From: peterjc <p.j.a.cock@googlemail.com>
Date: Tue, 12 Jun 2012 14:29:26 +0000 (+0100)
Subject: SAM/BAM input to 'samtools depad' not linked to FASTA reference
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=09ad722ca25bd51716d24531bd199ca24269786d;hp=8919a745585a68d671a1301b444e6edf7f4fdd4b

SAM/BAM input to 'samtools depad' not linked to FASTA reference
---

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);
 		}