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May 14, 2020
Merged

Update KC metric to work on samples not leaves #610

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72 changes: 71 additions & 1 deletion c/tests/test_trees.c
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Original file line number Diff line number Diff line change
Expand Up @@ -4383,6 +4383,44 @@ test_internal_sample_sample_sets(void)
tsk_treeseq_free(&ts);
}

static void
test_non_sample_leaf_sample_lists(void)
{
const char *nodes = "1 0 0\n"
"0 0 0\n"
"1 2 0\n";
const char *edges = "0 1 2 0,1\n";
const tsk_id_t left_sample[3] = { 0, -1, 1 };
const tsk_id_t right_sample[3] = { 0, -1, 0 };
const tsk_id_t next_sample[2] = { -1, 0 };
const tsk_id_t samples[2] = { 0, 2 };
const tsk_id_t sample_index_map[3] = { 0, -1, 1 };
tsk_treeseq_t ts;
tsk_tree_t t;
tsk_id_t i;
int ret;

tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, NULL, NULL, NULL, NULL);

ret = tsk_tree_init(&t, &ts, TSK_SAMPLE_LISTS);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_tree_first(&t);
CU_ASSERT_EQUAL_FATAL(ret, 1);

for (i = 0; i < 3; i++) {
CU_ASSERT_EQUAL_FATAL(left_sample[i], t.left_sample[i]);
CU_ASSERT_EQUAL_FATAL(right_sample[i], t.right_sample[i]);
CU_ASSERT_EQUAL_FATAL(sample_index_map[i], ts.sample_index_map[i]);
}
for (i = 0; i < 2; i++) {
CU_ASSERT_EQUAL_FATAL(next_sample[i], t.next_sample[i]);
CU_ASSERT_EQUAL_FATAL(samples[i], t.samples[i]);
}

tsk_treeseq_free(&ts);
tsk_tree_free(&t);
}

/*=======================================================
* KC Distance tests.
*=======================================================*/
Expand Down Expand Up @@ -4644,7 +4682,37 @@ test_internal_samples_kc(void)
ret = tsk_tree_first(&t);
CU_ASSERT_EQUAL_FATAL(ret, 1);
ret = tsk_tree_kc_distance(&t, &t, 0, &result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_INTERNAL_SAMPLES);
CU_ASSERT_EQUAL_FATAL(ret, 0);
tsk_treeseq_free(&ts);
tsk_tree_free(&t);
}

static void
test_non_sample_leaf_kc(void)
{
const char *nodes = "1 0 0\n"
"0 0 0\n"
"0 1 0\n";
const char *edges = "0 1 2 0,1\n";
tsk_treeseq_t ts;
tsk_tree_t t;
int ret;
double result = 0;

tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, NULL, NULL, NULL, NULL);

ret = tsk_treeseq_kc_distance(&ts, &ts, 0, &result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_EQUAL_FATAL(result, 0.0);

ret = tsk_tree_init(&t, &ts, TSK_SAMPLE_LISTS);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_tree_first(&t);
CU_ASSERT_EQUAL_FATAL(ret, 1);
ret = tsk_tree_kc_distance(&t, &t, 0, &result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_EQUAL_FATAL(result, 0.0);

tsk_treeseq_free(&ts);
tsk_tree_free(&t);
}
Expand Down Expand Up @@ -5647,6 +5715,7 @@ main(int argc, char **argv)
{ "test_simple_sample_sets", test_simple_sample_sets },
{ "test_nonbinary_sample_sets", test_nonbinary_sample_sets },
{ "test_internal_sample_sample_sets", test_internal_sample_sample_sets },
{ "test_non_sample_leaf_sample_lists", test_non_sample_leaf_sample_lists },

/* KC distance tests */
{ "test_single_tree_kc", test_single_tree_kc },
Expand All @@ -5656,6 +5725,7 @@ main(int argc, char **argv)
{ "test_nonbinary_tree_kc", test_nonbinary_tree_kc },
{ "test_nonzero_samples_kc", test_nonzero_samples_kc },
{ "test_internal_samples_kc", test_internal_samples_kc },
{ "test_non_sample_leaf_kc", test_non_sample_leaf_kc },
{ "test_unequal_sample_size_kc", test_unequal_sample_size_kc },
{ "test_unequal_samples_kc", test_unequal_samples_kc },
{ "test_unary_nodes_kc", test_unary_nodes_kc },
Expand Down
3 changes: 0 additions & 3 deletions c/tskit/core.c
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Original file line number Diff line number Diff line change
Expand Up @@ -390,9 +390,6 @@ tsk_strerror_internal(int err)
case TSK_ERR_SAMPLES_NOT_EQUAL:
ret = "Samples must be identical in trees to compare.";
break;
case TSK_ERR_INTERNAL_SAMPLES:
ret = "Internal samples are not supported.";
break;
case TSK_ERR_MULTIPLE_ROOTS:
ret = "Trees with multiple roots not supported.";
break;
Expand Down
9 changes: 4 additions & 5 deletions c/tskit/core.h
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Original file line number Diff line number Diff line change
Expand Up @@ -241,11 +241,10 @@ not found in the file.
/* Distance metric errors */
#define TSK_ERR_SAMPLE_SIZE_MISMATCH -1200
#define TSK_ERR_SAMPLES_NOT_EQUAL -1201
#define TSK_ERR_INTERNAL_SAMPLES -1202
#define TSK_ERR_MULTIPLE_ROOTS -1203
#define TSK_ERR_UNARY_NODES -1204
#define TSK_ERR_SEQUENCE_LENGTH_MISMATCH -1205
#define TSK_ERR_NO_SAMPLE_LISTS -1206
#define TSK_ERR_MULTIPLE_ROOTS -1202
#define TSK_ERR_UNARY_NODES -1203
#define TSK_ERR_SEQUENCE_LENGTH_MISMATCH -1204
#define TSK_ERR_NO_SAMPLE_LISTS -1205

/* Haplotype matching errors */
#define TSK_ERR_NULL_VITERBI_MATRIX -1300
Expand Down
87 changes: 35 additions & 52 deletions c/tskit/trees.c
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Expand Up @@ -4529,7 +4529,7 @@ kc_vectors_free(kc_vectors *self)
}

static inline void
update_kc_vectors_single_leaf(
update_kc_vectors_single_sample(
tsk_treeseq_t *ts, kc_vectors *kc_vecs, tsk_id_t u, double time)
{
const tsk_id_t *sample_index_map = ts->sample_index_map;
Expand All @@ -4543,25 +4543,19 @@ static inline void
update_kc_vectors_all_pairs(tsk_tree_t *tree, kc_vectors *kc_vecs, tsk_id_t u,
tsk_id_t v, tsk_size_t depth, double time)
{
tsk_id_t leaf1_index, leaf2_index, leaf1, leaf2, n1, n2, tmp, pair_index;
tsk_treeseq_t *ts = tree->tree_sequence;
const tsk_id_t *restrict samples = ts->samples;
tsk_id_t sample1_index, sample2_index, n1, n2, tmp, pair_index;
const tsk_id_t *restrict left_sample = tree->left_sample;
const tsk_id_t *restrict right_sample = tree->right_sample;
const tsk_id_t *restrict next_sample = tree->next_sample;
const tsk_id_t *restrict sample_index_map = ts->sample_index_map;
tsk_size_t *restrict kc_m = kc_vecs->m;
double *restrict kc_M = kc_vecs->M;

leaf1_index = left_sample[u];
while (true) {
leaf1 = samples[leaf1_index];
leaf2_index = left_sample[v];
while (true) {
leaf2 = samples[leaf2_index];

n1 = sample_index_map[leaf1];
n2 = sample_index_map[leaf2];
sample1_index = left_sample[u];
while (sample1_index != TSK_NULL) {
sample2_index = left_sample[v];
while (sample2_index != TSK_NULL) {
n1 = sample1_index;
n2 = sample2_index;
if (n1 > n2) {
tmp = n1;
n1 = n2;
Expand All @@ -4574,15 +4568,15 @@ update_kc_vectors_all_pairs(tsk_tree_t *tree, kc_vectors *kc_vecs, tsk_id_t u,
kc_m[pair_index] = depth;
kc_M[pair_index] = time;

if (leaf2_index == right_sample[v]) {
if (sample2_index == right_sample[v]) {
break;
}
leaf2_index = next_sample[leaf2_index];
sample2_index = next_sample[sample2_index];
}
if (leaf1_index == right_sample[u]) {
if (sample1_index == right_sample[u]) {
break;
}
leaf1_index = next_sample[leaf1_index];
sample1_index = next_sample[sample1_index];
}
}

Expand Down Expand Up @@ -4620,22 +4614,21 @@ fill_kc_vectors(tsk_tree_t *t, kc_vectors *kc_vecs)
depth = stack[stack_top].depth;
stack_top--;

if (t->left_child[u] == TSK_NULL) {
if (u == root) {
time = 0;
} else {
time = times[t->parent[u]] - times[u];
}
update_kc_vectors_single_leaf(ts, kc_vecs, u, time);
} else {
if (tsk_tree_is_sample(t, u)) {
time = tsk_tree_branch_length(t, u);
update_kc_vectors_single_sample(ts, kc_vecs, u, time);
}

/* Don't bother going deeper if there are no samples under this node */
if (t->left_sample[u] != TSK_NULL) {
for (c1 = t->left_child[u]; c1 != TSK_NULL; c1 = t->right_sib[c1]) {
stack_top++;
stack[stack_top].node = c1;
stack[stack_top].depth = depth + 1;

for (c2 = t->right_sib[c1]; c2 != TSK_NULL; c2 = t->right_sib[c2]) {
update_kc_vectors_all_pairs(
t, kc_vecs, c1, c2, depth, times[root] - times[u]);
time = times[root] - times[u];
update_kc_vectors_all_pairs(t, kc_vecs, c1, c2, depth, time);
}
}
}
Expand Down Expand Up @@ -4718,7 +4711,7 @@ check_kc_distance_samples_inputs(tsk_treeseq_t *self, tsk_treeseq_t *other)
int
tsk_tree_kc_distance(tsk_tree_t *self, tsk_tree_t *other, double lambda, double *result)
{
tsk_id_t n, i, j, u, num_samples;
tsk_id_t n, i;
kc_vectors vecs[2];
tsk_tree_t *trees[2] = { self, other };
int ret = 0;
Expand All @@ -4732,17 +4725,6 @@ tsk_tree_kc_distance(tsk_tree_t *self, tsk_tree_t *other, double lambda, double
goto out;
}
for (i = 0; i < 2; i++) {
num_samples = (tsk_id_t) trees[i]->tree_sequence->num_samples;
for (j = 0; j < num_samples; j++) {
u = trees[i]->tree_sequence->samples[j];
if (trees[i]->left_child[u] != TSK_NULL) {
/* It's probably possible to support this, but it's too awkward
* to deal with and seems like a fairly niche requirement. */
ret = TSK_ERR_INTERNAL_SAMPLES;
goto out;
}
}

ret = check_kc_distance_tree_inputs(trees[i]);
if (ret != 0) {
goto out;
Expand Down Expand Up @@ -4789,22 +4771,24 @@ check_kc_distance_tree_sequence_inputs(tsk_treeseq_t *self, tsk_treeseq_t *other
}

static void
update_kc_pairs_with_leaf(tsk_tree_t *self, kc_vectors *kc, tsk_id_t leaf,
update_kc_pair_with_sample(tsk_tree_t *self, kc_vectors *kc, tsk_id_t sample,
tsk_size_t *depths, double root_time)
{
tsk_id_t c, p, sib;
double time;
tsk_size_t depth;
double *times = self->tree_sequence->tables->nodes.time;

for (c = leaf, p = self->parent[leaf]; p != TSK_NULL; c = p, p = self->parent[p]) {
c = sample;
for (p = self->parent[sample]; p != TSK_NULL; p = self->parent[p]) {
time = root_time - times[p];
depth = depths[p];
for (sib = self->left_child[p]; sib != TSK_NULL; sib = self->right_sib[sib]) {
if (sib != c) {
update_kc_vectors_all_pairs(self, kc, leaf, sib, depth, time);
update_kc_vectors_all_pairs(self, kc, sample, sib, depth, time);
}
}
c = p;
}
}

Expand All @@ -4830,14 +4814,13 @@ update_kc_subtree_state(
stack_top--;

if (tsk_tree_is_sample(t, v)) {
update_kc_pairs_with_leaf(t, kc, v, depths, root_time);
} else {
for (c = t->left_child[v]; c != TSK_NULL; c = t->right_sib[c]) {
if (depths[c] != 0) {
depths[c] = depths[v] + 1;
stack_top++;
stack[stack_top] = c;
}
update_kc_pair_with_sample(t, kc, v, depths, root_time);
}
for (c = t->left_child[v]; c != TSK_NULL; c = t->right_sib[c]) {
if (depths[c] != 0) {
depths[c] = depths[v] + 1;
stack_top++;
stack[stack_top] = c;
}
}
}
Expand Down Expand Up @@ -4889,7 +4872,7 @@ update_kc_incremental(tsk_tree_t *self, kc_vectors *kc, tsk_edge_list_t *edges_o

if (tsk_tree_is_sample(self, u)) {
time = tsk_tree_branch_length(self, u);
update_kc_vectors_single_leaf(self->tree_sequence, kc, u, time);
update_kc_vectors_single_sample(self->tree_sequence, kc, u, time);
}
}

Expand Down
3 changes: 3 additions & 0 deletions python/CHANGELOG.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,9 @@ In development

**New features**

- Add support for trees with internal samples for the Kendall-Colijn tree distance
metric. (:user:`daniel-goldstein`, :pr:`610`)

- Add background shading to SVG tree sequences to reflect tree position along the
sequence (:user:`hyanwong`, :pr:`563`)

Expand Down
5 changes: 2 additions & 3 deletions python/tests/test_lowlevel.py
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Expand Up @@ -1976,8 +1976,7 @@ def test_kc_distance_errors(self):
t2 = _tskit.Tree(ts1, options=_tskit.SAMPLE_LISTS)
# If we don't seek to a specific tree, it has multiple roots (i.e., it's
# in the null state). This fails because we don't accept multiple roots.
with self.assertRaises(_tskit.LibraryError):
t1.get_kc_distance(t2, 0)
self.verify_kc_library_error(t2, t2)

# Different numbers of samples fail.
ts2 = self.get_example_tree_sequence(11)
Expand All @@ -1991,7 +1990,7 @@ def test_kc_distance_errors(self):
t2.first()
self.verify_kc_library_error(t1, t2)

# Internal samples cause errors.
# Unary nodes cause errors.
tables = _tskit.TableCollection(1.0)
tables.nodes.add_row(flags=1)
tables.nodes.add_row(flags=1, time=1)
Expand Down
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