{
samfile_t *in = 0, *out = 0;
int c, is_bamin = 1, compress_level = -1, is_bamout = 1, is_long_help = 0;
{
samfile_t *in = 0, *out = 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;
+ 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");
int ret=0;
/* parse command-line options */
strcpy(in_mode, "r"); strcpy(out_mode, "w");
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;
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;
// open file handlers
if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
fprintf(stderr, "[depad] fail to open \"%s\" for reading.\n", argv[optind]);
// open file handlers
if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
fprintf(stderr, "[depad] fail to open \"%s\" for reading.\n", argv[optind]);
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, " -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");
- //TODO - These are the arguments I think make sense to support:
- //fprintf(stderr, " -@ INT number of BAM compression threads [0]\n");
- //fprintf(stderr, " -T FILE reference sequence file (force -S) [null]\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\
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\