From 09ad722ca25bd51716d24531bd199ca24269786d Mon Sep 17 00:00:00 2001
From: peterjc <p.j.a.cock@googlemail.com>
Date: Tue, 12 Jun 2012 15:29:26 +0100
Subject: [PATCH] SAM/BAM input to 'samtools depad' not linked to FASTA
 reference

---
 padding.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/padding.c b/padding.c
index d5fd15f..27bbd4b 100644
--- a/padding.c
+++ b/padding.c
@@ -261,7 +261,7 @@ int main_pad2unpad(int argc, char *argv[])
 		case 'o': fn_out = strdup(optarg); break;
 		case 'u': assert(is_bamout == 1); compress_level = 0; break;
 		case '1': assert(is_bamout == 1); compress_level = 1; break;
-		case 'T': fn_ref = strdup(optarg); is_bamin = 0; break;
+		case 'T': fn_ref = strdup(optarg); break;
                 case '?': is_long_help = 1; break;
 		default: return usage(is_long_help);
 		}
-- 
2.39.2