+ samfile_t *in = 0, *out = 0;
+ bam_header_t *h = 0;
+ faidx_t *fai = 0;
+ int c, is_bamin = 1, compress_level = -1, is_bamout = 1, is_long_help = 0;
+ char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0;
+ int ret=0;
+
+ /* parse command-line options */
+ strcpy(in_mode, "r"); strcpy(out_mode, "w");
+ while ((c = getopt(argc, argv, "Sso:u1T:?")) >= 0) {
+ switch (c) {
+ case 'S': is_bamin = 0; break;
+ case 's': assert(compress_level == -1); is_bamout = 0; break;
+ case 'o': fn_out = strdup(optarg); break;
+ case 'u': assert(is_bamout == 1); compress_level = 0; break;
+ case '1': assert(is_bamout == 1); compress_level = 1; break;
+ case 'T': fn_ref = strdup(optarg); break;
+ case '?': is_long_help = 1; break;
+ default: return usage(is_long_help);
+ }
+ }
+ if (argc == optind) return usage(is_long_help);
+
+ if (is_bamin) strcat(in_mode, "b");
+ if (is_bamout) strcat(out_mode, "b");
+ strcat(out_mode, "h");
+ if (compress_level >= 0) {
+ char tmp[2];
+ tmp[0] = compress_level + '0'; tmp[1] = '\0';
+ strcat(out_mode, tmp);
+ }
+
+ // Load FASTA reference (also needed for SAM -> BAM if missing header)
+ if (fn_ref) {
+ fn_list = samfaipath(fn_ref);
+ fai = fai_load(fn_ref);
+ }
+ // open file handlers
+ if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
+ fprintf(stderr, "[depad] failed to open \"%s\" for reading.\n", argv[optind]);
+ ret = 1;
+ goto depad_end;
+ }
+ if (in->header == 0) {
+ fprintf(stderr, "[depad] failed to read the header from \"%s\".\n", argv[optind]);
+ ret = 1;
+ goto depad_end;
+ }
+ if (in->header->text == 0 || in->header->l_text == 0) {
+ fprintf(stderr, "[depad] Warning - failed to read any header text from \"%s\".\n", argv[optind]);
+ assert (0 == in->header->l_text);
+ assert (0 == in->header->text);
+ }
+ if (fn_ref) {
+ h = fix_header(in->header, fai);
+ } else {
+ fprintf(stderr, "[depad] Warning - reference lengths will not be corrected without FASTA reference\n");
+ h = in->header;
+ }
+ if ((out = samopen(fn_out? fn_out : "-", out_mode, h)) == 0) {
+ fprintf(stderr, "[depad] failed to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
+ ret = 1;
+ goto depad_end;
+ }
+
+ // Do the depad
+ ret = bam_pad2unpad(in, out, fai);
+
+depad_end:
+ // close files, free and return
+ if (fai) fai_destroy(fai);
+ if (h != in->header) bam_header_destroy(h);
+ samclose(in);
+ samclose(out);
+ free(fn_list); free(fn_out);
+ return ret;
+}
+
+static int usage(int is_long_help)
+{
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: samtools depad <in.bam>\n\n");
+ fprintf(stderr, "Options: -s output is SAM (default is BAM)\n");
+ fprintf(stderr, " -S input is SAM (default is BAM)\n");
+ fprintf(stderr, " -u uncompressed BAM output (can't use with -s)\n");
+ fprintf(stderr, " -1 fast compression BAM output (can't use with -s)\n");
+ fprintf(stderr, " -T FILE reference sequence file [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\
+ with the future aim to also support a FASTA padded reference sequence file.\n\
+\n\
+ 2. The input padded alignment read's CIGAR strings must not use P or I operators.\n\
+\n");
+ return 1;