From efc19a36de7236c21b3ae1fe7601e0503bc9c4b7 Mon Sep 17 00:00:00 2001 From: peterjc Date: Fri, 19 Apr 2013 15:18:49 +0100 Subject: [PATCH] Update 'samtools depad' help text regarding FASTA reference file --- padding.c | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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"); -- 2.39.2