comment for --reference

It isn't recommended and is tripping up too many users. Figure out how
to remove it without messing up pipelines.

truvari/matching.py

@@ -90,7 +90,8 @@ def __init__(self, args=None):
 
         self.reference = None
         if self.params.reference is not None:
-            #logging.warning("`--reference` is being deprecated and is only
+            #sys.stderr.write("WARNING `--reference` is no longer recommended for use with bench/collapse ")
+            #sys.stderr.write("results will be slower and less accurate.\n")
             self.reference = pysam.FastaFile(self.params.reference)
 
     @staticmethod