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 <in.bam>\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");
bam_close(in); bam_close(out);
return result;
}
+
+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");
+ //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");
+ //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;
+}