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Fix segfault in tsk_variant_restricted_copy #2437

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Jul 27, 2022
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Fix segfault in tsk_variant_restricted_copy #2437

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6 changes: 5 additions & 1 deletion c/CHANGELOG.rst
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Original file line number Diff line number Diff line change
@@ -1,8 +1,12 @@
--------------------
[1.2.0] - 2022-XX-XX
[1.1.1] - 2022-XX-XX
--------------------

**Bug fixes**

- Fix segfault in tsk_variant_restricted_copy in tree sequences with large
numbers of alleles or very long alleles
(:user:`jeromekelleher`, :pr:`2437`, :issue:`2429`).

--------------------
[1.1.0] - 2022-07-14
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163 changes: 133 additions & 30 deletions c/tests/test_genotypes.c
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Expand Up @@ -958,53 +958,154 @@ test_variant_decode_errors(void)
tsk_treeseq_free(&ts);
}

/* Checks that the data represented by the specified pair of variants exposed
* by the public API is equal. */
static void
assert_variants_equal(const tsk_variant_t *v1, const tsk_variant_t *v2)
{
tsk_size_t j;

CU_ASSERT_EQUAL(v1->num_samples, v2->num_samples);
CU_ASSERT_EQUAL(v1->num_alleles, v2->num_alleles);
for (j = 0; j < v1->num_alleles; j++) {
CU_ASSERT_EQUAL(v1->allele_lengths[j], v2->allele_lengths[j]);
CU_ASSERT_EQUAL(
0, memcmp(v1->alleles[j], v2->alleles[j], (size_t) v1->allele_lengths[j]));
}
CU_ASSERT_EQUAL(v1->has_missing_data, v2->has_missing_data);
CU_ASSERT_EQUAL(v1->num_samples, v2->num_samples);
for (j = 0; j < v1->num_samples; j++) {
CU_ASSERT_EQUAL(v1->samples[j], v2->samples[j]);
CU_ASSERT_EQUAL(v1->genotypes[j], v2->genotypes[j]);
}
CU_ASSERT_EQUAL(v1->site.id, v2->site.id);
CU_ASSERT_EQUAL(v1->site.position, v2->site.position);
CU_ASSERT_EQUAL(v1->site.ancestral_state_length, v2->site.ancestral_state_length);
CU_ASSERT_EQUAL(0, memcmp(v1->site.ancestral_state, v2->site.ancestral_state,
(size_t) v1->site.ancestral_state_length));
CU_ASSERT_EQUAL(v1->site.mutations_length, v2->site.mutations_length);
/* We're pointing back to the same memory for embedded pointers */
CU_ASSERT_EQUAL(v1->site.mutations, v2->site.mutations);
CU_ASSERT_EQUAL(v1->site.metadata, v2->site.metadata);
}

static void
test_variant_copy(void)
{
int ret = 0;
tsk_size_t j;
tsk_treeseq_t ts;
tsk_variant_t var;
tsk_variant_t var_copy;
tsk_variant_t var, var_copy;

tsk_treeseq_from_text(&ts, 10, paper_ex_nodes, paper_ex_edges, NULL, paper_ex_sites,
paper_ex_mutations, paper_ex_individuals, NULL, 0);

ret = tsk_variant_init(&var, &ts, NULL, 0, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_variant_decode(&var, 0, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_variant_restricted_copy(&var, &var_copy);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_variant_decode(&var_copy, 0, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_VARIANT_CANT_DECODE_COPY);

CU_ASSERT_EQUAL(
0, memcmp(var.tree_sequence, var.tree_sequence, sizeof(*var.tree_sequence)));
CU_ASSERT_EQUAL(0, memcmp(&var.tree, &var_copy.tree, sizeof(tsk_tree_t)));
CU_ASSERT_EQUAL(0, memcmp(&var.site, &var_copy.site, sizeof(tsk_site_t)));
CU_ASSERT_EQUAL(0, memcmp(var.genotypes, var_copy.genotypes,
sizeof(int32_t) * (size_t) var.num_samples));
CU_ASSERT_EQUAL(var.num_alleles, var_copy.num_alleles);
CU_ASSERT_EQUAL(
0, memcmp(var.allele_lengths, var_copy.allele_lengths, sizeof(tsk_size_t)));
for (j = 0; j < var.num_alleles; j++) {
CU_ASSERT_EQUAL(0,
memcmp(var.alleles[j], var_copy.alleles[j], (size_t) var.allele_lengths[j]));
for (j = 0; j < tsk_treeseq_get_num_sites(&ts); j++) {
ret = tsk_variant_decode(&var, (tsk_id_t) j, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_variant_restricted_copy(&var, &var_copy);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_variant_decode(&var_copy, 0, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_VARIANT_CANT_DECODE_COPY);

assert_variants_equal(&var, &var_copy);
CU_ASSERT_EQUAL(
0, memcmp(var.tree_sequence, var.tree_sequence, sizeof(*var.tree_sequence)));
CU_ASSERT_EQUAL(0, memcmp(&var.tree, &var_copy.tree, sizeof(tsk_tree_t)));
CU_ASSERT_EQUAL(0, memcmp(&var.site, &var_copy.site, sizeof(tsk_site_t)));
CU_ASSERT_EQUAL(var_copy.traversal_stack, NULL);
CU_ASSERT_EQUAL(var_copy.sample_index_map, NULL);
CU_ASSERT_EQUAL(var_copy.alt_samples, NULL);
CU_ASSERT_EQUAL(var_copy.alt_sample_index_map, NULL);
tsk_variant_free(&var_copy);
}
CU_ASSERT_EQUAL(var.has_missing_data, var_copy.has_missing_data);
CU_ASSERT_EQUAL(var.num_alleles, var_copy.num_alleles);
CU_ASSERT_EQUAL(var.num_samples, var_copy.num_samples);
CU_ASSERT_EQUAL(0, memcmp(var.samples, var_copy.samples,
sizeof(*var.samples) * (size_t) var.num_samples));

CU_ASSERT_EQUAL(var_copy.traversal_stack, NULL);
CU_ASSERT_EQUAL(var_copy.sample_index_map, NULL);
CU_ASSERT_EQUAL(var_copy.alt_samples, NULL);
CU_ASSERT_EQUAL(var_copy.alt_sample_index_map, NULL);
tsk_variant_free(&var);
tsk_treeseq_free(&ts);
}

static void
test_variant_copy_long_alleles(void)
{
int ret = 0;
const char *sites = "0.0 GGGG\n"
"0.125 AAAAA\n"
"0.25 CCCCCC\n"
"0.5 AAAAAAA\n";
const char *mutations = "0 0 TTT -1\n"
"1 1 CCCCCCC -1\n"
"2 0 GGGGGGG -1\n"
"2 1 AG -1\n"
"2 2 TTTTTTT -1\n"
"3 4 TGGGGGG -1\n"
"3 0 AAA 5\n";
tsk_treeseq_t ts;
tsk_variant_t var, copy, copy_of_copy;
tsk_size_t j;

tsk_treeseq_from_text(&ts, 1, single_tree_ex_nodes, single_tree_ex_edges, NULL,
sites, mutations, NULL, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);

ret = tsk_variant_init(&var, &ts, NULL, 0, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
for (j = 0; j < tsk_treeseq_get_num_sites(&ts); j++) {
ret = tsk_variant_decode(&var, (tsk_id_t) j, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_variant_restricted_copy(&var, &copy);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_variants_equal(&var, &copy);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_variant_restricted_copy(&copy, &copy_of_copy);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_variants_equal(&var, &copy_of_copy);
CU_ASSERT_EQUAL_FATAL(ret, 0);
tsk_variant_free(&copy_of_copy);
tsk_variant_free(&copy);
}
tsk_variant_free(&var);
tsk_variant_free(&var_copy);
tsk_treeseq_free(&ts);
}

static void
test_variant_copy_memory_management(void)
{
int ret = 0;
tsk_size_t j;
tsk_treeseq_t ts;
tsk_variant_t *var;
tsk_variant_t copy, copy_of_copy;

tsk_treeseq_from_text(&ts, 10, paper_ex_nodes, paper_ex_edges, NULL, paper_ex_sites,
paper_ex_mutations, paper_ex_individuals, NULL, 0);

for (j = 0; j < tsk_treeseq_get_num_sites(&ts); j++) {
var = tsk_malloc(sizeof(*var));
CU_ASSERT_FATAL(var != NULL);
ret = tsk_variant_init(var, &ts, NULL, 0, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_variant_decode(var, (tsk_id_t) j, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_variant_restricted_copy(var, &copy);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_variants_equal(var, &copy);
/* Free var to make sure we're not pointing to any of the original memory. */
tsk_variant_free(var);
free(var);
ret = tsk_variant_restricted_copy(&copy, &copy_of_copy);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_variants_equal(&copy, &copy_of_copy);
ret = tsk_variant_decode(&copy, 0, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_VARIANT_CANT_DECODE_COPY);
ret = tsk_variant_decode(&copy_of_copy, 0, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_VARIANT_CANT_DECODE_COPY);

tsk_variant_free(&copy);
tsk_variant_free(&copy_of_copy);
}
tsk_treeseq_free(&ts);
}

Expand All @@ -1030,6 +1131,8 @@ main(int argc, char **argv)
{ "test_multiple_variant_decode", test_multiple_variant_decode },
{ "test_variant_decode_errors", test_variant_decode_errors },
{ "test_variant_copy", test_variant_copy },
{ "test_variant_copy_long_alleles", test_variant_copy_long_alleles },
{ "test_variant_copy_memory_management", test_variant_copy_memory_management },
{ NULL, NULL },
};

Expand Down
16 changes: 8 additions & 8 deletions c/tskit/genotypes.c
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Expand Up @@ -463,7 +463,6 @@ tsk_variant_decode(
tsk_id_t allele_index;
tsk_size_t j, num_missing;
int no_longer_missing;

tsk_mutation_t mutation;
bool impute_missing = !!(self->options & TSK_ISOLATED_NOT_MISSING);
bool by_traversal = self->alt_samples != NULL;
Expand Down Expand Up @@ -582,11 +581,11 @@ tsk_variant_restricted_copy(const tsk_variant_t *self, tsk_variant_t *other)
tsk_size_t total_len, offset, j;

/* Copy everything */
tsk_memcpy(other, self, sizeof(tsk_variant_t));
tsk_memcpy(other, self, sizeof(*other));
/* Tree sequence left as NULL and zero'd tree is a way of indicating this variant is
* fixed and cannot be further decoded. */
other->tree_sequence = NULL;
tsk_memset(&other->tree, sizeof(tsk_tree_t), 0);
tsk_memset(&other->tree, sizeof(other->tree), 0);
other->traversal_stack = NULL;
other->samples = NULL;
other->sample_index_map = NULL;
Expand All @@ -598,9 +597,9 @@ tsk_variant_restricted_copy(const tsk_variant_t *self, tsk_variant_t *other)
for (j = 0; j < self->num_alleles; j++) {
total_len += self->allele_lengths[j];
}
other->samples = tsk_malloc(other->num_samples * sizeof(tsk_id_t));
other->genotypes = tsk_malloc(other->num_samples * sizeof(int32_t));
other->user_alleles_mem = tsk_malloc(total_len * sizeof(char *));
other->samples = tsk_malloc(other->num_samples * sizeof(*other->samples));
other->genotypes = tsk_malloc(other->num_samples * sizeof(*other->genotypes));
other->user_alleles_mem = tsk_malloc(total_len * sizeof(*other->user_alleles_mem));
other->allele_lengths
= tsk_malloc(other->num_alleles * sizeof(*other->allele_lengths));
other->alleles = tsk_malloc(other->num_alleles * sizeof(*other->alleles));
Expand All @@ -612,13 +611,14 @@ tsk_variant_restricted_copy(const tsk_variant_t *self, tsk_variant_t *other)
}
tsk_memcpy(
other->samples, self->samples, other->num_samples * sizeof(*other->samples));
tsk_memcpy(other->genotypes, self->genotypes, other->num_samples * sizeof(int32_t));
tsk_memcpy(other->genotypes, self->genotypes,
other->num_samples * sizeof(*other->genotypes));
tsk_memcpy(other->allele_lengths, self->allele_lengths,
other->num_alleles * sizeof(*other->allele_lengths));
offset = 0;
for (j = 0; j < other->num_alleles; j++) {
tsk_memcpy(other->user_alleles_mem + offset, self->alleles[j],
other->allele_lengths[j] * sizeof(char *));
other->allele_lengths[j] * sizeof(*other->user_alleles_mem));
other->alleles[j] = other->user_alleles_mem + offset;
offset += other->allele_lengths[j];
}
Expand Down
5 changes: 4 additions & 1 deletion python/CHANGELOG.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,10 @@

**Fixes**

- Iterating over ``ts.variants()`` could cause a segfault in tree sequences
with large numbers of alleles or very long alleles
(:user:`jeromekelleher`, :pr:`2437`, :issue:`2429`).

- Various memory leaks fixed (:user:`jeromekelleher`, :pr:`2424`, :issue:`2423`,
:issue:`2427`).

Expand All @@ -24,7 +28,6 @@
- Variant objects now have a ``.num_missing`` attribute and ``.counts()`` and
``.frequencies`` methods (:user:`hyanwong`, :issue:`2390` :pr:`2393`)


- Add the `Tree.num_lineages(t)` method to return the number of lineages present
at time t in the tree (:user:`jeromekelleher`, :issue:`386`, :pr:`2422`)

Expand Down
1 change: 0 additions & 1 deletion python/tests/test_lowlevel.py
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Expand Up @@ -2502,7 +2502,6 @@ def test_copy(self, isolated_as_missing, samples, alleles):
variant2 = variant.restricted_copy()
assert variant.site_id == variant2.site_id
assert variant.alleles == variant2.alleles
print(variant.alleles)
assert np.array_equal(variant.genotypes, variant2.genotypes)
assert np.array_equal(variant.samples, variant2.samples)
assert variant.isolated_as_missing == variant2.isolated_as_missing
Expand Down