From: peterjc <p.j.a.cock@googlemail.com>
Date: Fri, 19 Apr 2013 14:18:49 +0000 (+0100)
Subject: Update 'samtools depad' help text regarding FASTA reference file
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=efc19a36de7236c21b3ae1fe7601e0503bc9c4b7

Update 'samtools depad' help text regarding FASTA reference file
---

diff --git a/padding.c b/padding.c
index 476e393..71dfc25 100644
--- 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");