Added option to write output to file

Josiah1 · Jun 27, 2017 · d28da05 · d28da05
1 parent ab3a92b
commit d28da05
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/fastmap.c b/fastmap.c
@@ -130,7 +130,7 @@ int main_mem(int argc, char *argv[])
 
 	aux.opt = opt = mem_opt_init();
 	memset(&opt0, 0, sizeof(mem_opt_t));
-	while ((c = getopt(argc, argv, "51paMCSPVYjk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:W:x:G:h:y:K:X:H:")) >= 0) {
+	while ((c = getopt(argc, argv, "51paMCSPVYjk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:m:I:N:f:W:x:G:h:y:K:X:H:")) >= 0) {
 		if (c == 'k') opt->min_seed_len = atoi(optarg), opt0.min_seed_len = 1;
 		else if (c == '1') no_mt_io = 1;
 		else if (c == 'x') mode = optarg;
@@ -158,6 +158,7 @@ int main_mem(int argc, char *argv[])
 		else if (c == 's') opt->split_width = atoi(optarg), opt0.split_width = 1;
 		else if (c == 'G') opt->max_chain_gap = atoi(optarg), opt0.max_chain_gap = 1;
 		else if (c == 'N') opt->max_chain_extend = atoi(optarg), opt0.max_chain_extend = 1;
+		else if (c == 'f') xreopen(optarg, "wb", stdout);
 		else if (c == 'W') opt->min_chain_weight = atoi(optarg), opt0.min_chain_weight = 1;
 		else if (c == 'y') opt->max_mem_intv = atol(optarg), opt0.max_mem_intv = 1;
 		else if (c == 'C') aux.copy_comment = 1;