From: peterjc
Date: Tue, 3 Apr 2012 11:05:17 +0000 (+0100)
Subject: Minimal 'samtools depad' command line parsing (-? only so far)
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=6714aa07f8d3ec25225cc691066da89ca1bd0e9b;hp=507c3e9db23c24b97d15bd1b34f321b6d21ecaee;p=samtools.git
Minimal 'samtools depad' command line parsing (-? only so far)
---
diff --git a/padding.c b/padding.c
index a406612..9fbdb53 100644
--- a/padding.c
+++ b/padding.c
@@ -1,5 +1,6 @@
#include
#include
+#include
#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 \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] |\n\n");
//fprintf(stderr, "Options: -b output BAM\n");