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

[samtools.git] / padding.c

diff --git a/padding.c b/padding.c
index 19b95a9fff07a81759343ee165c2abd3f2d4a0e3..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);
                }
@@ -284,18 +284,18 @@ int main_pad2unpad(int argc, char *argv[])
        }
        // open file handlers
        if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
-               fprintf(stderr, "[depad] fail to open \"%s\" for reading.\n", argv[optind]);
+               fprintf(stderr, "[depad] failed to open \"%s\" for reading.\n", argv[optind]);
                ret = 1;
                goto depad_end;
        }
        if (in->header == 0) {
-               fprintf(stderr, "[depad] fail to read the header from \"%s\".\n", argv[optind]);
+               fprintf(stderr, "[depad] failed to read the header from \"%s\".\n", argv[optind]);
                ret = 1;
                goto depad_end;
        }
        /* TODO - The reference sequence lengths in the BAM + SAM headers should be updated */
        if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
-               fprintf(stderr, "[depad] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
+               fprintf(stderr, "[depad] failed to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
                ret = 1;
                goto depad_end;
        }