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

[samtools.git] / padding.c

diff --git a/padding.c b/padding.c
index d5fd15fb6a7cf49e782d506ebe74201748f9467e..27bbd4b6cd982864262dc909cb068df8f9355f3c 100644 (file)
--- 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);
                }