chore: get to 100% test coverage

fgpyo/sam/__init__.py

@@ -1223,7 +1223,7 @@ def set_tag(
             rec.set_tag(tag, value)
 
     def with_aux_alignments(self) -> "Template":
-        """Rebuild this template by adding auxiliary alignments from primary alignment tags."""
+        """Rebuild this template by adding auxiliary alignments from the primary alignment tags."""
         r1_aux = iter([]) if self.r1 is None else AuxAlignment.many_pysam_from_rec(self.r1)
         r2_aux = iter([]) if self.r2 is None else AuxAlignment.many_pysam_from_rec(self.r2)
         return self.build(recs=chain(self.all_recs(), r1_aux, r2_aux))

tests/fgpyo/sam/test_aux_alignment.py

@@ -185,12 +185,30 @@ def test_from_tag_value_invalid_number_of_commas(tag: str) -> None:
         AuxAlignment.from_tag_value(tag, "chr9,104599381")
 
 
+def test_from_tag_value_raises_invalid_multi_value() -> None:
+    """Test that we raise an exception if we receive a multi-value."""
+    with pytest.raises(
+        ValueError,
+        match=(
+            r"Cannot parse a multi-value string! Found: "
+            + r"chr3,\+170653467,49M,4;chr3,\+170653467,49M,4 for tag XA"
+        ),
+    ):
+        AuxAlignment.from_tag_value("XA", "chr3,+170653467,49M,4;chr3,+170653467,49M,4")
+
+
 def test_from_tag_value_raises_invalid_tag() -> None:
     """Test that we raise an exception if we receive an unsupported SAM tag."""
     with pytest.raises(ValueError, match="Tag XF is not one of SA, XA, XB!"):
         AuxAlignment.from_tag_value("XF", "chr3,+170653467,49M,4")
 
 
+def test_from_tag_value_raises_for_invalid_sa_strand() -> None:
+    """Test that we raise an exception when strand is malformed for an SA value."""
+    with pytest.raises(ValueError, match=r"The strand field is not either '\+' or '-': !"):
+        AuxAlignment.from_tag_value("SA", "chr3,2000,!,49M,60,4")
+
+
 @pytest.mark.parametrize("stranded_start", ["!1", "1"])
 def test_from_tag_value_raises_for_invalid_xa_stranded_start(stranded_start: str) -> None:
     """Test that we raise an exception when stranded start is malformed for an XA value."""