r198: made VERBOSE_GFA a CL option --dbg-gfa

CommandLines.cpp

@@ -9,6 +9,12 @@
 
 hifiasm_opt_t asm_opt;
 
+static ko_longopt_t long_options[] = {
+	{ "version",      ko_no_argument,       300 },
+	{ "dbg-gfa",      ko_no_argument,       301 },
+	{ 0, 0, 0 }
+};
+
 double Get_T(void)
 {
   struct timeval t;
@@ -90,6 +96,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
     asm_opt->max_short_tip = 3;
     asm_opt->min_cnt = 2;
     asm_opt->mid_cnt = 5;
+	asm_opt->verbose_gfa = 0;
 }
 
 void destory_opt(hifiasm_opt_t* asm_opt)
@@ -301,13 +308,13 @@ int CommandLine_process(int argc, char *argv[], hifiasm_opt_t* asm_opt)
 
     int c;
 
-    while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:lw:m:n:r:a:b:z:x:y:p:c:d:M:P:if:D:FN:", 0)) >= 0) {
+    while ((c = ketopt(&opt, argc, argv, 1, "hvt:o:k:lw:m:n:r:a:b:z:x:y:p:c:d:M:P:if:D:FN:", long_options)) >= 0) {
         if (c == 'h')
         {
             Print_H(asm_opt);
             return 0;
         } 
-        else if (c == 'v')
+        else if (c == 'v' || c == 300)
         {
 			puts(HA_VERSION);
             return 0;
@@ -335,6 +342,7 @@ 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 == 301) asm_opt->verbose_gfa = 1;
         else if (c == ':') 
         {
 			fprintf(stderr, "[ERROR] missing option argument in \"%s\"\n", argv[opt.i - 1]);

CommandLines.h

@@ -3,10 +3,9 @@
 
 #include <pthread.h>
 
-#define HA_VERSION "0.3.0-dirty-r197"
+#define HA_VERSION "0.3.0-dirty-r198"
 
 #define VERBOSE 0
-#define VERBOSE_GFA 1
 
 typedef struct {
     int num_reads;
@@ -38,6 +37,7 @@ typedef struct {
     int max_short_tip;
     int min_cnt;
     int mid_cnt;
+	int verbose_gfa;
 
     float max_hang_rate;
     float min_drop_rate;

Overlaps.cpp

@@ -26464,7 +26464,7 @@ ma_sub_t **coverage_cut_ptr, int debug_g)
 
     asg_arc_del_simple_circle_untig(sources, coverage_cut, sg, 100, 0);
 
-    if(VERBOSE_GFA >= 1)
+    if (asm_opt.verbose_gfa)
     {
         /*******************************for debug***************************************/
         write_debug_graph(sg, sources, coverage_cut, output_file_name, n_read, reverse_sources, ruIndex);
@@ -26543,7 +26543,7 @@ long long bubble_dist, int read_graph, int write)
     ///actually min_thres = asm_opt.max_short_tip + 1 there are asm_opt.max_short_tip reads
     min_thres = asm_opt.max_short_tip + 1;
 
-    if(VERBOSE_GFA >= 1)
+    if (asm_opt.verbose_gfa)
     {
         if(load_debug_graph(&sg, &sources, &coverage_cut, output_file_name, &reverse_sources, &ruIndex))
         {

hifiasm.1

@@ -202,7 +202,11 @@ but occurs <
 times in the other sample.
 
 
+.SS Debugging options
 
+.TP 10
+.B --dbg-gfa
+Write additional files to speed up the debugging of graph cleaning
 
 
 .SH EXAMPLES

ketopt.h

@@ -17,7 +17,7 @@ typedef struct {
 } ketopt_t;
 
 typedef struct {
-	char *name;
+	const char *name;
 	int has_arg;
 	int val;
 } ko_longopt_t;