+
+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;
+}