mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-26 02:28:12 +08:00
fix slow running time vs r726
This commit is contained in:
chhylp123
+1
-1
@@ -5,7 +5,7 @@
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#include <pthread.h>
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#include <stdint.h>
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#define HA_VERSION "0.25.0-r873"
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#define HA_VERSION "0.25.0-r877"
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#define VERBOSE 0
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+2
-6
@@ -32001,6 +32001,8 @@ void reassign_gaps(overlap_region *z, overlap_region *aux, char* qstr, int64_t q
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if(rr) update_overlap_region(z, aux, ql, ((rref)?(Get_READ_LENGTH((*rref), z->y_id)):(tl)));
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z->non_homopolymer_errors -= re;
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if(!qhpf) return;
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// if(z->x_id == 142 && z->y_id == 207) {
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// fprintf(stderr, "-c-[M::%s::]\tqid::%u\ttid::%u\t%.*s\tq::[%u,%u)\tt::[%u,%u)\tis_match::%u\terr::%u\trr::%ld\tre::%ld\tw_err::%d\n", __func__, z->x_id,
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// z->y_id, (int)Get_NAME_LENGTH(R_INF, z->y_id), Get_NAME(R_INF, z->y_id),
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@@ -35287,9 +35289,6 @@ uint8_t hc_aln_simd(overlap_region* ol, uint64_t *ffa, uint32_t *ia, uint64_t in
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}
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// for (k = 0; k < mm_k; k++) {
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// ed_band_cal_semi_64_w_absent_diag(tstr[k], bt_pri_l[k], qstr, wql, thre, baux_beg[k], exz); ez_er[k] = exz->err; ez_pe[k] = exz->pe;
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// }
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if(mm_k > 1) {
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ed_band_cal_semi_64_w_absent_diag_avx8(tstr, bt_pri_l, qstr, wql, thre, baux_beg, ez_er, ez_pe);
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} else {
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@@ -35334,9 +35333,6 @@ uint64_t gen_hc_r_alin_adp_mmp_1(overlap_region_alloc* ol, Candidates_list *cl,
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for (i = 0; i < wsrt_n; i++) {
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z = &(ol->list[(uint32_t)wsrt[i]]);
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// if(z->x_id == 63 && z->y_id == 9) {
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// fprintf(stderr, "-a-[M::%s]\tqid::%u\ttid::%u\tqa::[%u,%u)\tta::[%u,%u)\n", __func__, z->x_id, z->y_id, z->x_pos_s, z->x_pos_e + 1, z->y_pos_s, z->y_pos_e + 1);
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// }
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if(z->is_match == 0) {
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z->w_list.n = 0; z->align_length = 0;
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}
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+286
-17
@@ -3368,8 +3368,8 @@ uint64_t gen_hc_r_alin_ea_flt_mmp(ha_abuf_t *ab, overlap_region_alloc* ol, Candi
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}
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if(!(srt->n)) {
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gen_ff_hpc(hpz, qu->seq, qu->length, HPC_RR_Q, HPC_CC_Q);
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tot_b = gen_hc_r_alin_adp_mmp_1(ol, cl, rref, qu, tu, exz, aux_o, e_rate, wl, rid, khit, move_gap, buf, chem_drop, align_gap_rate, align_gap_max, sec_aln_win, sec_aln_cov, sec_aln_err_rate, sec_aln_max, srt, ocw, hpz->a,
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// gen_ff_hpc(hpz, qu->seq, qu->length, HPC_RR_Q, HPC_CC_Q);
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tot_b = gen_hc_r_alin_adp_mmp_1(ol, cl, rref, qu, tu, exz, aux_o, e_rate, wl, rid, khit, move_gap, buf, chem_drop, align_gap_rate, align_gap_max, sec_aln_win, sec_aln_cov, sec_aln_err_rate, sec_aln_max, srt, ocw, NULL/**hpz->a**/,
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v32, bp, max_n_chain>0?max_n_chain:1, max_n_chain_f>0?max_n_chain_f:1, chain_cutoff, ((asm_opt.hom_cov*HC_AV_MIN)>0)?(asm_opt.hom_cov*HC_AV_MIN):(1), 1);
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} else {
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kv_resize(uint64_t, *srt, (srt->n + ol->length));
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@@ -3400,8 +3400,8 @@ uint64_t gen_hc_r_alin_ea_flt_mmp(ha_abuf_t *ab, overlap_region_alloc* ol, Candi
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}
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if(on > nec) {
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gen_ff_hpc(hpz, qu->seq, qu->length, HPC_RR_Q, HPC_CC_Q);
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tot_b = gen_hc_r_alin_adp_mmp_1(ol, cl, rref, qu, tu, exz, aux_o, e_rate, wl, rid, khit, move_gap, buf, chem_drop, align_gap_rate, align_gap_max, sec_aln_win, sec_aln_cov, sec_aln_err_rate, sec_aln_max, srt, ocw, hpz->a,
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// gen_ff_hpc(hpz, qu->seq, qu->length, HPC_RR_Q, HPC_CC_Q);
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tot_b = gen_hc_r_alin_adp_mmp_1(ol, cl, rref, qu, tu, exz, aux_o, e_rate, wl, rid, khit, move_gap, buf, chem_drop, align_gap_rate, align_gap_max, sec_aln_win, sec_aln_cov, sec_aln_err_rate, sec_aln_max, srt, ocw, NULL/**hpz->a**/,
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v32, bp, max_n_chain>0?max_n_chain:1, max_n_chain_f>0?max_n_chain_f:1, chain_cutoff, ((asm_opt.hom_cov*HC_AV_MIN)>0)?(asm_opt.hom_cov*HC_AV_MIN):(1), 0);
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}
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}
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@@ -3428,8 +3428,8 @@ uint64_t gen_hc_r_alin_ea(overlap_region_alloc* ol, Candidates_list *cl, All_rea
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}
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if(!(srt->n)) {
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gen_ff_hpc(hpz, qu->seq, qu->length, HPC_RR_Q, HPC_CC_Q);
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tot_b = gen_hc_r_alin(ol, cl, rref, qu, tu, exz, aux_o, e_rate, wl, rid, khit, move_gap, buf, chem_drop, align_gap_rate, align_gap_max, sec_aln_win, sec_aln_cov, sec_aln_err_rate, sec_aln_max, kp, hpz->a);
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// gen_ff_hpc(hpz, qu->seq, qu->length, HPC_RR_Q, HPC_CC_Q);
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tot_b = gen_hc_r_alin(ol, cl, rref, qu, tu, exz, aux_o, e_rate, wl, rid, khit, move_gap, buf, chem_drop, align_gap_rate, align_gap_max, sec_aln_win, sec_aln_cov, sec_aln_err_rate, sec_aln_max, kp, NULL/**hpz->a**/);
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} else {
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///debug for memory
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// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
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@@ -3464,8 +3464,8 @@ uint64_t gen_hc_r_alin_ea(overlap_region_alloc* ol, Candidates_list *cl, All_rea
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// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
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if(on > nec) {
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gen_ff_hpc(hpz, qu->seq, qu->length, HPC_RR_Q, HPC_CC_Q);
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tot_b = gen_hc_r_alin_nec(ol, cl, rref, qu, tu, exz, aux_o, e_rate, wl, rid, khit, move_gap, buf, chem_drop, align_gap_rate, align_gap_max, sec_aln_win, sec_aln_cov, sec_aln_err_rate, sec_aln_max, kp, hpz->a);
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// gen_ff_hpc(hpz, qu->seq, qu->length, HPC_RR_Q, HPC_CC_Q);
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tot_b = gen_hc_r_alin_nec(ol, cl, rref, qu, tu, exz, aux_o, e_rate, wl, rid, khit, move_gap, buf, chem_drop, align_gap_rate, align_gap_max, sec_aln_win, sec_aln_cov, sec_aln_err_rate, sec_aln_max, kp, NULL/**hpz->a**/);
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}
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// fprintf(stderr, "[M::%s] srt->n::%u, nec::%lu, on::%lu\n", __func__, (uint32_t)srt->n, nec, on);
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@@ -4374,6 +4374,251 @@ static void worker_hap_ec(void *data, long i, int tid)
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// prt_chain(&b->olist);
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// ul_map_lchain(b->abl, (uint32_t)-1, s->seq[i], s->len[i], s->opt->w, s->opt->k, s->uu, &b->olist, &b->clist, s->opt->bw_thres,
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// s->opt->max_n_chain, 1, NULL, &(b->tmp_region), NULL, &(b->sp), &high_occ, NULL, 0, 1, 0.2/**0.75**/, 2, 3);
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/**
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int fully_cov, abnormal;
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// if(i != 12578) return;
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// fprintf(stderr, "[M::%s-beg] rid->%ld\n", __func__, i);
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// if (memcmp("7897e875-76e5-42c8-bc37-94b370c4cc8d", Get_NAME((R_INF), i), Get_NAME_LENGTH((R_INF),i)) == 0) {
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// fprintf(stderr, "[M::%s-beg] rid->%ld\n", __func__, i);
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// } else {
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// return;
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// }
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ha_get_candidates_interface(b->ab, i, &b->self_read, &b->olist, &b->olist_hp, &b->clist,
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0.02, asm_opt.max_n_chain, 1, NULL, &b->r_buf, &(R_INF.paf[i]), &(R_INF.reverse_paf[i]), &(b->tmp_region), NULL, &(b->sp));
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clear_Cigar_record(&b->cigar1);
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clear_Round2_alignment(&b->round2);
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correct_overlap(&b->olist, &R_INF, &b->self_read, &b->correct, &b->ovlp_read, &b->POA_Graph, &b->DAGCon,
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&b->cigar1, &b->hap, &b->round2, &b->r_buf, &(b->tmp_region.w_list), 0, 1, &fully_cov, &abnormal);
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b->num_read_base += b->self_read.length;
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b->num_correct_base += b->correct.corrected_base;
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b->num_recorrect_base += b->round2.dumy.corrected_base;
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push_cigar(R_INF.cigars, i, &b->cigar1);
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push_cigar(R_INF.second_round_cigar, i, &b->round2.cigar);
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R_INF.paf[i].is_fully_corrected = 0;
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if (fully_cov) {
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if (get_cigar_errors(&b->cigar1) == 0 && get_cigar_errors(&b->round2.cigar) == 0)
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R_INF.paf[i].is_fully_corrected = 1;
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}
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R_INF.paf[i].is_abnormal = abnormal;
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R_INF.trio_flag[i] = AMBIGU;
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///need to be fixed in r305
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// if(ha_idx_hp == NULL)
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// {
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// R_INF.trio_flag[i] += collect_hp_regions(&b->olist, &R_INF, &(b->k_flag), RESEED_HP_RATE, Get_READ_LENGTH(R_INF, i), NULL);
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// }
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if (R_INF.trio_flag[i] != AMBIGU || b->save_ov) {
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int is_rev = (asm_opt.number_of_round % 2 == 0);
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push_overlaps(&(R_INF.paf[i]), &b->olist, 1, &R_INF, is_rev);
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push_overlaps(&(R_INF.reverse_paf[i]), &b->olist, 2, &R_INF, is_rev);
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}
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if(het_cnt) het_cnt[i] = get_het_cnt(&b->hap);
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// fprintf(stderr, "[M::%s-end] rid->%ld\n", __func__, i);
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**/
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// exit(1);
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refresh_ec_ovec_buf_t0(b, REFRESH_N);
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/**
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fprintf(stderr, "%ld\t---\n", i);
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**/
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//fprintf(stderr, "-[M::%s]\trid::%ld\t%.*s\n", __func__, i, (int)Get_NAME_LENGTH(R_INF, i), Get_NAME(R_INF, i));
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}
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// void dbg_gen_ovlp_lst()
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// {
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// ;
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// }
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void worker_hap_ec_back_dbg(void *data, long i, int tid)
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{
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ec_ovec_buf_t0 *b = &(((ec_ovec_buf_t*)data)->a[tid]);
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uint32_t high_occ = asm_opt.hom_cov * (2.0 - HA_KMER_GOOD_RATIO);
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uint32_t low_occ = asm_opt.hom_cov * HA_KMER_GOOD_RATIO; int64_t het_a, hom_a; ///gen_hc_aln_t ez;
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overlap_region *aux_o = NULL/**, *rse_o = NULL**/; asg64_v buf0; uint32_t qlen = 0, qw = 0; uint64_t tot_b = 0; double tt0 = 0, tt1 = 0;
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b->v8q.n = b->v8t.n = 0; set_ec_cov(asm_opt.het_cov, asm_opt.hom_cov, asm_opt.het_cov_set, asm_opt.polyploidy, het_a, hom_a);
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// if(i != 0) return;
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if(DBG_TIME && dbg_a) {
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dbg_a[i].chn_tm = dbg_a[i].aln_tm = dbg_a[i].phs_tm = dbg_a[i].cns_tm = 0;
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}
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// debug_retrive_bqual(D, &b->v8t, i, 256); return;
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if(DBG_TIME && dbg_a) {
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if(DBG_TIME == 1) {
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tt0 = yak_realtime_0();
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}
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}
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recover_UC_Read(&b->self_read, &R_INF, i); qlen = b->self_read.length;
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qw = ((qlen < (COV_W_AC<<1))?(qlen>>1):(COV_W_AC)); if(!qw) qw = 1;
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// if(qlen <= 0) return;
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/**
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h_ec_lchain(b->ab, i, b->self_read.seq, b->self_read.length, asm_opt.mz_win, asm_opt.k_mer_length, &R_INF, &b->olist, &b->clist, ((asm_opt.is_ont)?(0.05):(0.02)), asm_opt.max_n_chain, 1, NULL, NULL, &(b->sp), &high_occ, &low_occ, 1, 1, 3, 0.7, 2, 32, COV_W, 1);///ONT high error
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**/
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h_ec_lchain(b->ab, i, b->self_read.seq, b->self_read.length, asm_opt.mz_win, asm_opt.k_mer_length, &R_INF, &b->olist, &b->clist, ((asm_opt.is_ont)?(0.05):(0.02)), asm_opt.max_n_chain, 1, NULL, NULL, &(b->sp), &high_occ, &low_occ, 1, 1, 3, 0.7, 2, 32, COV_W, 0);///ONT high error
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// b->num_read_base += b->olist.length;
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b->cnt[0] += b->self_read.length;
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aux_o = fetch_aux_ovlp(&b->olist, NULL/**&rse_o**/);///must be here
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if(DBG_TIME && dbg_a) {
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if(DBG_TIME == 1) {
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tt1 = yak_realtime_0();
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dbg_a[i].chn_tm = tt1 - tt0;
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tt0 = tt1;
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} else if(DBG_TIME == 2) {
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dbg_a[i].fbs = b->olist.length;
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}
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}
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// stderr_phase_ovlp(&b->olist);
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///debug for memory
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// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
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///mz1_ha_sketch(rs, rl, mz_w, mz_k, 0, !(asm_opt.flag & HA_F_NO_HPC), &ab->mz, ha_flt_tab, asm_opt.mz_sample_dist, k_flag, dbg_ct, NULL, -1, asm_opt.dp_min_len, -1, sp, asm_opt.mz_rewin, 0, NULL);
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// if((asm_opt.is_ont) && (b->olist.length)) get_mz1(qu->seq, qu->length, RES_W, RES_K, 0, !(asm_opt.flag & HA_F_NO_HPC), b->ab, NULL, NULL, asm_opt.mz_sample_dist, NULL, NULL, NULL, -1, asm_opt.dp_min_len, -1, &(b->sp), asm_opt.mz_rewin, 0, NULL, 0);
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// fprintf(stderr, "\n+[M::%s]\trid::%ld\t%.*s\n", __func__, i, (int)Get_NAME_LENGTH(R_INF, i), Get_NAME(R_INF, i));
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///r769: kp (gen_hc_r_alin_ea) -> NULL; site_sc (rphase_hc) -> 0
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///r770: kp (gen_hc_r_alin_ea) -> buf0; site_sc (rphase_hc) -> 0
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///r789: kp (gen_hc_r_alin_ea) -> NULL; site_sc (rphase_hc) -> 0
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///r791: kp (gen_hc_r_alin_ea) -> buf0; site_sc (rphase_hc) -> 0
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/**
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copy_asg_arr(buf0, b->sp);
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// tot_b = gen_hc_r_alin_ea_flt(b->ab, &b->olist, &b->clist, &R_INF, &b->self_read, &b->ovlp_read, &b->exz, aux_o, asm_opt.max_n_chain, asm_opt.max_n_chain*HC_MF_R, asm_opt.chn_occ, asm_opt.max_ov_diff_ec, (asm_opt.is_ont)?(WINDOW_OHC):(WINDOW_HC), i, E_KHIT,
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// 1, &b->v16, &b->v64, &(R_INF.paf[i]), asm_opt.is_ont, (asm_opt.is_ont)?(0.006):(-1), (asm_opt.is_ont)?(64):(-1), (asm_opt.is_ont)?(512):(0), (asm_opt.is_ont)?(6):(0), (asm_opt.is_ont)?(1.5):(-1), (asm_opt.is_ont)?(0.1):(-1), &buf0, qw, &b->v8q, &b->v32, 1);
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tot_b = gen_hc_r_alin_ea_flt_mmp(b->ab, &b->olist, &b->clist, &R_INF, &b->self_read, &b->ovlp_read, &b->exz, aux_o, asm_opt.max_n_chain, asm_opt.max_n_chain*HC_MF_R, asm_opt.chn_occ, asm_opt.max_ov_diff_ec, (asm_opt.is_ont)?(WINDOW_OHC):(WINDOW_HC), i, E_KHIT,
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1, &b->v16, &b->v64, &(R_INF.paf[i]), asm_opt.is_ont, (asm_opt.is_ont)?(0.006):(-1), (asm_opt.is_ont)?(64):(-1), (asm_opt.is_ont)?(512):(0), (asm_opt.is_ont)?(6):(0), (asm_opt.is_ont)?(1.5):(-1), (asm_opt.is_ont)?(0.1):(-1), &buf0, qw, &b->v8q, &b->v32);
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copy_asg_arr(b->sp, buf0);
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**/
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// exit(1);
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copy_asg_arr(buf0, b->sp);
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//kp: r763 -> r765: buf0 -> NULL
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//kp: r766 -> r767: NULL -> buf0
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tot_b = gen_hc_r_alin_ea(&b->olist, &b->clist, &R_INF, &b->self_read, &b->ovlp_read, &b->exz, aux_o, asm_opt.max_ov_diff_ec, (asm_opt.is_ont)?(WINDOW_OHC):(WINDOW_HC), i, E_KHIT,
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1, &b->v16, &b->v64, &(R_INF.paf[i]), asm_opt.is_ont, (asm_opt.is_ont)?(0.006):(-1), (asm_opt.is_ont)?(64):(-1), (asm_opt.is_ont)?(512):(0), (asm_opt.is_ont)?(6):(0),
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(asm_opt.is_ont)?(1.5):(-1), (asm_opt.is_ont)?(0.1):(-1), /**(asm_opt.is_ont)?(&buf0):**/(NULL), &b->v8q);
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copy_asg_arr(b->sp, buf0);
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// init_gen_hc_aln_t(&ez, &b->olist, &b->clist, &R_INF, &b->self_read, &b->ovlp_read, &b->exz, aux_o,
|
||||
// asm_opt.max_ov_diff_ec, asm_opt.max_ov_diff_ec, (asm_opt.is_ont)?(WINDOW_OHC):(WINDOW_HC), (asm_opt.is_ont)?(WINDOW_OHC):(WINDOW_HC), i, E_KHIT, 1, &b->v16, &b->v64, &(R_INF.paf[i]),
|
||||
// asm_opt.is_ont, asm_opt.is_ont, (asm_opt.is_ont)?(0.006):(-1), (asm_opt.is_ont)?(0.006):(-1), (asm_opt.is_ont)?(64):(-1), (asm_opt.is_ont)?(64):(-1),
|
||||
// (asm_opt.is_ont)?(512):(0), (asm_opt.is_ont)?(6):(0), (asm_opt.is_ont)?(1.5):(-1), (asm_opt.is_ont)?(0.1):(-1), (asm_opt.is_ont)?(&buf0):(NULL), (uint64_t)-1);
|
||||
// gen_hc_r_alin_ea_adv(&ez);
|
||||
|
||||
|
||||
|
||||
if(DBG_TIME && dbg_a) {
|
||||
if(DBG_TIME == 1) {
|
||||
tt1 = yak_realtime_0();
|
||||
dbg_a[i].aln_tm = tt1 - tt0;
|
||||
tt0 = tt1;
|
||||
|
||||
dbg_a[i].faln = cal_aln_bs(&b->olist);
|
||||
dbg_a[i].fbs = tot_b;
|
||||
} else if(DBG_TIME == 2) {
|
||||
dbg_a[i].faln = b->olist.length;
|
||||
}
|
||||
}
|
||||
|
||||
// fprintf(stderr, "-[M::%s] rid::%ld\n", __func__, i);
|
||||
//for debug indel
|
||||
// prt_ovlp_sam(&b->olist, &b->ovlp_read, b->self_read.seq, b->self_read.length);
|
||||
// stderr_phase_ovlp(&b->olist);
|
||||
|
||||
|
||||
// fprintf(stderr, "\n[M::%s] rid::%ld\t%.*s\tlen::%lld\tocc::%lu\n", __func__, i, (int)Get_NAME_LENGTH(R_INF, i), Get_NAME(R_INF, i), b->self_read.length, b->olist.length);
|
||||
|
||||
// fprintf(stderr, "[M::%s] rid::%ld\n", __func__, i);
|
||||
// debug_mm_exact_cigar(&b->olist, i, &b->self_read, &b->ovlp_read);
|
||||
|
||||
// b->num_correct_base += b->olist.length;
|
||||
/**
|
||||
* ///r779: enable this
|
||||
copy_asg_arr(buf0, b->sp);
|
||||
gen_reseed_re(&b->olist, &b->clist, aux_o, rse_o, &R_INF, &b->self_read, &b->ovlp_read, &b->exz, &b->pidx, &b->v64, &buf0, 0, asm_opt.mz_win, 19, i, asm_opt.max_ov_diff_ec, asm_opt.max_ov_diff_ec, &b->v16, R_INF.tqn, b->v8q.a);
|
||||
copy_asg_arr(b->sp, buf0);
|
||||
**/
|
||||
|
||||
copy_asg_arr(buf0, b->sp);
|
||||
//site_sc: r765 -> r766: 1 -> 0
|
||||
rphase_hc(&b->olist, &R_INF, &b->hap, &b->self_read, &b->ovlp_read, &b->pidx, &b->v64, &buf0, 0, WINDOW_MAX_SIZE, b->self_read.length, 1/**, 0**/, i, (asm_opt.is_ont)?HPC_PL:0, asm_opt.is_ont, ((asm_opt.is_ont)?&(b->clist.chainDP):NULL), ((asm_opt.is_sc)?&(b->v8q):NULL), /**((asm_opt.is_sc)?&(b->v8t):NULL)**/&(b->v8t), (asm_opt.is_ont)?1:0, ((uint64_t)-1), 0, HC0_W, &b->v32,
|
||||
asm_opt.s_hap_cov, asm_opt.infor_cov, het_a, hom_a, asm_opt.polyploidy, -1.0);
|
||||
copy_asg_arr(b->sp, buf0);
|
||||
///for debug indel
|
||||
// stderr_phase_ovlp(&b->olist);
|
||||
|
||||
// est_rep_err_rate(&b->olist, &b->v64, &b->pidx, qlen, (asm_opt.is_ont)?(WINDOW_OHC):(WINDOW_HC), NULL);
|
||||
|
||||
if(DBG_TIME && dbg_a) {
|
||||
if(DBG_TIME == 1) {
|
||||
tt1 = yak_realtime_0();
|
||||
dbg_a[i].phs_tm = tt1 - tt0;
|
||||
tt0 = tt1;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
dedup_chains(&b->olist);
|
||||
|
||||
|
||||
|
||||
copy_asg_arr(buf0, b->sp);
|
||||
b->cnt[1] += wcns_gen(&b->olist, &R_INF, i, &b->self_read, &b->ovlp_read, &b->exz, &b->pidx, &b->v64, &buf0, 0, 512, b->self_read.length, 3, 0.500001, aux_o, &b->v32, &b->cns, 256, i, ((uint64_t)-1),
|
||||
R_INF.tr[0], R_INF.tr[1], asm_opt.ont_rate, asm_opt.hf_rate, asm_opt.hf_rate_max, NULL);
|
||||
copy_asg_arr(b->sp, buf0);
|
||||
|
||||
if(DBG_TIME && dbg_a) {
|
||||
if(DBG_TIME == 1) {
|
||||
tt1 = yak_realtime_0();
|
||||
dbg_a[i].cns_tm = tt1 - tt0;
|
||||
tt0 = tt1;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
push_nec_re(aux_o, &(scc.a[i]));
|
||||
push_nec_re(aux_o, &(scb.a[i]));
|
||||
|
||||
// if((asm_opt.is_ont) && is_chemical_r_qual(&b->olist, &b->v64, qlen, 1, 16, &(b->v8q), i)/**(is_uncorrected_read(&b->olist, &b->v64, qlen, 1600))**/) {
|
||||
// // b->olist.length = 0;
|
||||
// fprintf(stderr, "[M::%s] rid::%ld\t%.*s\n\n", __func__, i, (int)Get_NAME_LENGTH(R_INF, i), Get_NAME(R_INF, i));
|
||||
// }
|
||||
|
||||
push_ne_ovlp(&(R_INF.paf[i]), &b->olist, 1, &R_INF, &(scc.a[i])/**, i, &b->self_read, &b->ovlp_read**/);
|
||||
push_ne_ovlp(&(R_INF.reverse_paf[i]), &b->olist, 2, &R_INF, NULL/**, i, NULL, NULL**/);
|
||||
|
||||
|
||||
check_well_cal(&(scc.a[i]), &b->v64, &(R_INF.paf[i].is_fully_corrected), &(R_INF.paf[i].is_abnormal), qlen, (MIN_COVERAGE_THRESHOLD*2), &(R_INF.paf[i]));
|
||||
R_INF.trio_flag[i] = AMBIGU;
|
||||
|
||||
// uint32_t k;
|
||||
// for (k = 0; k < b->olist.length; k++) {
|
||||
// if(b->olist.list[k].is_match == 1) b->num_recorrect_base++;
|
||||
// }
|
||||
///for debug indel
|
||||
// exit(1);
|
||||
|
||||
|
||||
|
||||
// prt_chain(&b->olist);
|
||||
|
||||
// ul_map_lchain(b->abl, (uint32_t)-1, s->seq[i], s->len[i], s->opt->w, s->opt->k, s->uu, &b->olist, &b->clist, s->opt->bw_thres,
|
||||
@@ -8279,19 +8524,43 @@ dbg_cnt_ss* fetch_dbg_cnt_ss(char *in, int64_t n_a, dbg_cnt_ss *in_p)
|
||||
return p;
|
||||
}
|
||||
|
||||
void prt_dbg_stats(dbg_cnt_ss *p, uint64_t n_a, char *fn_n, uint64_t rr)
|
||||
void prt_dbg_stats(dbg_cnt_ss *p, uint64_t n_a, char *fn_n, uint64_t rr, uint8_t stat_only)
|
||||
{
|
||||
uint64_t k;
|
||||
char* ga_n = (char*)malloc(strlen(fn_n)+64);
|
||||
sprintf(ga_n, "%s.%lu.run.stat.log", fn_n, rr);
|
||||
FILE *fn = fopen(ga_n, "w");
|
||||
free(ga_n);
|
||||
uint64_t k; char *ga_n = NULL; FILE *fn = NULL; double chn_tm = 0, aln_tm = 0, phs_tm = 0, cns_tm = 0;
|
||||
uint64_t fbs = 0, faln = 0;
|
||||
if(!stat_only) {
|
||||
ga_n = (char*)malloc(strlen(fn_n)+64);
|
||||
sprintf(ga_n, "%s.%lu.run.stat.log", fn_n, rr);
|
||||
fn = fopen(ga_n, "w");
|
||||
free(ga_n);
|
||||
}
|
||||
|
||||
|
||||
for (k = 0; k < n_a; k++) {
|
||||
fprintf(fn, "rid::%lu\ttot_bs::%lu\taln_bs::%lu\tchn_tm::%f\taln_tm::%f\tphs_tm::%f\tcns_tm::%f\n", k, p[k].fbs, p[k].faln, p[k].chn_tm, p[k].aln_tm, p[k].phs_tm, p[k].cns_tm);
|
||||
if(!stat_only) {
|
||||
if(DBG_TIME == 1) {
|
||||
fprintf(fn, "rid::%lu\ttot_bs::%lu\taln_bs::%lu\tchn_tm::%f\taln_tm::%f\tphs_tm::%f\tcns_tm::%f\n", k, p[k].fbs, p[k].faln, p[k].chn_tm, p[k].aln_tm, p[k].phs_tm, p[k].cns_tm);
|
||||
} else {
|
||||
fprintf(fn, "rid::%lu\ttot_bs::%lu\taln_bs::%lu\n", k, p[k].fbs, p[k].faln);
|
||||
}
|
||||
|
||||
}
|
||||
chn_tm += p[k].chn_tm;
|
||||
aln_tm += p[k].aln_tm;
|
||||
phs_tm += p[k].phs_tm;
|
||||
cns_tm += p[k].cns_tm;
|
||||
fbs += p[k].fbs;
|
||||
faln += p[k].faln;
|
||||
}
|
||||
|
||||
fclose(fn);
|
||||
if(!stat_only) {
|
||||
fprintf(stderr, "[M::%s] chn_tm::%f, aln_tm:%f, phs_tm:%f, cns_tm:%f, fbs::%lu, faln::%lu\n", __func__, chn_tm, aln_tm, phs_tm, cns_tm, fbs, faln);
|
||||
fclose(fn);
|
||||
exit(1);
|
||||
} else {
|
||||
fprintf(stderr, "[M::%s] chn_tm::%f, aln_tm:%f, phs_tm:%f, cns_tm:%f, fbs::%lu, faln::%lu\n", __func__, chn_tm, aln_tm, phs_tm, cns_tm, fbs, faln);
|
||||
exit(1);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@@ -8912,7 +9181,7 @@ void cal_ec_r(uint64_t n_thre, uint64_t round, uint64_t n_round, uint64_t n_a, u
|
||||
}
|
||||
|
||||
if(DBG_TIME && dbg_a) {
|
||||
prt_dbg_stats(dbg_a, n_a, asm_opt.output_file_name, round);
|
||||
prt_dbg_stats(dbg_a, n_a, asm_opt.output_file_name, round, 0);
|
||||
free(dbg_a); dbg_a = NULL;
|
||||
}
|
||||
sl_ec_r(n_thre, n_a);
|
||||
|
||||
Reference in New Issue
Block a user