Fixes #602: Fixed bug in transcript bounds check that caused n. varia…

…nts outside bounds to be deemed valid
biocommons · Jun 23, 2020 · c05c85f · c05c85f
1 parent 376f8ac
commit c05c85f
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/hgvs/validator.py b/hgvs/validator.py
@@ -82,6 +82,7 @@ def validate(self, var, strict=None):
             var_n = var
         elif var.type == "c":
             var_n = self.vm.c_to_n(var)
+
         if var_n is not None:
             res, msg = self._n_within_transcript_bounds(var_n)
             if res != ValidationLevel.VALID:
@@ -166,9 +167,9 @@ def _n_within_transcript_bounds(self, var):
         if tx_info is None:
             return (ValidationLevel.WARNING,
                     "No transcript data for accession: {ac}".format(ac=var.ac))
-        if var.posedit.pos.start.datum == Datum.SEQ_START and var.posedit.pos.end.base <= 0:
+        if var.posedit.pos.start.datum == Datum.SEQ_START and var.posedit.pos.start.base <= 0:
             return (ValidationLevel.ERROR, TX_BOUND_ERROR_MSG.format())
-        if var.posedit.pos.end.datum == Datum.SEQ_START and var.posedit.pos.start.base > tx_len:
+        if var.posedit.pos.end.datum == Datum.SEQ_START and var.posedit.pos.end.base > tx_len:
             return (ValidationLevel.ERROR, TX_BOUND_ERROR_MSG.format())
         return (ValidationLevel.VALID, None)