add options

Assembly.cpp

@@ -1201,9 +1201,10 @@ int ha_assemble(void)
 		if (asm_opt.flag & HA_F_WRITE_PAF) Output_PAF();
 		ha_triobin(&asm_opt);
 	}
-	build_string_graph_without_clean(asm_opt.min_overlap_coverage, R_INF.paf, R_INF.reverse_paf, 
+
-			R_INF.total_reads, R_INF.read_length, asm_opt.min_overlap_Len, asm_opt.max_hang_Len, asm_opt.clean_round, 
+    build_string_graph_without_clean(asm_opt.min_overlap_coverage, R_INF.paf, R_INF.reverse_paf, 
-			asm_opt.gap_fuzz, asm_opt.min_drop_rate, asm_opt.max_drop_rate, asm_opt.output_file_name, asm_opt.large_pop_bubble_size, 0, !ovlp_loaded);
+        R_INF.total_reads, R_INF.read_length, asm_opt.min_overlap_Len, asm_opt.max_hang_Len, asm_opt.clean_round, 
+        asm_opt.gap_fuzz, asm_opt.min_drop_rate, asm_opt.max_drop_rate, asm_opt.output_file_name, asm_opt.large_pop_bubble_size, 0, !ovlp_loaded);
 	destory_All_reads(&R_INF);
 	return 0;
 }

CommandLines.cpp

@@ -50,6 +50,7 @@ void Print_H(hifiasm_opt_t* asm_opt)
     fprintf(stderr, "    -n INT        small removed unitig threshold [%d]\n", asm_opt->max_short_tip);
     fprintf(stderr, "    -x FLOAT      max overlap drop ratio [%.2g]\n", asm_opt->max_drop_rate);
     fprintf(stderr, "    -y FLOAT      min overlap drop ratio [%.2g]\n", asm_opt->min_drop_rate);
+    fprintf(stderr, "    -u            disable post join contigs step which may improve N50. Don't disable in default.\n");
     fprintf(stderr, "    --version     show version number\n");
     fprintf(stderr, "    -h            show help information\n");
 
@@ -361,7 +362,7 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
 
     int c;
 
-    while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:w:m:n:r:a:b:z:x:y:p:c:d:M:P:if:D:FN:1:2:3:4:l:s:O:", long_options)) >= 0) {
+    while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:w:m:n:r:a:b:z:x:y:p:c:d:M:P:if:D:FN:1:2:3:4:l:s:O:eu", long_options)) >= 0) {
         if (c == 'h')
         {
             Print_H(asm_opt);
@@ -396,6 +397,8 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
         else if (c == 'p') asm_opt->small_pop_bubble_size = atoll(opt.arg);
         else if (c == 'm') asm_opt->large_pop_bubble_size = atoll(opt.arg);
         else if (c == 'n') asm_opt->max_short_tip = atoll(opt.arg);
+        else if (c == 'e') asm_opt->flag |= HA_F_BAN_ASSEMBLY;
+        else if (c == 'u') asm_opt->flag |= HA_F_BAN_POST_JOIN;
 		else if (c == 301) asm_opt->flag |= HA_F_VERBOSE_GFA;
 		else if (c == 302) asm_opt->flag |= HA_F_WRITE_PAF;
 		else if (c == 303) asm_opt->flag |= HA_F_WRITE_EC;

CommandLines.h

@@ -3,7 +3,7 @@
 
 #include <pthread.h>
 
-#define HA_VERSION "0.7-dirty-r255"
+#define HA_VERSION "0.7-dirty-r256"
 
 #define VERBOSE 0
 
@@ -15,6 +15,8 @@
 #define HA_F_SKIP_TRIOBIN    0x20
 #define HA_F_PURGE_CONTAIN   0x40
 #define HA_F_PURGE_JOIN      0x80
+#define HA_F_BAN_POST_JOIN   0x100
+#define HA_F_BAN_ASSEMBLY    0x200
 
 #define HA_MIN_OV_DIFF       0.02 // min sequence divergence in an overlap
 

Overlaps.cpp

@@ -13251,15 +13251,18 @@ kvec_asg_arc_t_warp* new_rtg_edges)
 
     renew_utg(ug, read_g, new_rtg_edges);
 
-    rescue_missing_overlaps_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang,
+    if (!(asm_opt.flag & HA_F_BAN_POST_JOIN))
-    min_ovlp, 0, 0, 1, NULL);
+    {
+        rescue_missing_overlaps_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang,
+        min_ovlp, 0, 0, 1, NULL);
 
-    renew_utg(ug, read_g, new_rtg_edges);
+        renew_utg(ug, read_g, new_rtg_edges);
 
-    rescue_contained_reads_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang, 
+        rescue_contained_reads_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang, 
-    min_ovlp, 0, 10, 0, 1, NULL, NULL);
+        min_ovlp, 0, 10, 0, 1, NULL, NULL);
 
-    renew_utg(ug, read_g, new_rtg_edges);
+        renew_utg(ug, read_g, new_rtg_edges);
+    }
     
     update_unitig_graph((*ug), read_g, reverse_sources, ruIndex, 1, flag, drop_rate);
 
@@ -22084,27 +22087,27 @@ kvec_asg_arc_t_warp* new_rtg_edges)
         renew_utg(ug, read_g, new_rtg_edges);
     }
     
-
+    if (!(asm_opt.flag & HA_F_BAN_POST_JOIN))
-
-    rescue_missing_overlaps_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang,
-    min_ovlp, 0, 0, 1, NULL);
-    renew_utg(ug, read_g, new_rtg_edges);
-
-    rescue_contained_reads_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang, 
-    min_ovlp, 0, 10, 0, 1, NULL, NULL);
-    renew_utg(ug, read_g, new_rtg_edges);
-
-
-    if(asm_opt.purge_level_primary > 0)
     {
-        just_contain = 0;
+        rescue_missing_overlaps_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang,
-        if(asm_opt.purge_level_primary == 1) just_contain = 1;
+        min_ovlp, 0, 0, 1, NULL);
-
-        purge_dups(*ug, read_g, coverage_cut, reverse_sources, ruIndex, new_rtg_edges, 
-        asm_opt.purge_simi_rate, asm_opt.purge_overlap_len, max_hang, min_ovlp, bubble_dist, 
-        drop_ratio, just_contain);
-        delete_useless_nodes(ug);
         renew_utg(ug, read_g, new_rtg_edges);
+
+        rescue_contained_reads_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang, 
+        min_ovlp, 0, 10, 0, 1, NULL, NULL);
+        renew_utg(ug, read_g, new_rtg_edges);
+
+        if(asm_opt.purge_level_primary > 0)
+        {
+            just_contain = 0;
+            if(asm_opt.purge_level_primary == 1) just_contain = 1;
+
+            purge_dups(*ug, read_g, coverage_cut, reverse_sources, ruIndex, new_rtg_edges, 
+            asm_opt.purge_simi_rate, asm_opt.purge_overlap_len, max_hang, min_ovlp, bubble_dist, 
+            drop_ratio, just_contain);
+            delete_useless_nodes(ug);
+            renew_utg(ug, read_g, new_rtg_edges);
+        }
     }
     
 
@@ -26107,7 +26110,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
     normalize_ma_hit_t_single_side_advance(sources, n_read);
     normalize_ma_hit_t_single_side_advance(reverse_sources, n_read);
     
-    // debug_info_of_specfic_read(">m64011_190830_220126/117834372/ccs", sources, reverse_sources, 
+    // debug_info_of_specfic_read("m64062_190803_042216/122882911/ccs", sources, reverse_sources, 
     // -1, "clean");
 
 
@@ -26369,13 +26372,17 @@ long long bubble_dist, int read_graph, int write)
         &R_INF, output_file_name);
     }
 
-    try_rescue_overlaps(sources, reverse_sources, n_read, 4); 
+    if (!(asm_opt.flag & HA_F_BAN_ASSEMBLY))
+    {
+        try_rescue_overlaps(sources, reverse_sources, n_read, 4); 
 
-    clean_graph(min_dp, sources, reverse_sources, n_read, readLen, mini_overlap_length, 
+        clean_graph(min_dp, sources, reverse_sources, n_read, readLen, mini_overlap_length, 
-    max_hang_length, clean_round, gap_fuzz, min_ovlp_drop_ratio, max_ovlp_drop_ratio, 
+        max_hang_length, clean_round, gap_fuzz, min_ovlp_drop_ratio, max_ovlp_drop_ratio, 
-    output_file_name, bubble_dist, read_graph, &ruIndex, &sg, &coverage_cut, 0);
+        output_file_name, bubble_dist, read_graph, &ruIndex, &sg, &coverage_cut, 0);
+        
+        asg_destroy(sg);
+        free(coverage_cut);
+    }
 
-    asg_destroy(sg);
-    free(coverage_cut);
     destory_R_to_U(&ruIndex);
 }