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avoid possible infinite loop in canonicalize #1198

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Merged
merged 1 commit into from
Feb 12, 2021
Merged

avoid possible infinite loop in canonicalize #1198

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43 changes: 43 additions & 0 deletions c/tests/test_tables.c
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Original file line number Diff line number Diff line change
Expand Up @@ -4087,6 +4087,48 @@ test_sort_tables_mutation_times(void)
tsk_treeseq_free(&ts);
}

static void
test_sort_tables_canonical_errors(void)
{
int ret;
tsk_table_collection_t tables;
ret = tsk_table_collection_init(&tables, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
tables.sequence_length = 1;

ret = tsk_node_table_add_row(&tables.nodes, 0, 0.0, TSK_NULL, TSK_NULL, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_site_table_add_row(&tables.sites, 0.0, "x", 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, 2, 0.0, "a", 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, 3, 0.0, "b", 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, 1, 0.0, "c", 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, 2, 0.0, "d", 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);

ret = tsk_table_collection_canonicalise(&tables, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_MUTATION_PARENT_INCONSISTENT);

ret = tsk_mutation_table_clear(&tables.mutations);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, 2, 0.0, "a", 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, 3, 0.0, "b", 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, 1, 0.0, "c", 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, -1, 0.0, "d", 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);

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

tsk_table_collection_free(&tables);
}

static void
test_sort_tables_canonical(void)
{
Expand Down Expand Up @@ -6028,6 +6070,7 @@ main(int argc, char **argv)
{ "test_edge_update_invalidates_index", test_edge_update_invalidates_index },
{ "test_copy_table_collection", test_copy_table_collection },
{ "test_sort_tables_errors", test_sort_tables_errors },
{ "test_sort_tables_canonical_errors", test_sort_tables_canonical_errors },
{ "test_sort_tables_canonical", test_sort_tables_canonical },
{ "test_sorter_interface", test_sorter_interface },
{ "test_dump_unindexed", test_dump_unindexed },
Expand Down
3 changes: 3 additions & 0 deletions c/tskit/core.c
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Original file line number Diff line number Diff line change
Expand Up @@ -281,6 +281,9 @@ tsk_strerror_internal(int err)
case TSK_ERR_MUTATION_PARENT_AFTER_CHILD:
ret = "Parent mutation ID must be < current ID";
break;
case TSK_ERR_MUTATION_PARENT_INCONSISTENT:
ret = "Mutation parent references form a loop.";
break;
case TSK_ERR_INCONSISTENT_MUTATIONS:
ret = "Inconsistent mutations: state already equal to derived state";
break;
Expand Down
3 changes: 2 additions & 1 deletion c/tskit/core.h
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Expand Up @@ -246,7 +246,8 @@ not found in the file.
#define TSK_ERR_MUTATION_PARENT_DIFFERENT_SITE -500
#define TSK_ERR_MUTATION_PARENT_EQUAL -501
#define TSK_ERR_MUTATION_PARENT_AFTER_CHILD -502
#define TSK_ERR_INCONSISTENT_MUTATIONS -503
#define TSK_ERR_MUTATION_PARENT_INCONSISTENT -503
#define TSK_ERR_INCONSISTENT_MUTATIONS -504
#define TSK_ERR_UNSORTED_MUTATIONS -505
#define TSK_ERR_NON_SINGLE_CHAR_MUTATION -506
#define TSK_ERR_MUTATION_TIME_YOUNGER_THAN_NODE -507
Expand Down
4 changes: 4 additions & 0 deletions c/tskit/tables.c
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Original file line number Diff line number Diff line change
Expand Up @@ -4905,6 +4905,10 @@ tsk_table_sorter_sort_mutations_canonical(tsk_table_sorter_t *self)
p = mutations->parent[j];
while (p != TSK_NULL) {
sorted_mutations[p].num_descendants += 1;
if (sorted_mutations[p].num_descendants > (int) num_mutations) {
ret = TSK_ERR_MUTATION_PARENT_INCONSISTENT;
goto out;
}
p = mutations->parent[p];
}
}
Expand Down