite(link->bed.a[k].a, sizeof(uint64_t)*link->bed.a[k].n, 1, fp); - // } fclose(fp); free(buf); @@ -3844,21 +3835,6 @@ int load_hc_links(hc_links* link, const char *fn) flag += fread(&link->enzymes.n, sizeof(link->enzymes.n), 1, fp); link->enzymes.m = link->enzymes.n; MALLOC(link->enzymes.a, link->enzymes.n); flag += fread(link->enzymes.a, sizeof(uint64_t), link->enzymes.n, fp); - // fread(&link->r_num, sizeof(link->r_num), 1, fp); - // MALLOC(link->u_idx, link->r_num); - // fread(link->u_idx, sizeof(uint32_t), 1, fp); - - // kv_init(link->bed); - // flag += fread(&(link->bed.n), sizeof(link->bed.n), 1, fp); - // link->bed.m = link->bed.n; CALLOC(link->bed.a, link->bed.n); - // for (k = 0; k < link->bed.n; k++) - // { - // flag += fread(&(link->bed.a[k].n), sizeof(link->bed.a[k].n), 1, fp); - // link->bed.a[k].m = link->bed.a[k].n; MALLOC(link->bed.a[k].a, link->bed.a[k].n); - // flag += fread(link->bed.a[k].a, sizeof(uint64_t)*link->bed.a[k].n, 1, fp); - // } - - fclose(fp); free(buf);