From 507c3e9db23c24b97d15bd1b34f321b6d21ecaee Mon Sep 17 00:00:00 2001
From: peterjc
Date: Tue, 3 Apr 2012 11:51:41 +0100
Subject: [PATCH 1/1] Adding a usage function to 'samtools depad' following
'samtools view' style
---
padding.c | 33 ++++++++++++++++++++++++++++++---
1 file changed, 30 insertions(+), 3 deletions(-)
diff --git a/padding.c b/padding.c
index 6d97b18..a406612 100644
--- a/padding.c
+++ b/padding.c
@@ -175,14 +175,15 @@ int bam_pad2unpad(bamFile in, bamFile out)
return 0;
}
+static int usage(int is_long_help);
+
int main_pad2unpad(int argc, char *argv[])
{
bamFile in, out;
+ int is_long_help = 1;
int result=0;
if (argc == 1) {
- fprintf(stderr, "Usage: samtools depad \n");
- fprintf(stderr, "\nRequires embedded reference sequences (before the reads for that reference).\n");
- return 1;
+ 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");
@@ -190,3 +191,29 @@ int main_pad2unpad(int argc, char *argv[])
bam_close(in); bam_close(out);
return result;
}
+
+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");
+ //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");
+ //fprintf(stderr, " -S input is SAM\n");
+ //fprintf(stderr, " -u uncompressed BAM output (force -b)\n");
+ //fprintf(stderr, " -1 fast compression (force -b)\n");
+ //fprintf(stderr, " -@ INT number of BAM compression threads [0]\n");
+ //fprintf(stderr, " -T FILE reference sequence file (force -S) [null]\n");
+ //fprintf(stderr, " -o FILE output file name [stdout]\n");
+ //fprintf(stderr, " -? longer help\n");
+ fprintf(stderr, "\n");
+ if (is_long_help)
+ fprintf(stderr, "Notes:\n\
+\n\
+ 1. Requires embedded reference sequences (before the reads for that reference).\n\
+\n\
+ 2. The input padded alignment read's CIGAR strings must not use P or I operators.\n\
+\n");
+ return 1;
+}
--
2.39.2