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, " -T FILE padded reference sequence file [null]\n");
fprintf(stderr, " -o FILE output file name [stdout]\n");
fprintf(stderr, " -? longer help\n");
fprintf(stderr, "\n");
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\
+ or ideally a FASTA file of the padded reference sequences (via the -T argument).\n\
\n\
2. The input padded alignment read's CIGAR strings must not use P or I operators.\n\
\n");