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Reject sample and ancestor IDs equal to num_nodes in link_ancestors (fixes #3484) #3492

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Reject sample and ancestor IDs equal to num_nodes in link_ancestors (fixes #3484) #3492

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b18239f
Reject sample and ancestor IDs equal to num_nodes in link_ancestors
Oct 18, 2026
4a5f92f
Fill in the PR number in the changelogs
Oct 18, 2026
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5 changes: 5 additions & 0 deletions c/CHANGELOG.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,11 @@ In development
- Update to kastore 2.1.3 to include file security fix (:user:`jeromekelleher`,
:pr:`3478`).

- Fix ``tsk_table_collection_link_ancestors`` accepting a sample or ancestor ID
equal to the number of nodes, which indexed node-sized arrays one past their
end. Such IDs now return ``TSK_ERR_NODE_OUT_OF_BOUNDS``.
(:user:`asystemoffields`, :issue:`3484`, :pr:`3492`)

--------------------
[1.3.1] - 2026-03-06
--------------------
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13 changes: 13 additions & 0 deletions c/tests/test_tables.c
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Expand Up @@ -7625,6 +7625,19 @@ test_link_ancestors_input_errors(void)
&tables, samples, 2, ancestors, 2, 0, &result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_NODE_OUT_OF_BOUNDS);

/* Sample and ancestor IDs one past the last node */
ancestors[0] = 4;
samples[0] = (tsk_id_t) tables.nodes.num_rows;
ret = tsk_table_collection_link_ancestors(
&tables, samples, 2, ancestors, 2, 0, &result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_NODE_OUT_OF_BOUNDS);

samples[0] = 0;
ancestors[0] = (tsk_id_t) tables.nodes.num_rows;
ret = tsk_table_collection_link_ancestors(
&tables, samples, 2, ancestors, 2, 0, &result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_NODE_OUT_OF_BOUNDS);

/* Duplicate sample IDs */
ancestors[0] = 4;
samples[0] = 1;
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5 changes: 3 additions & 2 deletions c/tskit/tables.c
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Expand Up @@ -7905,7 +7905,7 @@ ancestor_mapper_init_samples(ancestor_mapper_t *self, tsk_id_t *samples)

/* Go through the samples to check for errors. */
for (j = 0; j < self->num_samples; j++) {
if (samples[j] < 0 || samples[j] > (tsk_id_t) self->tables->nodes.num_rows) {
if (samples[j] < 0 || samples[j] >= (tsk_id_t) self->tables->nodes.num_rows) {
ret = tsk_trace_error(TSK_ERR_NODE_OUT_OF_BOUNDS);
goto out;
}
Expand All @@ -7932,7 +7932,8 @@ ancestor_mapper_init_ancestors(ancestor_mapper_t *self, tsk_id_t *ancestors)

/* Go through the samples to check for errors. */
for (j = 0; j < self->num_ancestors; j++) {
if (ancestors[j] < 0 || ancestors[j] > (tsk_id_t) self->tables->nodes.num_rows) {
if (ancestors[j] < 0
|| ancestors[j] >= (tsk_id_t) self->tables->nodes.num_rows) {
ret = tsk_trace_error(TSK_ERR_NODE_OUT_OF_BOUNDS);
goto out;
}
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3 changes: 3 additions & 0 deletions python/CHANGELOG.rst
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Expand Up @@ -22,6 +22,9 @@

- Update to kastore C version 2.1.3 to include file security fix (:user:`jeromekelleher`,
:pr:`3478`).
- ``link_ancestors`` now raises ``LibraryError`` (node out of bounds) for a sample or
ancestor ID equal to the number of nodes, instead of reading and writing past the
end of its node arrays. (:user:`asystemoffields`, :issue:`3484`, :pr:`3492`)

--------------------
[1.0.3] - 2026-05-14
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7 changes: 6 additions & 1 deletion python/tests/test_python_c.py
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Expand Up @@ -390,11 +390,16 @@ def test_link_ancestors_bad_args(self):
tc.link_ancestors(samples=[0, 1], ancestors=[11, -1])
with pytest.raises(_tskit.LibraryError):
tc.link_ancestors(samples=[0, -1], ancestors=[11])
# One past the last node ID is out of bounds too
with pytest.raises(_tskit.LibraryError, match="out of bounds"):
tc.link_ancestors(samples=[0, tc.nodes.num_rows], ancestors=[11])
with pytest.raises(_tskit.LibraryError, match="out of bounds"):
tc.link_ancestors(samples=[0, 1], ancestors=[tc.nodes.num_rows])

def test_link_ancestors(self):
ts = msprime.simulate(2, random_seed=1)
tc = ts.dump_tables()._ll_tables
edges = tc.link_ancestors([0, 1], [3])
edges = tc.link_ancestors([0, 1], [2])
assert isinstance(edges, _tskit.EdgeTable)
del edges
assert tc.edges.num_rows == 2
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