fill in documentation TODOs

Author: clwgg

c/tskit/tables.h

@@ -3485,6 +3485,8 @@ on how to sequentially load table collections from a stream.
 
 If the TSK_LOAD_SKIP_TABLES option is set, only the top-level
 information of the table collection will be read, leaving all tables empty.
+If the TSK_LOAD_SKIP_REFERENCE_SEQUENCE option is set, the table collection is
+read without loading the reference sequence.
 
 **Options**
 
@@ -3496,7 +3498,7 @@ TSK_NO_INIT
 TSK_LOAD_SKIP_TABLES
     Skip reading tables, and only load top-level information.
 TSK_LOAD_SKIP_REFERENCE_SEQUENCE
-    TODO
+    Do not load reference sequence.
 
 **Examples**
 
@@ -3545,10 +3547,13 @@ different error conditions. Please see the
 sequentially load tree sequences from a stream.
 
 Please note that this streaming behaviour is not supported if the
-TSK_LOAD_SKIP_TABLES option is set. With this option, only the top-level
-information of the table collection will be read, leaving all tables empty. When
-attempting to read from a stream with multiple table collection definitions and
-the TSK_LOAD_SKIP_TABLES option set, only the top-level information of the first
+TSK_LOAD_SKIP_TABLES or TSK_LOAD_SKIP_REFERENCE_SEQUENCE option is set.
+If the TSK_LOAD_SKIP_TABLES option is set, only the top-level
+information of the table collection will be read, leaving all tables empty.
+If the TSK_LOAD_SKIP_REFERENCE_SEQUENCE option is set, the table collection is
+read without loading the reference sequence.
+When attempting to read from a stream with multiple table collection definitions
+and either of these two options set, the requested information from the first
 table collection will be read on the first call to
 :c:func:`tsk_table_collection_loadf`, with subsequent calls leading to errors.
 
@@ -3562,7 +3567,7 @@ TSK_NO_INIT
 TSK_LOAD_SKIP_TABLES
     Skip reading tables, and only load top-level information.
 TSK_LOAD_SKIP_REFERENCE_SEQUENCE
-    TODO
+    Do not load reference sequence.
 
 @endrst
 

python/tskit/tables.py

@@ -2831,7 +2831,8 @@ def equals(
             parameter has no effect.
         :param bool ignore_tables: If True no tables are included in the
             comparison, thus comparing only the top-level information.
-        :param bool ignore_reference_sequence: If True TODO.
+        :param bool ignore_reference_sequence: If True the reference sequence
+            is not included in the comparison.
         :return: True if other is equal to this table collection; False otherwise.
         :rtype: bool
         """
@@ -2879,7 +2880,8 @@ def assert_equals(
             parameter has no effect.
         :param bool ignore_tables: If True no tables are included in the
             comparison, thus comparing only the top-level information.
-        :param bool ignore_reference_sequence: If True TODO.
+        :param bool ignore_reference_sequence: If True the reference sequence
+            is not included in the comparison.
         """
         if type(other) is not type(self):
             raise AssertionError(f"Types differ: self={type(self)} other={type(other)}")

python/tskit/trees.py

@@ -2997,7 +2997,11 @@ def load(file, *, skip_tables=False, skip_reference_sequence=False):
         Please note that with this option set, it is not possible to load data from
         a stream of multiple tree sequences using consecutive calls to
         :meth:`tskit.load`.
-    :param bool skip_reference_sequence: If True, TODO
+    :param bool skip_reference_sequence: If True, the tree sequence is read
+        without loading its reference sequence.
+        Please note that with this option set, it is not possible to load data from
+        a stream of multiple tree sequences using consecutive calls to
+        :meth:`tskit.load`.
     :return: The tree sequence object containing the information
         stored in the specified file path.
     :rtype: :class:`tskit.TreeSequence`