raising warnings about --reference deprecation

it will be removed at some point

truvari/bench.py

@@ -143,8 +143,10 @@ def check_params(args):
     if args.includebed and not os.path.exists(args.includebed):
         logging.error("Include bed %s does not exist", args.includebed)
         check_fail = True
-    if args.reference and not os.path.exists(args.reference):
-        logging.error("Reference %s does not exist", args.reference)
+    if args.reference:
+        logging.warning("`--reference` is no longer recommended and will be deprecated by v5")
+        not os.path.exists(args.reference):
+            logging.error("Reference %s does not exist", args.reference)
         check_fail = True
     return check_fail
 

truvari/collapse.py

@@ -566,6 +566,11 @@ def check_params(args):
     if args.hap and args.keep != "first":
         check_fail = True
         logging.error("Using --hap must use --keep first")
+    if args.reference:
+        logging.warning("`--reference` is no longer recommended and will be deprecated by v5")
+        not os.path.exists(args.reference):
+            logging.error("Reference %s does not exist", args.reference)
+        check_fail = True
     return check_fail
 
 

truvari/matching.py

@@ -89,8 +89,6 @@ def __init__(self, args=None):
 
         self.reference = None
         if self.params.reference is not None:
-            #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