From e5e011cdde4bb4650390587f9c51b5ad3e6ee25f Mon Sep 17 00:00:00 2001
From: SophiaPerzan-DG <sophia.perzan@deepgenomics.com>
Date: Tue, 6 Oct 2026 11:49:30 -0400
Subject: [PATCH 1/2] fix: IntervalData write fails with single-length
 Interval-like objects

---
 genome_kit/interval_data.py |  2 +-
 tests/test_interval_data.py | 30 ++++++++++++++++++++++++++++++
 2 files changed, 31 insertions(+), 1 deletion(-)

diff --git a/genome_kit/interval_data.py b/genome_kit/interval_data.py
index 607415ae..5dddc9c4 100644
--- a/genome_kit/interval_data.py
+++ b/genome_kit/interval_data.py
@@ -435,7 +435,7 @@ def _concat_pieces(self, intervals: list[Interval]):
         """Fetch and concatenate the data slices for ``intervals`` (in order)
         along the aligned axis.
         """
-        pieces = [self._get_interval_like(iv).data for iv in intervals]
+        pieces = [self._get_interval_like(iv)._data for iv in intervals]
         return pieces[0] if len(pieces) == 1 else np.concatenate(pieces, axis=self._axis)
 
     # The forms a value assigned via an interval-like key may take. See
diff --git a/tests/test_interval_data.py b/tests/test_interval_data.py
index 41aec87c..c10bba51 100644
--- a/tests/test_interval_data.py
+++ b/tests/test_interval_data.py
@@ -155,6 +155,36 @@ def test_set_dis(self):
                 interval_data[0] = -interval_data[0]
                 np.testing.assert_equal(-data[0], interval_data[0])
 
+    def test_data_read_only_does_not_affect_backing_array(self):
+        position = Interval('chr1', '+', 100, 100, self.genome)
+        interval = position.expand(0, 3)
+        data = np.arange(0, 30).reshape(3, 10)
+        interval_data = IntervalData(interval, data)
+
+        view = interval_data.data
+        self.assertFalse(view.flags.writeable)
+        with self.assertRaises(ValueError):
+            view[0, 0] = 1
+
+        self.assertTrue(data.flags.writeable)
+        interval_data[0] = -interval_data[0]
+        np.testing.assert_equal(-np.arange(0, 10), interval_data[0])
+
+    def test_set_after_single_piece_concat(self):
+        base = Interval('chr1', '+', 100, 106, self.genome)
+        piece = Interval('chr1', '+', 101, 103, self.genome)
+        keys = {
+            'list': [piece],
+            'dis': DisjointIntervalSequence.from_intervals([piece]),
+        }
+        for name, key in keys.items():
+            with self.subTest(name):
+                interval_data = IntervalData(base, np.zeros((6, 4), dtype=int))
+                sub = interval_data[key]
+                sub[0] = 1
+                np.testing.assert_equal(np.ones(4), sub[0])
+                np.testing.assert_equal(np.ones(4), interval_data[1])
+
 
 class TestIntervalDataSliceIndex(unittest.TestCase):
     rank = 3

From 96dd15677b872329cc5e3094dcb93e258c7aaf14 Mon Sep 17 00:00:00 2001
From: SophiaPerzan-DG <sophia.perzan@deepgenomics.com>
Date: Mon, 19 Oct 2026 12:35:21 -0400
Subject: [PATCH 2/2] chore: update data property typing

---
 genome_kit/interval_data.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/genome_kit/interval_data.py b/genome_kit/interval_data.py
index 5dddc9c4..6ab5e439 100644
--- a/genome_kit/interval_data.py
+++ b/genome_kit/interval_data.py
@@ -161,8 +161,8 @@ def interval(self) -> IntervalLike:
         return self._interval
 
     @property
-    def data(self):
-        """Return the backing data array."""
+    def data(self) -> np.ndarray:
+        """Return the backing data array as read-only."""
         if isinstance(self._data, np.ndarray):
             read_only_view = self._data.view()
             read_only_view.flags.writeable = False