X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_md.c;h=3ca730993cbc01065eb2c76bd66df1640808e032;hp=8d074870d336677cee2e606ab05ee81a2b4a6f1e;hb=8af6e7eac6605aab3bd8b1a1f874309b59789b08;hpb=4a17fa7e1f91b2fe04ad334a63fc2b0d5e859d8a

diff --git a/bam_md.c b/bam_md.c
index 8d07487..3ca7309 100644
--- a/bam_md.c
+++ b/bam_md.c
@@ -132,8 +132,11 @@ int bam_fillmd(int argc, char *argv[])
 				free(ref);
 				ref = fai_fetch(fai, fp->header->target_name[b->core.tid], &len);
 				tid = b->core.tid;
+				if (ref == 0)
+					fprintf(stderr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n",
+							fp->header->target_name[tid]);
 			}
-			bam_fillmd1(b, ref, is_equal);
+			if (ref) bam_fillmd1(b, ref, is_equal);
 		}
 		samwrite(fpout, b);
 	}