Make variant region at boundary configurable

src/hgvs/_data/defaults.ini

@@ -6,6 +6,7 @@ inferred_p_is_uncertain = True
 normalize = True
 prevalidation_level = EXTRINSIC
 replace_reference = True
+ref_at_boundary_is_intronic = True
 
 # strict_bounds: require transcript variants to be within transcript sequence bounds
 strict_bounds = True

src/hgvs/utils/altseqbuilder.py

@@ -9,6 +9,7 @@
 import logging
 import math
 
+from hgvs import global_config
 from hgvs.exceptions import HGVSError
 
 from bioutils.sequences import reverse_complement, translate_cds
@@ -198,16 +199,16 @@ def _get_variant_region(self):
             result = self.WHOLE_GENE
         elif self._var_c.posedit.edit.type == "ins" and self._var_c.posedit.pos.start.offset == -1 and self._var_c.posedit.pos.end.offset == 0:
             # ins at intron-exon boundary
-            result = self.EXON
+            result = self.INTRON if global_config.mapping.ref_at_boundary_is_intronic else self.EXON
         elif self._var_c.posedit.edit.type == "ins" and self._var_c.posedit.pos.start.offset == 0 and self._var_c.posedit.pos.end.offset == 1:
             # ins at exon-intron boundary
-            result = self.EXON
+            result = self.INTRON if global_config.mapping.ref_at_boundary_is_intronic else self.EXON
         elif self._var_c.posedit.edit.type == "dup" and self._var_c.posedit.pos.end.offset == -1:
             # dup at intron-exon boundary
-            result = self.EXON
+            result = self.INTRON if global_config.mapping.ref_at_boundary_is_intronic else self.EXON
         elif self._var_c.posedit.edit.type == "dup" and self._var_c.posedit.pos.start.offset == 1:
             # dup at exon-intron boundary
-            result = self.EXON
+            result = self.INTRON if global_config.mapping.ref_at_boundary_is_intronic else self.EXON
         elif self._var_c.posedit.pos.start.offset != 0 or self._var_c.posedit.pos.end.offset != 0:
             # leave out anything else intronic for now
             result = self.INTRON

tests/issues/test_655.py

@@ -124,8 +124,18 @@ def mock_vm(mock_hdp):
     return hgvs.variantmapper.VariantMapper(mock_hdp, prevalidation_level="INTRINSIC")
 
 
+@pytest.fixture()
+def ref_at_boundary_is_exonic():
+    original = hgvs.global_config.mapping.ref_at_boundary_is_intronic
+    hgvs.global_config.mapping.ref_at_boundary_is_intronic = False
+    try:
+        yield
+    finally:
+        hgvs.global_config.mapping.ref_at_boundary_is_intronic = original
+
+
 @pytest.mark.parametrize("case", sanity_cases)
-def test_sanity_c_to_p(case, hp, mock_vm):
+def test_sanity_c_to_p(case, hp, mock_vm, ref_at_boundary_is_exonic):
     var_c = hp.parse(case["var_c"])
     if "exc" in case:
         with pytest.raises(case["exc"]):
@@ -135,7 +145,7 @@ def test_sanity_c_to_p(case, hp, mock_vm):
 
 
 @pytest.mark.parametrize("case", real_cases)
-def test_real_c_to_p(case, hp, vm, am37):
+def test_real_c_to_p(case, hp, vm, am37, ref_at_boundary_is_exonic):
     var_c = hp.parse(case["var_c"])
     if "exc" in case:
         with pytest.raises(case["exc"]):