r246: made purge_dups optional for trio binning

CommandLines.cpp

@@ -15,6 +15,7 @@ static ko_longopt_t long_options[] = {
 	{ "write-paf",    ko_no_argument,       302 },
 	{ "write-ec",     ko_no_argument,       303 },
 	{ "skip-triobin", ko_no_argument,       304 },
+	{ "purge-trio",   ko_no_argument,       305 },
 	{ 0, 0, 0 }
 };
 
@@ -355,19 +356,20 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
 		else if (c == 302) asm_opt->flag |= HA_F_WRITE_PAF;
 		else if (c == 303) asm_opt->flag |= HA_F_WRITE_EC;
 		else if (c == 304) asm_opt->flag |= HA_F_SKIP_TRIOBIN;
+		else if (c == 305) asm_opt->flag |= HA_F_PURGE_TRIO;
         else if (c == ':') 
         {
 			fprintf(stderr, "[ERROR] missing option argument in \"%s\"\n", argv[opt.i - 1]);
-			return 0;
+			return 1;
 		} 
         else if (c == '?') 
         {
 			fprintf(stderr, "[ERROR] unknown option in \"%s\"\n", argv[opt.i - 1]);
-			return 0;
+			return 1;
 		}
     }
 
-    if (argc == 1)
+    if (argc == opt.ind)
     {
         Print_H(asm_opt);
         return 0;

CommandLines.h

@@ -3,7 +3,7 @@
 
 #include <pthread.h>
 
-#define HA_VERSION "0.5.0"
+#define HA_VERSION "0.5-dirty-r246"
 
 #define VERBOSE 0
 
@@ -13,6 +13,7 @@
 #define HA_F_WRITE_EC     0x8
 #define HA_F_WRITE_PAF    0x10
 #define HA_F_SKIP_TRIOBIN 0x20
+#define HA_F_PURGE_TRIO   0x40
 
 typedef struct {
 	int flag;

Overlaps.cpp

@@ -13222,10 +13222,12 @@ kvec_asg_arc_t_warp* new_rtg_edges)
     renew_utg(ug, read_g, new_rtg_edges);
 
     delete_useless_nodes(ug);
-    purge_dups(*ug, read_g, coverage_cut, reverse_sources, ruIndex, new_rtg_edges, 0.75, 50, 50, 0.5, max_hang,
-    min_ovlp, bubble_dist, drop_ratio, 1);
-    delete_useless_nodes(ug);
 
+	if (asm_opt.flag & HA_F_PURGE_TRIO) {
+		purge_dups(*ug, read_g, coverage_cut, reverse_sources, ruIndex, new_rtg_edges, 0.75, 50, 50, 0.5, max_hang,
+				min_ovlp, bubble_dist, drop_ratio, 1);
+		delete_useless_nodes(ug);
+	}
 
     set_drop_trio_flag(*ug);