argument checking for update-ref-alt

gymrek-lab · Sep 9, 2024 · 6cb53fc · 6cb53fc
1 parent 1703b33
commit 6cb53fc
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diff --git a/trtools/annotaTR/annotaTR.py b/trtools/annotaTR/annotaTR.py
@@ -480,6 +480,10 @@ def main(args):
         common.WARNING("Error: you cannot use --update-ref-alt unless "
                        " --match-refpanel-on is set to locid")
         return 1
+    if args.update_ref_alt and args.ref_panel is None:
+        common.WARNING("Error: --update-ref-alt only works with "
+                       " --ref-panel.")
+        return 1
 
     outtypes = set()
     for outtype in args.outtype:

diff --git a/trtools/annotaTR/tests/test_annotaTR.py b/trtools/annotaTR/tests/test_annotaTR.py
@@ -141,6 +141,11 @@ def test_UpdateRefAlt(args, vcfdir):
     args.match_refpanel_on = "rawalleles"
     retcode = main(args)
     assert retcode==1
+    # Won't work with no ref panel
+    args.match_refpanel_on = "locid"
+    args.ref_panel = None
+    retcode = main(args)
+    assert retcode==1
 
     # Try on good file with alleles that do match refpanel
     args.match_refpanel_on = "locid"