fix bubble on-the-fly

CommandLines.h

@@ -5,7 +5,7 @@
 #include <pthread.h>
 #include <stdint.h>
 
-#define HA_VERSION "0.19.4-r575"
+#define HA_VERSION "0.19.4-r583"
 
 #define VERBOSE 0
 

Overlaps.h

@@ -1066,7 +1066,7 @@ ma_ug_t* copy_untig_graph(ma_ug_t *src);
 ma_ug_t* output_trio_unitig_graph(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name, 
 uint8_t flag, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, 
 long long tipsLen, float tip_drop_ratio, long long stops_threshold, R_to_U* ruIndex, 
-float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, int is_bench, bub_label_t* b_mask_t, char *f_prefix, uint8_t *kpt_buf, kvec_asg_arc_t_warp *r_edges);
+float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, int gap_fuzz, int is_bench, bub_label_t* b_mask_t, char *f_prefix, uint8_t *kpt_buf, kvec_asg_arc_t_warp *r_edges);
 asg_t* copy_read_graph(asg_t *src);
 ma_ug_t *ma_ug_gen(asg_t *g);
 void ma_ug_destroy(ma_ug_t *ug);
@@ -1135,7 +1135,7 @@ void adjust_utg_by_trio(ma_ug_t **ug, asg_t* read_g, uint8_t flag, float drop_ra
 ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, ma_sub_t* coverage_cut, 
 long long tipsLen, float tip_drop_ratio, long long stops_threshold, 
 R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp,
-kvec_asg_arc_t_warp* new_rtg_edges, bub_label_t* b_mask_t);
+int gap_fuzz, kvec_asg_arc_t_warp* new_rtg_edges, bub_label_t* b_mask_t);
 uint32_t cmp_untig_graph(ma_ug_t *src, ma_ug_t *dest);
 void reduce_hamming_error(asg_t *sg, ma_hit_t_alloc* sources, ma_sub_t *coverage_cut, 
 int max_hang, int min_ovlp, long long gap_fuzz);

README.md

@@ -51,7 +51,7 @@ Its latest release could support the telomere-to-telomere assembly by utilizing
 
 ## <a name="why"></a>Why Hifiasm?
 
-* Hifiasm delivers high-quality assemblies. It tends to generate longer contigs
+* Hifiasm delivers high-quality telomere-to-telomere assemblies. It tends to generate longer contigs
   and resolve more segmental duplications than other assemblers.
 
 * Given Hi-C reads or short reads from the parents, hifiasm can produce overall the best

gfa_ut.cpp

@@ -15686,6 +15686,9 @@ void u2g_hybrid_clean(ul_resolve_t *uidx, ulg_opt_t *ulopt, usg_t *ng, asg64_v *
         // prt_usg_t(uidx, ng, sb);
         // usg_arc_cut_length(ng, b, ub, mm_tip>>1, drop, ulopt->is_trio, 1, NULL);
         usg_bub_clean(ng, &bb, b, ub, mm_tip>>1, drop, 1, bs, f);
+        // fprintf(stderr, "-1bub-[M::%s::] i::%ld, drop::%f\n", __func__, i, drop);
+        // sprintf(sb, "ng_ss::%ld_i::%ld_drop::%f_b::bub", ss, i, drop);
+        // prt_usg_t(uidx, ng, sb);
         usg_arc_cut_srt_length(ng, b, ub, mm_tip>>1, drop, ulopt->is_trio, 1, NULL, bs);
         // fprintf(stderr, "-1-[M::%s::] i::%ld, drop::%f\n", __func__, i, drop);
         // sprintf(sb, "ng_ss::%ld_i::%ld_drop::%f_b", ss, i, drop);
@@ -16580,7 +16583,7 @@ ma_ug_t* output_trio_unitig_graph_ul(ug_opt_t *uopt, ul_resolve_t *uidx, char* o
 
     adjust_utg_by_trio(&ug, uidx->sg, flag, TRIO_THRES, uopt->sources, uopt->reverse_sources, 
     uopt->coverage_cut, uopt->tipsLen, uopt->tip_drop_ratio, uopt->stops_threshold, uopt->ruIndex, 
-    uopt->chimeric_rate, uopt->drop_ratio, uopt->max_hang, uopt->min_ovlp, &ne, uopt->b_mask_t);    
+    uopt->chimeric_rate, uopt->drop_ratio, uopt->max_hang, uopt->min_ovlp, uopt->gap_fuzz, &ne, uopt->b_mask_t);    
 
     // if(asm_opt.b_low_cov > 0) {
     //     break_ug_contig(&ug, uidx->sg, &R_INF, uopt->coverage_cut, uopt->sources, uopt->ruIndex, &ne, 

horder.cpp

@@ -781,7 +781,7 @@ ma_ug_t* get_trio_unitig_graph(asg_t *sg, uint8_t flag, ug_opt_t *opt)
     adjust_utg_by_trio(&ug, sg, flag, TRIO_THRES, opt->sources, opt->reverse_sources, 
     opt->coverage_cut, opt->tipsLen, opt->tip_drop_ratio, opt->stops_threshold, 
     opt->ruIndex, opt->chimeric_rate, opt->drop_ratio, opt->max_hang, opt->min_ovlp,
-    &new_rtg_edges, opt->b_mask_t);
+    opt->gap_fuzz, &new_rtg_edges, opt->b_mask_t);
 
     kv_destroy(new_rtg_edges.a);
     return ug;