bug fixed

hic.cpp

@@ -7406,7 +7406,7 @@ void update_bsg(asg_t *bsg, kvec_asg_arc_t_warp* edges)
 
 void resolve_bubble_chain_tangle(ma_ug_t* ug, bubble_type* bub)
 {
-    double index_time = yak_realtime();
+    // double index_time = yak_realtime();
     ma_ug_t *bub_ug = bub->b_ug;
     asg_t *bsg = bub->b_g;
     uint32_t k, i, v, n_vx, new_bub;
@@ -7575,7 +7575,7 @@ void resolve_bubble_chain_tangle(ma_ug_t* ug, bubble_type* bub)
     kv_destroy(res_btg.a); kv_destroy(res_utg.a); kv_destroy(edges.a);
 
     ///print_debug_bubble_graph(bub, ug, asm_opt.output_file_name);
-    fprintf(stderr, "[M::%s::%.3f]\n", __func__, yak_realtime()-index_time);
+    // fprintf(stderr, "[M::%s::%.3f]\n", __func__, yak_realtime()-index_time);
 }
 
 void update_bubble_chain(ma_ug_t* ug, bubble_type* bub, uint32_t is_middle, uint32_t is_end)
@@ -13931,11 +13931,11 @@ int hic_short_align(const enzyme *fn1, const enzyme *fn2, ha_ug_index* idx)
         }
 
         renew_kv_u_trans(&k_trans, &link, &sl.hits, &(idx->t_ch->k_trans), idx, &bub, s->s, 0);
-        // if(bub.round_id == 0) init_phase(idx, &k_trans, &bub, s); 
+        if(bub.round_id == 0) init_phase(idx, &k_trans, &bub, s); 
         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, 0, /**&bub**/NULL);
+        /**(bub.round_id == 0? 1 : 0)**/0, s->s, 0, /**&bub**/NULL);
         /*******************************for debug************************************/
         label_unitigs_sm(s->s, idx->ug);
         /**

hifiasm.1

@@ -1,4 +1,4 @@
-.TH hifiasm 1 "20 Mar 2021" "hifiasm-0.14.2 (r315)" "Bioinformatics tools"
+.TH hifiasm 1 "16 April 2021" "hifiasm-0.15 (r327)" "Bioinformatics tools"
 
 .SH NAME
 .PP
@@ -349,11 +349,7 @@ RNG seed [11].
 .SH OUTPUTS
 
 .PP
-Without trio partition options
+In general, hifiasm generates the following assembly graphs in the GFA format:
-.B -1
-and
-.BR -2 ,
-hifiasm generates the following assembly graphs in the GFA format:
 
 .RS 2
 .TP 2
@@ -380,40 +376,106 @@ assembly graph of primary contigs. This graph collapses different haplotypes.
 assembly graph of alternate contigs. This graph consists of all assemblies that
 are discarded in primary contig graph.
 
+.TP
+*
+.IR prefix .hap*.p_ctg.gfa:
+phased contig graph. This graph keeps the phased assembly.
+
 .RE
 
 .PP
-With trio partition, hifiasm outputs the following assembly graphs:
+Hifiasm outputs
+.B *.r_utg.gfa
+and
+.B *.p_utg.gfa
+in any cases.
+Specifically, hifiasm outputs the following assembly graphs
+with trio-binning options:
 
 .RS 2
 .TP 2
 *
-.IR prefix .dip.r_utg.gfa:
+.IR prefix .dip.hap1.p_ctg.gfa:
-haplotype-resolved raw unitig graph. This graph keeps all haplotype information.
+phased paternal/haplotype1 contig graph keeping the phased
-
-.TP
-*
-.IR prefix .hap1.p_ctg.gfa:
-phased paternal/haplotype1 contig graph. This graph keeps the phased
 paternal/haplotype1 assembly.
 
 .TP
 *
-.IR prefix .hap2.p_ctg.gfa:
+.IR prefix .dip.hap2.p_ctg.gfa:
-phased maternal/haplotype2 contig graph. This graph keeps the phased
+phased maternal/haplotype2 contig graph keeping the phased
 maternal/haplotype2 assembly.
 .RE
 
 .PP
-With Hi-C partition, hifiasm outputs the assembly graphs like trio partition,
+With Hi-C partition options, hifiasm outputs:
-but with additional prefix
+
-.B [hic].
+.RS 2
-In this mode, hifiasm keeps Hi-C alignment results and Hi-C index in two bin 
+.TP 2
+*
+.IR prefix .hic.p_ctg.gfa:
+assembly graph of primary contigs. This graph collapses different haplotypes.
+
+.TP
+*
+.IR prefix .hic.hap1.p_ctg.gfa:
+phased contig graph where each contig is fully phased.
+
+.TP
+*
+.IR prefix .hic.hap2.p_ctg.gfa:
+phased contig graph where each contig is fully phased.
+.RE
+
+
+.PP
+Hifiasm keeps Hi-C alignment results and Hi-C index in two bin 
 files: 
 .B *hic.lk.bin
 and 
 .B *hic.tlb.bin.
-Rerunning hifiasm with different Hi-C reads needs to delete these bin files.
+Rerunning hifiasm with different Hi-C reads needs to delete these bin files
+or enable 
+.BR -i .
+.RE
+
+.PP
+Hifiasm generates the following assembly graphs only with HiFi reads:
+
+.RS 2
+.TP 2
+*
+.IR prefix .p_ctg.gfa:
+assembly graph of primary contigs. This graph collapses different haplotypes.
+
+.TP
+*
+.IR prefix .bp.hap1.p_ctg.gfa:
+balanced contig graph where each contig is partially phased.
+
+.TP
+*
+.IR prefix .bp.hap2.p_ctg.gfa:
+balanced contig graph where each contig is partially phased.
+.RE
+
+.PP
+If the option
+.BR -p
+or
+.BR --primary
+is specified, hifiasm outputs:
+
+.RS 2
+.TP 2
+*
+.IR prefix .p_ctg.gfa:
+assembly graph of primary contigs. This graph collapses different haplotypes.
+
+.TP
+*
+.IR prefix .a_ctg.gfa:
+assembly graph of alternate contigs. This graph consists of all assemblies that
+are discarded in primary contig graph.
 .RE
 
 

rcut.cpp

@@ -842,6 +842,7 @@ t_w_t mc_init_spin(const mc_opt_t *opt, const mc_match_t *ma, mc_svaux_t *b)
 	b->cc_edge.n = 0;
 	for (i = 0; i < b->cc_size; ++i) {///how many nodes
 		uint32_t k = (uint32_t)ma->cc[b->cc_off + i];///node id
+		b->cc_node[i] = k;
 		if(b->s[k] == 0) break;
 	}
 	if(i >= b->cc_size)
@@ -1234,10 +1235,8 @@ uint32_t mc_solve_cc(const mc_opt_t *opt, const mc_g_t *mg, mc_svaux_t *b, uint3
 {
 	uint32_t j, k, n_iter = 0;
 	t_w_t sc_opt = -(1<<30), sc;///problem-w
-
 	b->cc_off = cc_off, b->cc_size = cc_size;
 	if (b->cc_size < 2) return 0;
-
 	// print_sc(opt, mg->e, b, sc_opt, (uint32_t)-1);
 	sc_opt = mc_init_spin(opt, mg->e, b);
 	if (b->cc_size == 2) return 0;
@@ -1305,25 +1304,19 @@ void mc_init_spin_all(const mc_opt_t *opt, mc_g_t *mg, mc_svaux_t *b)
 
 void mc_solve_core(const mc_opt_t *opt, mc_g_t *mg, bubble_type* bub)
 {
-	fprintf(stderr, "#######0#######\n");
 	double index_time = yak_realtime();
 	uint32_t st, i;
 	mc_svaux_t *b;
 	mc_bp_t *bp = NULL;
-	fprintf(stderr, "#######1#######\n");
 	mc_g_cc(mg->e);
-	fprintf(stderr, "#######2#######\n");
 	b = mc_svaux_init(mg, opt->seed);
-	fprintf(stderr, "#######3#######\n");
 	if(bub) bp = mc_bp_t_init(mg->e, b, bub, asm_opt.thread_num);
-	fprintf(stderr, "#######4#######\n");
 	/*******************************for debug************************************/
 	if(bp)
 	{
 		mc_init_spin_all(opt, mg, b);
 		mc_solve_bp(bp);
 	} 
-	fprintf(stderr, "#######5#######\n");
 	/*******************************for debug************************************/
 	// fprintf(stderr, "\n\n\n\n\n*************beg-[M::%s::score->%f] ==> Partition\n", __func__, mc_score_all(mg->e, b));
 	for (st = 0, i = 1; i <= mg->e->n_seq; ++i) {
@@ -1333,14 +1326,10 @@ void mc_solve_core(const mc_opt_t *opt, mc_g_t *mg, bubble_type* bub)
 		}
 	}
 	// fprintf(stderr, "##############end-[M::%s::score->%f] ==> Partition\n", __func__, mc_score_all(mg->e, b));
-	fprintf(stderr, "#######6#######\n");
 	if(bp) mc_solve_bp(bp);	
-	fprintf(stderr, "#######7#######\n");
 	///mc_write_info(g, b);
 	mc_svaux_destroy(b);
-	fprintf(stderr, "#######8#######\n");
 	if(bp) destroy_mc_bp_t(&bp);
-	fprintf(stderr, "#######9#######\n");
 	fprintf(stderr, "[M::%s::%.3f] ==> Partition\n", __func__, yak_realtime()-index_time);
 }
 
@@ -1450,16 +1439,11 @@ void p_nodes(mc_g_t *mg, trans_chain* t_ch, uint8_t* trio_flag)
 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)
 {
 	mc_opt_t opt;
-	fprintf(stderr, "*****0******\n");
 	mc_opt_init(&opt, asm_opt.n_perturb, asm_opt.f_perturb, asm_opt.seed);
-	fprintf(stderr, "*****1******\n");
 	mc_g_t *mg = init_mc_g_t(ug, read_g, s, renew_s);
-	fprintf(stderr, "*****2******\n");
 	update_mc_edges(mg, ovlp, ta, t_ch, f_rate, is_sys);
-	fprintf(stderr, "*****3******\n");
 	///debug_mc_g_t(mg);
 	mc_solve_core(&opt, mg, bub);
-	fprintf(stderr, "*****4******\n");
 
 	if((asm_opt.flag & HA_F_PARTITION) && t_ch)
 	{