Update 'samtools depad' help text regarding FASTA reference file

diff --git a/padding.c b/padding.c
index 476e393166983b0d00434789ad8596f0403a8f34..71dfc25957bf38214e899cbd92b653bd729f3373 100644 (file)
--- a/padding.c
+++ b/padding.c
@@ -465,7 +465,7 @@ static int usage(int is_long_help)
        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");
@@ -473,7 +473,7 @@ static int usage(int 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\
+     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");