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fill in documentation TODOs
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c/tskit/tables.h

Lines changed: 11 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -3485,6 +3485,8 @@ on how to sequentially load table collections from a stream.
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If the TSK_LOAD_SKIP_TABLES option is set, only the top-level
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information of the table collection will be read, leaving all tables empty.
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If the TSK_LOAD_SKIP_REFERENCE_SEQUENCE option is set, the table collection is
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read without loading the reference sequence.
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**Options**
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@@ -3496,7 +3498,7 @@ TSK_NO_INIT
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TSK_LOAD_SKIP_TABLES
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Skip reading tables, and only load top-level information.
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TSK_LOAD_SKIP_REFERENCE_SEQUENCE
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TODO
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Do not load reference sequence.
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**Examples**
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@@ -3545,10 +3547,13 @@ different error conditions. Please see the
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sequentially load tree sequences from a stream.
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Please note that this streaming behaviour is not supported if the
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TSK_LOAD_SKIP_TABLES option is set. With this option, only the top-level
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information of the table collection will be read, leaving all tables empty. When
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attempting to read from a stream with multiple table collection definitions and
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the TSK_LOAD_SKIP_TABLES option set, only the top-level information of the first
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TSK_LOAD_SKIP_TABLES or TSK_LOAD_SKIP_REFERENCE_SEQUENCE option is set.
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If the TSK_LOAD_SKIP_TABLES option is set, only the top-level
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information of the table collection will be read, leaving all tables empty.
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If the TSK_LOAD_SKIP_REFERENCE_SEQUENCE option is set, the table collection is
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read without loading the reference sequence.
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When attempting to read from a stream with multiple table collection definitions
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and either of these two options set, the requested information from the first
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table collection will be read on the first call to
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:c:func:`tsk_table_collection_loadf`, with subsequent calls leading to errors.
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@@ -3562,7 +3567,7 @@ TSK_NO_INIT
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TSK_LOAD_SKIP_TABLES
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Skip reading tables, and only load top-level information.
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TSK_LOAD_SKIP_REFERENCE_SEQUENCE
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TODO
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Do not load reference sequence.
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@endrst
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python/tskit/tables.py

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2831,7 +2831,8 @@ def equals(
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parameter has no effect.
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:param bool ignore_tables: If True no tables are included in the
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comparison, thus comparing only the top-level information.
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:param bool ignore_reference_sequence: If True TODO.
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:param bool ignore_reference_sequence: If True the reference sequence
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is not included in the comparison.
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:return: True if other is equal to this table collection; False otherwise.
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:rtype: bool
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"""
@@ -2879,7 +2880,8 @@ def assert_equals(
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parameter has no effect.
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:param bool ignore_tables: If True no tables are included in the
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comparison, thus comparing only the top-level information.
2882-
:param bool ignore_reference_sequence: If True TODO.
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:param bool ignore_reference_sequence: If True the reference sequence
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is not included in the comparison.
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"""
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if type(other) is not type(self):
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raise AssertionError(f"Types differ: self={type(self)} other={type(other)}")

python/tskit/trees.py

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2997,7 +2997,11 @@ def load(file, *, skip_tables=False, skip_reference_sequence=False):
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Please note that with this option set, it is not possible to load data from
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a stream of multiple tree sequences using consecutive calls to
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:meth:`tskit.load`.
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:param bool skip_reference_sequence: If True, TODO
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:param bool skip_reference_sequence: If True, the tree sequence is read
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without loading its reference sequence.
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Please note that with this option set, it is not possible to load data from
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a stream of multiple tree sequences using consecutive calls to
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:meth:`tskit.load`.
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:return: The tree sequence object containing the information
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stored in the specified file path.
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:rtype: :class:`tskit.TreeSequence`

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