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Nov 4, 2025
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Tolerate invalid parents when computing mutation parents #3309

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83 changes: 83 additions & 0 deletions c/tests/test_tables.c
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Original file line number Diff line number Diff line change
Expand Up @@ -10775,6 +10775,85 @@ test_check_integrity_bad_mutation_parent_topology(void)
tsk_table_collection_free(&tables);
}

static void
test_table_collection_compute_mutation_parents_tolerates_invalid_input(void)
{
int ret;
tsk_id_t ret_id;
tsk_table_collection_t tables;
tsk_id_t site;

ret = tsk_table_collection_init(&tables, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
tables.sequence_length = 1.0;

ret_id = tsk_node_table_add_row(&tables.nodes, 0, 1.0, TSK_NULL, TSK_NULL, NULL, 0);
CU_ASSERT_FATAL(ret_id >= 0);
ret_id = tsk_node_table_add_row(
&tables.nodes, TSK_NODE_IS_SAMPLE, 0.0, TSK_NULL, TSK_NULL, NULL, 0);
CU_ASSERT_FATAL(ret_id >= 0);
ret_id = tsk_edge_table_add_row(&tables.edges, 0.0, 1.0, 0, 1, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret_id, 0);
site = tsk_site_table_add_row(&tables.sites, 0.0, "A", 1, NULL, 0);
CU_ASSERT_FATAL(site >= 0);
ret_id = tsk_mutation_table_add_row(
&tables.mutations, site, 1, TSK_NULL, TSK_UNKNOWN_TIME, "C", 1, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret_id, 0);

ret = tsk_table_collection_build_index(&tables, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
tables.mutations.parent[0] = 42;

ret = tsk_table_collection_compute_mutation_parents(&tables, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_FATAL(tables.mutations.parent[0] == TSK_NULL);

tsk_table_collection_free(&tables);
}

static void
test_table_collection_compute_mutation_parents_restores_on_error(void)
{
int ret;
tsk_id_t ret_id;
tsk_table_collection_t tables;
tsk_id_t site;

ret = tsk_table_collection_init(&tables, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
tables.sequence_length = 1.0;

ret_id = tsk_node_table_add_row(&tables.nodes, 0, 1.0, TSK_NULL, TSK_NULL, NULL, 0);
CU_ASSERT_FATAL(ret_id >= 0);
ret_id = tsk_node_table_add_row(
&tables.nodes, TSK_NODE_IS_SAMPLE, 0.0, TSK_NULL, TSK_NULL, NULL, 0);
CU_ASSERT_FATAL(ret_id >= 0);
ret_id = tsk_edge_table_add_row(&tables.edges, 0.0, 1.0, 0, 1, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret_id, 0);
site = tsk_site_table_add_row(&tables.sites, 0.5, "A", 1, NULL, 0);
CU_ASSERT_FATAL(site >= 0);

ret_id = tsk_mutation_table_add_row(
&tables.mutations, site, 1, TSK_NULL, TSK_UNKNOWN_TIME, "C", 1, NULL, 0);
CU_ASSERT_FATAL(ret_id >= 0);
ret_id = tsk_mutation_table_add_row(
&tables.mutations, site, 0, TSK_NULL, TSK_UNKNOWN_TIME, "G", 1, NULL, 0);
CU_ASSERT_FATAL(ret_id >= 0);

ret = tsk_table_collection_build_index(&tables, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);

tables.mutations.parent[0] = 111;
tables.mutations.parent[1] = 222;

ret = tsk_table_collection_compute_mutation_parents(&tables, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_MUTATION_PARENT_AFTER_CHILD);
CU_ASSERT_EQUAL(tables.mutations.parent[0], 111);
CU_ASSERT_EQUAL(tables.mutations.parent[1], 222);

tsk_table_collection_free(&tables);
}

static void
test_table_collection_subset_with_options(tsk_flags_t options)
{
Expand Down Expand Up @@ -11934,6 +12013,10 @@ main(int argc, char **argv)
test_table_collection_check_integrity_bad_indexes },
{ "test_check_integrity_bad_mutation_parent_topology",
test_check_integrity_bad_mutation_parent_topology },
{ "test_table_collection_compute_mutation_parents_tolerates_invalid_input",
test_table_collection_compute_mutation_parents_tolerates_invalid_input },
{ "test_table_collection_compute_mutation_parents_restores_on_error",
test_table_collection_compute_mutation_parents_restores_on_error },
{ "test_table_collection_subset", test_table_collection_subset },
{ "test_table_collection_subset_unsorted",
test_table_collection_subset_unsorted },
Expand Down
24 changes: 24 additions & 0 deletions c/tskit/tables.c
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Original file line number Diff line number Diff line change
Expand Up @@ -12436,8 +12436,27 @@ tsk_table_collection_compute_mutation_parents(
tsk_table_collection_t *self, tsk_flags_t options)
{
int ret = 0;
tsk_mutation_table_t *mutations = &self->mutations;
tsk_id_t *parent_backup = NULL;
bool restore_parents = false;

if (!(options & TSK_NO_CHECK_INTEGRITY)) {
if (mutations->num_rows > 0) {
/* We need to wipe the parent column before computing, as otherwise invalid
* parents can cause integrity checks to fail. We take a copy to restore on
* error */
parent_backup = tsk_malloc(mutations->num_rows * sizeof(*parent_backup));
if (parent_backup == NULL) {
ret = tsk_trace_error(TSK_ERR_NO_MEMORY);
goto out;
}
tsk_memcpy(parent_backup, mutations->parent,
mutations->num_rows * sizeof(*parent_backup));
/* Set the parent pointers to TSK_NULL */
tsk_memset(mutations->parent, 0xff,
mutations->num_rows * sizeof(*mutations->parent));
restore_parents = true;
}
/* Safe to cast here as we're not counting trees */
ret = (int) tsk_table_collection_check_integrity(self, TSK_CHECK_TREES);
if (ret < 0) {
Expand All @@ -12452,6 +12471,11 @@ tsk_table_collection_compute_mutation_parents(
}

out:
if (ret != 0 && restore_parents) {
tsk_memcpy(mutations->parent, parent_backup,
mutations->num_rows * sizeof(*parent_backup));
}
tsk_safe_free(parent_backup);
return ret;
}

Expand Down
28 changes: 28 additions & 0 deletions python/tests/test_tables.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3540,6 +3540,34 @@ def test_table_references(self):
assert str(populations) == before_populations
assert str(provenances) == before_provenances

def test_compute_mutation_parents_ignores_existing_values(self):
tables = tskit.TableCollection(sequence_length=1.0)
parent = tables.nodes.add_row(time=1.0)
child = tables.nodes.add_row(time=0, flags=tskit.NODE_IS_SAMPLE)
tables.edges.add_row(left=0.0, right=1.0, parent=parent, child=child)
site = tables.sites.add_row(position=0.0, ancestral_state="A")
tables.mutations.add_row(site=site, node=child, derived_state="C")
tables.build_index()
tables.mutations.parent[:] = 42
tables.compute_mutation_parents()
assert tables.mutations.parent[0] == tskit.NULL

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@jeromekelleher jeromekelleher Nov 3, 2025

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Another test checking the parent data is preserved on error

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@petrelharp petrelharp Nov 3, 2025

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if possible we should check the data is preserved on error even if TSK_NO_CHECK_INTEGRITY is on

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@benjeffery benjeffery Nov 4, 2025

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a3e12f7

def test_compute_mutation_parents_restores_on_index_error(self):
tables = tskit.TableCollection(sequence_length=1.0)
parent = tables.nodes.add_row(time=1.0)
child = tables.nodes.add_row(time=0, flags=tskit.NODE_IS_SAMPLE)
tables.edges.add_row(left=0.0, right=1.0, parent=parent, child=child)
site = tables.sites.add_row(position=0.0, ancestral_state="A")
tables.mutations.add_row(site=site, node=child, derived_state="C")

mutation_columns = tables.mutations.asdict()
mutation_columns["parent"] = np.array([123], dtype=np.int32)
tables.mutations.set_columns(**mutation_columns)

with pytest.raises(tskit.LibraryError, match="TSK_ERR_TABLES_NOT_INDEXED"):
tables.compute_mutation_parents()
assert tables.mutations.parent[0] == 123

def test_str(self):
ts = msprime.simulate(10, random_seed=1)
tables = ts.tables
Expand Down