Initial high-level stuff

python/_tskitmodule.c

@@ -5864,7 +5864,7 @@ ReferenceSequence_check_write(ReferenceSequence *self)
     }
     if (self->read_only) {
         PyErr_SetString(PyExc_AttributeError,
-            "ReferenceSequence is read-only mode and can only be modified "
+            "ReferenceSequence is read-only and can only be modified "
             "in a TableCollection");
         ret = -1;
         goto out;

python/tests/test_lowlevel.py

@@ -3280,7 +3280,7 @@ def test_state(self):
         refseq.data = ""
         assert refseq.state != 0
 
-    @pytest.mark.parametrize("ref_data", ["", "abc", "A" * 1000, "🎄🌳🌴🌲🎋"])
+    @pytest.mark.parametrize("ref_data", ["", "abc", "A" * 10, "🎄🌳🌴🌲🎋"])
     def test_data(self, ref_data):
         tables = _tskit.TableCollection()
         refseq = tables.reference_sequence

python/tests/test_reference_sequence.py

@@ -0,0 +1,70 @@
+# MIT License
+#
+# Copyright (c) 2021 Tskit Developers
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+"""
+Tests for reference sequence support.
+"""
+import pytest
+
+import tskit
+
+
+class TestTablesProperties:
+    def test_initially_unset(self):
+        tables = tskit.TableCollection(1)
+        assert tables.reference_sequence.is_unset()
+        tables.reference_sequence.data = "ABCDEF"
+        assert tables.reference_sequence.data == "ABCDEF"
+
+    def test_same_object(self):
+        tables = tskit.TableCollection(1)
+        refseq = tables.reference_sequence
+        tables.reference_sequence.data = "asdf"
+        assert refseq.data == "asdf"
+        # Not clear we want to do this, but keeping the same pattern as the
+        # tables for now.
+        assert tables.reference_sequence is not refseq
+
+    def test_write_object_fails(self):
+        tables = tskit.TableCollection(1)
+        with pytest.raises(AttributeError):
+            tables.reference_sequence = None
+
+
+class TestTreeSequenceProperties:
+    @pytest.mark.parametrize("data", ["", "abcd", "🎄🌳🌴"])
+    def test_data_inherited_from_tables(self, data):
+        tables = tskit.TableCollection(1)
+        tables.reference_sequence.data = data
+        ts = tables.tree_sequence()
+        assert ts.reference_sequence.data == data
+
+    def test_write_data_fails(self):
+        tables = tskit.TableCollection(1)
+        ts = tables.tree_sequence()
+        with pytest.raises(AttributeError, match="read-only"):
+            ts.reference_sequence.data = "xyz"
+
+    def test_write_object_fails(self):
+        tables = tskit.TableCollection(1)
+        ts = tables.tree_sequence()
+        with pytest.raises(AttributeError):
+            ts.reference_sequence = None

python/tskit/tables.py

@@ -2520,6 +2520,23 @@ def __len__(self):
         return self.num_pairs
 
 
+# TODO move to reference_sequence.py
+class ReferenceSequence:
+    def __init__(self, ll_reference_sequence):
+        self._ll_reference_sequence = ll_reference_sequence
+
+    def is_unset(self) -> bool:
+        return self._ll_reference_sequence.state == 0
+
+    @property
+    def data(self) -> str:
+        return self._ll_reference_sequence.data
+
+    @data.setter
+    def data(self, value):
+        self._ll_reference_sequence.data = value
+
+
 class TableCollection:
     """
     A collection of mutable tables defining a tree sequence. See the
@@ -2561,6 +2578,14 @@ class TableCollection:
     def __init__(self, sequence_length=0):
         self._ll_tables = _tskit.TableCollection(sequence_length)
 
+    @property
+    def reference_sequence(self):
+        # NOTE: arguably we should cache the reference to this object
+        # during init, rather than creating a new instance each time.
+        # However, following the pattern of the Table classes for now
+        # for consistency.
+        return ReferenceSequence(self._ll_tables.reference_sequence)
+
     @property
     def individuals(self):
         return IndividualTable(ll_table=self._ll_tables.individuals)

python/tskit/trees.py

@@ -3630,6 +3630,10 @@ def dump(self, file_or_path, zlib_compression=False):
             if local_file:
                 file.close()
 
+    @property
+    def reference_sequence(self):
+        return tables.ReferenceSequence(self._ll_tree_sequence.reference_sequence)
+
     @property
     def tables_dict(self):
         """