TST: more explicit conditions for selecting alignment records

[FIXED] any alignment record whose segment overlaps the query
    coordinates is now returned

src/ensembl_lite/_aligndb.py

@@ -81,15 +81,18 @@ def _get_block_id(
     ) -> list[int]:
         sql = f"SELECT block_id from {self.table_name} WHERE species = ? AND coord_name = ?"
         values = species, coord_name
-        if start and end:
-            sql = f"{sql} AND start > ? AND end < ?"
-            values += (start, end)
-        elif start:
-            sql = f"{sql} AND start > ?"
-            values += (start,)
-        elif end:
-            sql = f"{sql} AND end < ?"
-            values += (end,)
+        if start is not None and end is not None:
+            # as long as start or end are within the record start/end, it's a match
+            sql = f"{sql} AND ((start <= ? AND ? < end) OR (start <= ? AND ? < end))"
+            values += (start, start, end, end)
+        elif start is not None:
+            # the aligned segment overlaps start
+            sql = f"{sql} AND start <= ? AND ? < end"
+            values += (start, start)
+        elif end is not None:
+            # the aligned segment overlaps end
+            sql = f"{sql} AND start <= ? AND ? < end"
+            values += (end, end)
 
         return self.db.execute(sql, values).fetchall()
 

tests/test_aligndb.py

@@ -283,3 +283,53 @@ def test_select_alignment_rc():
         align_db=align_db, genomes=genomes, species="human", coord_name="s1"
     )
     assert got.to_dict() == expect.to_dict()
+
+
+@pytest.mark.parametrize(
+    "coord",
+    (
+        ("human", "s1", None, 11),  # finish within
+        ("human", "s1", 3, None),  # start within
+        ("human", "s1", 3, 9),  # within
+        ("human", "s1", 3, 13),  # extends past
+    ),
+)
+def test_align_db_get_records(coord):
+    kwargs = dict(zip(("species", "coord_name", "start", "end"), coord))
+    # records are, we should get a single hit from each query
+    # [('blah', 0, 'human', 's1', 1, 12, '+', array([], dtype=int32)),
+    _, align_db = make_sample(two_aligns=True)
+    got = list(align_db.get_records_matching(**kwargs))
+    assert len(got) == 1
+
+
+@pytest.mark.parametrize(
+    "coord",
+    (
+        ("human", "s1"),
+        ("mouse", "s2"),
+        ("dog", "s3"),
+    ),
+)
+def test_align_db_get_records_required_only(coord):
+    kwargs = dict(zip(("species", "coord_name"), coord))
+    # two hits for each species
+    _, align_db = make_sample(two_aligns=True)
+    got = list(align_db.get_records_matching(**kwargs))
+    assert len(got) == 2
+
+
+@pytest.mark.parametrize(
+    "coord",
+    (
+        ("human", "s2"),
+        ("mouse", "xx"),
+        ("blah", "s3"),
+    ),
+)
+def test_align_db_get_records_no_matches(coord):
+    kwargs = dict(zip(("species", "coord_name"), coord))
+    # no hits at all
+    _, align_db = make_sample()
+    got = list(align_db.get_records_matching(**kwargs))
+    assert not len(got)