-// if (n == 0) add_pair(sm, sm2id, fn, fn);
- add_pair(sm, sm2id, fn, fn);
+ if (n == 0) add_pair(sm, sm2id, fn, fn);
+ // If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but
+ // use the tag instead.
+ else if ( n==1 && first_sm.s )
+ add_pair(sm,sm2id,fn,first_sm.s);
+ if ( first_sm.s )
+ free(first_sm.s);
+
+// add_pair(sm, sm2id, fn, fn);