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);
}