mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-10-01 01:38:12 +08:00
bug fixed
This commit is contained in:
chhylp123
@@ -7406,7 +7406,7 @@ void update_bsg(asg_t *bsg, kvec_asg_arc_t_warp* edges)
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void resolve_bubble_chain_tangle(ma_ug_t* ug, bubble_type* bub)
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{
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double index_time = yak_realtime();
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// double index_time = yak_realtime();
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ma_ug_t *bub_ug = bub->b_ug;
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asg_t *bsg = bub->b_g;
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uint32_t k, i, v, n_vx, new_bub;
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@@ -7575,7 +7575,7 @@ void resolve_bubble_chain_tangle(ma_ug_t* ug, bubble_type* bub)
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kv_destroy(res_btg.a); kv_destroy(res_utg.a); kv_destroy(edges.a);
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///print_debug_bubble_graph(bub, ug, asm_opt.output_file_name);
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fprintf(stderr, "[M::%s::%.3f]\n", __func__, yak_realtime()-index_time);
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// fprintf(stderr, "[M::%s::%.3f]\n", __func__, yak_realtime()-index_time);
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}
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void update_bubble_chain(ma_ug_t* ug, bubble_type* bub, uint32_t is_middle, uint32_t is_end)
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@@ -13931,11 +13931,11 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
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}
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renew_kv_u_trans(&k_trans, &link, &sl.hits, &(idx->t_ch->k_trans), idx, &bub, s->s, 0);
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// if(bub.round_id == 0) init_phase(idx, &k_trans, &bub, s);
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if(bub.round_id == 0) init_phase(idx, &k_trans, &bub, s);
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update_trans_g(idx, &k_trans, &bub);
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/*******************************for debug************************************/
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mc_solve(NULL, NULL, &k_trans, idx->ug, idx->read_g, 0.8, R_INF.trio_flag,
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(bub.round_id == 0? 1 : 0), s->s, 0, /**&bub**/NULL);
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/**(bub.round_id == 0? 1 : 0)**/0, s->s, 0, /**&bub**/NULL);
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/*******************************for debug************************************/
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label_unitigs_sm(s->s, idx->ug);
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/**
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@@ -1,4 +1,4 @@
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.TH hifiasm 1 "20 Mar 2021" "hifiasm-0.14.2 (r315)" "Bioinformatics tools"
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.TH hifiasm 1 "16 April 2021" "hifiasm-0.15 (r327)" "Bioinformatics tools"
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.SH NAME
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.PP
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@@ -349,11 +349,7 @@ RNG seed [11].
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.SH OUTPUTS
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.PP
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Without trio partition options
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.B -1
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and
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.BR -2 ,
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hifiasm generates the following assembly graphs in the GFA format:
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In general, hifiasm generates the following assembly graphs in the GFA format:
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.RS 2
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.TP 2
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@@ -380,40 +376,106 @@ assembly graph of primary contigs. This graph collapses different haplotypes.
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assembly graph of alternate contigs. This graph consists of all assemblies that
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are discarded in primary contig graph.
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.TP
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*
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.IR prefix .hap*.p_ctg.gfa:
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phased contig graph. This graph keeps the phased assembly.
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.RE
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.PP
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With trio partition, hifiasm outputs the following assembly graphs:
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Hifiasm outputs
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.B *.r_utg.gfa
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and
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.B *.p_utg.gfa
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in any cases.
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Specifically, hifiasm outputs the following assembly graphs
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with trio-binning options:
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.RS 2
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.TP 2
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*
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.IR prefix .dip.r_utg.gfa:
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haplotype-resolved raw unitig graph. This graph keeps all haplotype information.
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.TP
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*
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.IR prefix .hap1.p_ctg.gfa:
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phased paternal/haplotype1 contig graph. This graph keeps the phased
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.IR prefix .dip.hap1.p_ctg.gfa:
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phased paternal/haplotype1 contig graph keeping the phased
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paternal/haplotype1 assembly.
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.TP
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*
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.IR prefix .hap2.p_ctg.gfa:
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phased maternal/haplotype2 contig graph. This graph keeps the phased
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.IR prefix .dip.hap2.p_ctg.gfa:
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phased maternal/haplotype2 contig graph keeping the phased
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maternal/haplotype2 assembly.
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.RE
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.PP
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With Hi-C partition, hifiasm outputs the assembly graphs like trio partition,
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but with additional prefix
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.B [hic].
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In this mode, hifiasm keeps Hi-C alignment results and Hi-C index in two bin
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With Hi-C partition options, hifiasm outputs:
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.RS 2
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.TP 2
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*
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.IR prefix .hic.p_ctg.gfa:
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assembly graph of primary contigs. This graph collapses different haplotypes.
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.TP
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*
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.IR prefix .hic.hap1.p_ctg.gfa:
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phased contig graph where each contig is fully phased.
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.TP
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*
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.IR prefix .hic.hap2.p_ctg.gfa:
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phased contig graph where each contig is fully phased.
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.RE
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.PP
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Hifiasm keeps Hi-C alignment results and Hi-C index in two bin
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files:
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.B *hic.lk.bin
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and
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.B *hic.tlb.bin.
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Rerunning hifiasm with different Hi-C reads needs to delete these bin files.
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Rerunning hifiasm with different Hi-C reads needs to delete these bin files
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or enable
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.BR -i .
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.RE
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.PP
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Hifiasm generates the following assembly graphs only with HiFi reads:
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.RS 2
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.TP 2
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*
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.IR prefix .p_ctg.gfa:
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assembly graph of primary contigs. This graph collapses different haplotypes.
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.TP
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*
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.IR prefix .bp.hap1.p_ctg.gfa:
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balanced contig graph where each contig is partially phased.
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.TP
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*
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.IR prefix .bp.hap2.p_ctg.gfa:
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balanced contig graph where each contig is partially phased.
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.RE
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.PP
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If the option
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.BR -p
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or
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.BR --primary
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is specified, hifiasm outputs:
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.RS 2
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.TP 2
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*
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.IR prefix .p_ctg.gfa:
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assembly graph of primary contigs. This graph collapses different haplotypes.
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.TP
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*
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.IR prefix .a_ctg.gfa:
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assembly graph of alternate contigs. This graph consists of all assemblies that
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are discarded in primary contig graph.
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.RE
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@@ -842,6 +842,7 @@ t_w_t mc_init_spin(const mc_opt_t *opt, const mc_match_t *ma, mc_svaux_t *b)
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b->cc_edge.n = 0;
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for (i = 0; i < b->cc_size; ++i) {///how many nodes
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uint32_t k = (uint32_t)ma->cc[b->cc_off + i];///node id
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b->cc_node[i] = k;
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if(b->s[k] == 0) break;
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}
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if(i >= b->cc_size)
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@@ -1234,10 +1235,8 @@ uint32_t mc_solve_cc(const mc_opt_t *opt, const mc_g_t *mg, mc_svaux_t *b, uint3
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{
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uint32_t j, k, n_iter = 0;
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t_w_t sc_opt = -(1<<30), sc;///problem-w
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b->cc_off = cc_off, b->cc_size = cc_size;
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if (b->cc_size < 2) return 0;
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// print_sc(opt, mg->e, b, sc_opt, (uint32_t)-1);
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sc_opt = mc_init_spin(opt, mg->e, b);
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if (b->cc_size == 2) return 0;
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@@ -1305,25 +1304,19 @@ void mc_init_spin_all(const mc_opt_t *opt, mc_g_t *mg, mc_svaux_t *b)
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void mc_solve_core(const mc_opt_t *opt, mc_g_t *mg, bubble_type* bub)
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{
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fprintf(stderr, "#######0#######\n");
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double index_time = yak_realtime();
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uint32_t st, i;
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mc_svaux_t *b;
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mc_bp_t *bp = NULL;
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fprintf(stderr, "#######1#######\n");
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mc_g_cc(mg->e);
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fprintf(stderr, "#######2#######\n");
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b = mc_svaux_init(mg, opt->seed);
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fprintf(stderr, "#######3#######\n");
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if(bub) bp = mc_bp_t_init(mg->e, b, bub, asm_opt.thread_num);
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fprintf(stderr, "#######4#######\n");
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/*******************************for debug************************************/
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if(bp)
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{
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mc_init_spin_all(opt, mg, b);
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mc_solve_bp(bp);
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}
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fprintf(stderr, "#######5#######\n");
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/*******************************for debug************************************/
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// fprintf(stderr, "\n\n\n\n\n*************beg-[M::%s::score->%f] ==> Partition\n", __func__, mc_score_all(mg->e, b));
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for (st = 0, i = 1; i <= mg->e->n_seq; ++i) {
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@@ -1333,14 +1326,10 @@ void mc_solve_core(const mc_opt_t *opt, mc_g_t *mg, bubble_type* bub)
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}
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}
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// fprintf(stderr, "##############end-[M::%s::score->%f] ==> Partition\n", __func__, mc_score_all(mg->e, b));
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fprintf(stderr, "#######6#######\n");
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if(bp) mc_solve_bp(bp);
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fprintf(stderr, "#######7#######\n");
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///mc_write_info(g, b);
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mc_svaux_destroy(b);
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fprintf(stderr, "#######8#######\n");
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if(bp) destroy_mc_bp_t(&bp);
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fprintf(stderr, "#######9#######\n");
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fprintf(stderr, "[M::%s::%.3f] ==> Partition\n", __func__, yak_realtime()-index_time);
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}
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@@ -1450,16 +1439,11 @@ void p_nodes(mc_g_t *mg, trans_chain* t_ch, uint8_t* trio_flag)
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void mc_solve(hap_overlaps_list* ovlp, trans_chain* t_ch, kv_u_trans_t *ta, ma_ug_t *ug, asg_t *read_g, double f_rate, uint8_t* trio_flag, uint32_t renew_s, int8_t *s, uint32_t is_sys, bubble_type* bub)
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{
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mc_opt_t opt;
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fprintf(stderr, "*****0******\n");
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mc_opt_init(&opt, asm_opt.n_perturb, asm_opt.f_perturb, asm_opt.seed);
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fprintf(stderr, "*****1******\n");
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mc_g_t *mg = init_mc_g_t(ug, read_g, s, renew_s);
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fprintf(stderr, "*****2******\n");
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update_mc_edges(mg, ovlp, ta, t_ch, f_rate, is_sys);
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fprintf(stderr, "*****3******\n");
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///debug_mc_g_t(mg);
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mc_solve_core(&opt, mg, bub);
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fprintf(stderr, "*****4******\n");
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if((asm_opt.flag & HA_F_PARTITION) && t_ch)
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{
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