From: peterjc
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/?a=commitdiff_plain;h=efc19a36de7236c21b3ae1fe7601e0503bc9c4b7;hp=8e3b3f229a04cb81b680987ce06ae1507c9d8b69;p=samtools.git
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");