Minimal 'samtools depad' command line parsing (-? only so far)

diff --git a/padding.c b/padding.c
index a4066122833620e8a68abec0368458e096048d8b..9fbdb53b797a6381408c9d32feb12333bfd54db8 100644 (file)
--- a/padding.c
+++ b/padding.c
@@ -1,5 +1,6 @@
 #include <string.h>
 #include <assert.h>
+#include <unistd.h>
 #include "kstring.h"
 #include "bam.h"
 
@@ -180,11 +181,18 @@ static int usage(int is_long_help);
 int main_pad2unpad(int argc, char *argv[])
 {
        bamFile in, out;
-       int is_long_help = 1;
+       int c, is_long_help = 0;
         int result=0;
-       if (argc == 1) {
-               return usage(is_long_help);
-       }
+
+       /* parse command-line options */
+       while ((c = getopt(argc, argv, "?")) >= 0) {
+               switch (c) {
+               case '?': is_long_help = 1; break;
+               default: return usage(is_long_help);
+               }
+        }
+       if (argc == optind) return usage(is_long_help);
+
        in = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
        out = bam_dopen(fileno(stdout), "w");
        result = bam_pad2unpad(in, out);
@@ -196,7 +204,7 @@ static int usage(int is_long_help)
 {
        fprintf(stderr, "\n");
        fprintf(stderr, "Usage:   samtools depad <in.bam>\n\n");
-       fprintf(stderr, "Currently there are no optional arguments.\n");
+       fprintf(stderr, "Options: -?       longer help\n");
        //TODO - These are the arguments I think make sense to support:
        //fprintf(stderr, "Usage:   samtools depad [options] <in.bam>|<in.sam>\n\n");
        //fprintf(stderr, "Options: -b       output BAM\n");