Skip to content

Better divmat site mode #2813

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Aug 15, 2023
Merged

Better divmat site mode #2813

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
33 changes: 26 additions & 7 deletions c/tests/test_stats.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1132,7 +1132,6 @@ test_single_tree_divergence_matrix_multi_root(void)
int ret;
double result[16];
double D_branch[16] = { 0, 2, 3, 3, 2, 0, 3, 3, 3, 3, 0, 4, 3, 3, 4, 0 };
double D_site[16] = { 0, 4, 6, 6, 4, 0, 6, 6, 6, 6, 0, 8, 6, 6, 8, 0 };

const char *nodes = "1 0 -1 -1\n"
"1 0 -1 -1\n" /* 2.00┊ 5 ┊ */
Expand All @@ -1142,7 +1141,7 @@ test_single_tree_divergence_matrix_multi_root(void)
"0 2 -1 -1\n"; /* 0 * * * * 1 */
const char *edges = "0 1 4 0,1\n"
"0 1 5 2,3\n";
/* Two mutations per branch unit so we get twice branch length value */
/* Two mutations per branch */
const char *sites = "0.1 A\n"
"0.2 A\n"
"0.3 A\n"
Expand All @@ -1166,9 +1165,8 @@ test_single_tree_divergence_matrix_multi_root(void)
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(16, result, D_branch);

ret = tsk_treeseq_divergence_matrix(&ts, 0, NULL, 0, NULL, TSK_STAT_SITE, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(16, result, D_site);
verify_divergence_matrix(&ts, TSK_STAT_SITE);
verify_divergence_matrix(&ts, TSK_STAT_BRANCH);

tsk_treeseq_free(&ts);
}
Expand Down Expand Up @@ -2041,6 +2039,13 @@ test_simplest_divergence_matrix(void)
ret = tsk_treeseq_divergence_matrix(&ts, 2, sample_ids, 0, NULL, 0, result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_NODE_OUT_OF_BOUNDS);

sample_ids[0] = 1;
ret = tsk_treeseq_divergence_matrix(&ts, 2, sample_ids, 0, NULL, 0, result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_DUPLICATE_SAMPLE);
ret = tsk_treeseq_divergence_matrix(
&ts, 2, sample_ids, 0, NULL, TSK_STAT_BRANCH, result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_DUPLICATE_SAMPLE);

tsk_treeseq_free(&ts);
}

Expand All @@ -2051,15 +2056,19 @@ test_simplest_divergence_matrix_windows(void)
"1 0 0\n"
"0 1 0\n";
const char *edges = "0 1 2 0,1\n";
const char *sites = "0.1 A\n"
"0.6 A\n";
const char *mutations = "0 0 B -1\n"
"1 0 B -1\n";
tsk_treeseq_t ts;
tsk_id_t sample_ids[] = { 0, 1 };
double D_branch[8] = { 0, 1, 1, 0, 0, 1, 1, 0 };
double D_site[8] = { 0, 0, 0, 0, 0, 0, 0, 0 };
double D_site[8] = { 0, 1, 1, 0, 0, 1, 1, 0 };
double result[8];
double windows[] = { 0, 0.5, 1 };
int ret;

tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, NULL, NULL, NULL, NULL, 0);
tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, sites, mutations, NULL, NULL, 0);

ret = tsk_treeseq_divergence_matrix(&ts, 2, sample_ids, 2, windows, 0, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
Expand All @@ -2069,6 +2078,16 @@ test_simplest_divergence_matrix_windows(void)
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(8, D_branch, result);

/* Windows for the second half */
ret = tsk_treeseq_divergence_matrix(
&ts, 2, sample_ids, 1, windows + 1, TSK_STAT_SITE, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(4, D_site, result);
ret = tsk_treeseq_divergence_matrix(
&ts, 2, sample_ids, 1, windows + 1, TSK_STAT_BRANCH, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(4, D_branch, result);

ret = tsk_treeseq_divergence_matrix(&ts, 2, sample_ids, 0, windows, 0, result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_NUM_WINDOWS);

Expand Down
210 changes: 133 additions & 77 deletions c/tskit/trees.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6597,43 +6597,62 @@ tsk_treeseq_divergence_matrix_branch(const tsk_treeseq_t *self, tsk_size_t num_s
return ret;
}

static tsk_size_t
count_mutations_on_path(tsk_id_t u, tsk_id_t v, const tsk_id_t *restrict parent,
const double *restrict time, const tsk_size_t *restrict mutations_per_node)
// FIXME see #2817
// Just including this here for now as it's the simplest option. Everything
// will probably move to stats.[c,h] in the near future though, and it
// can pull in ``genotypes.h`` without issues.
#include <tskit/genotypes.h>

static void
update_site_divergence(const tsk_variant_t *var, const tsk_id_t *restrict A,
const tsk_size_t *restrict offsets, double *D)

{
double tu, tv;
tsk_size_t count = 0;
const tsk_size_t num_alleles = var->num_alleles;
const tsk_id_t n = (tsk_id_t) var->num_samples;

tu = time[u];
tv = time[v];
while (u != v) {
if (tu < tv) {
count += mutations_per_node[u];
u = parent[u];
if (u == TSK_NULL) {
break;
}
tu = time[u];
} else {
count += mutations_per_node[v];
v = parent[v];
if (v == TSK_NULL) {
break;
tsk_size_t a, b, j, k;
tsk_id_t u, v;

for (a = 0; a < num_alleles; a++) {
for (b = a + 1; b < num_alleles; b++) {
for (j = offsets[a]; j < offsets[a + 1]; j++) {
for (k = offsets[b]; k < offsets[b + 1]; k++) {
u = A[j];
v = A[k];
/* Only increment the upper triangle to (hopefully) improve memory
* access patterns */
if (u > v) {
v = A[j];
u = A[k];
}
D[u * n + v]++;
}
}
tv = time[v];
}
}
if (u != v) {
while (u != TSK_NULL) {
count += mutations_per_node[u];
u = parent[u];
}
while (v != TSK_NULL) {
count += mutations_per_node[v];
v = parent[v];
}

static void
group_alleles(const tsk_variant_t *var, tsk_id_t *restrict A, tsk_size_t *offsets)
{
const tsk_size_t n = var->num_samples;
const int32_t *restrict genotypes = var->genotypes;
tsk_id_t a;
tsk_size_t j, k;

k = 0;
offsets[0] = 0;
for (a = 0; a < (tsk_id_t) var->num_alleles; a++) {
offsets[a + 1] = offsets[a];
for (j = 0; j < n; j++) {
if (genotypes[j] == a) {
offsets[a + 1]++;
A[k] = (tsk_id_t) j;
k++;
}
}
}
return count;
}

static int
Expand All @@ -6643,72 +6662,99 @@ tsk_treeseq_divergence_matrix_site(const tsk_treeseq_t *self, tsk_size_t num_sam
double *restrict result)
{
int ret = 0;
tsk_tree_t tree;
const tsk_size_t n = num_samples;
const tsk_size_t num_nodes = self->tables->nodes.num_rows;
const double *restrict nodes_time = self->tables->nodes.time;
tsk_size_t i, j, k, tree_site, tree_mut;
tsk_site_t site;
tsk_mutation_t mut;
tsk_id_t u, v;
double left, right, span_left, span_right;
tsk_size_t i;
tsk_id_t site_id;
double left, right;
double *restrict D;
tsk_size_t *mutations_per_node = tsk_malloc(num_nodes * sizeof(*mutations_per_node));

ret = tsk_tree_init(&tree, self, 0);
const tsk_id_t num_sites = (tsk_id_t) self->tables->sites.num_rows;
const double *restrict sites_position = self->tables->sites.position;
tsk_id_t *A = tsk_malloc(num_samples * sizeof(*A));
/* Allocate the allele offsets at the first variant */
tsk_size_t max_alleles = 0;
tsk_size_t *allele_offsets = NULL;
tsk_variant_t variant;

ret = tsk_variant_init(
&variant, self, samples, num_samples, NULL, TSK_ISOLATED_NOT_MISSING);
if (ret != 0) {
goto out;
}
if (mutations_per_node == NULL) {
if (A == NULL) {
ret = TSK_ERR_NO_MEMORY;
goto out;
}

site_id = 0;
while (site_id < num_sites && sites_position[site_id] < windows[0]) {
site_id++;
}

for (i = 0; i < num_windows; i++) {
left = windows[i];
right = windows[i + 1];
D = result + i * n * n;
ret = tsk_tree_seek(&tree, left, 0);
if (ret != 0) {
goto out;
}
while (tree.interval.left < right && tree.index != -1) {
span_left = TSK_MAX(tree.interval.left, left);
span_right = TSK_MIN(tree.interval.right, right);
D = result + i * num_samples * num_samples;

/* NOTE: we could avoid this full memset across all nodes by doing
* the same loops again and decrementing at the end of the main
* tree-loop. It's probably not worth it though, because of the
* overwhelming O(n^2) below */
tsk_memset(mutations_per_node, 0, num_nodes * sizeof(*mutations_per_node));
for (tree_site = 0; tree_site < tree.sites_length; tree_site++) {
site = tree.sites[tree_site];
if (span_left <= site.position && site.position < span_right) {
for (tree_mut = 0; tree_mut < site.mutations_length; tree_mut++) {
mut = site.mutations[tree_mut];
mutations_per_node[mut.node]++;
}
}
if (site_id < num_sites) {
tsk_bug_assert(sites_position[site_id] >= left);
}
while (site_id < num_sites && sites_position[site_id] < right) {
ret = tsk_variant_decode(&variant, site_id, 0);
if (ret != 0) {
goto out;
}

for (j = 0; j < n; j++) {
u = samples[j];
for (k = j + 1; k < n; k++) {
v = samples[k];
D[j * n + k] += (double) count_mutations_on_path(
u, v, tree.parent, nodes_time, mutations_per_node);
if (variant.num_alleles > max_alleles) {
/* could do some kind of doubling here, but there's no
* point - just keep it simple for testing. */
max_alleles = variant.num_alleles;
tsk_safe_free(allele_offsets);
allele_offsets = tsk_malloc((max_alleles + 1) * sizeof(*allele_offsets));
if (allele_offsets == NULL) {
ret = TSK_ERR_NO_MEMORY;
goto out;
}
}
ret = tsk_tree_next(&tree);
if (ret < 0) {
goto out;
}
group_alleles(&variant, A, allele_offsets);
update_site_divergence(&variant, A, allele_offsets, D);
site_id++;
}
}
ret = 0;
out:
tsk_tree_free(&tree);
tsk_safe_free(mutations_per_node);
tsk_variant_free(&variant);
tsk_safe_free(A);
tsk_safe_free(allele_offsets);
return ret;
}

static int
get_sample_index_map(const tsk_size_t num_nodes, const tsk_size_t num_samples,
const tsk_id_t *restrict samples, tsk_id_t **ret_sample_index_map)
{
int ret = 0;
tsk_size_t j;
tsk_id_t u;
tsk_id_t *sample_index_map = tsk_malloc(num_nodes * sizeof(*sample_index_map));

if (sample_index_map == NULL) {
ret = TSK_ERR_NO_MEMORY;
goto out;
}
/* Assign the output pointer here so that it will be freed in the case
* of an error raised in the input checking */
*ret_sample_index_map = sample_index_map;

for (j = 0; j < num_nodes; j++) {
sample_index_map[j] = TSK_NULL;
}
for (j = 0; j < num_samples; j++) {
u = samples[j];
if (sample_index_map[u] != TSK_NULL) {
ret = TSK_ERR_DUPLICATE_SAMPLE;
goto out;
}
sample_index_map[u] = (tsk_id_t) j;
}
out:
return ret;
}

Expand Down Expand Up @@ -6739,9 +6785,11 @@ tsk_treeseq_divergence_matrix(const tsk_treeseq_t *self, tsk_size_t num_samples,
const tsk_id_t *samples = self->samples;
tsk_size_t n = self->num_samples;
const double default_windows[] = { 0, self->tables->sequence_length };
const tsk_size_t num_nodes = self->tables->nodes.num_rows;
bool stat_site = !!(options & TSK_STAT_SITE);
bool stat_branch = !!(options & TSK_STAT_BRANCH);
bool stat_node = !!(options & TSK_STAT_NODE);
tsk_id_t *sample_index_map = NULL;

if (stat_node) {
ret = TSK_ERR_UNSUPPORTED_STAT_MODE;
Expand Down Expand Up @@ -6785,6 +6833,13 @@ tsk_treeseq_divergence_matrix(const tsk_treeseq_t *self, tsk_size_t num_samples,
}
}

/* NOTE: we're just using this here to check the input for duplicates.
*/
ret = get_sample_index_map(num_nodes, n, samples, &sample_index_map);
if (ret != 0) {
goto out;
}

tsk_memset(result, 0, num_windows * n * n * sizeof(*result));

if (stat_branch) {
Expand All @@ -6801,5 +6856,6 @@ tsk_treeseq_divergence_matrix(const tsk_treeseq_t *self, tsk_size_t num_samples,
fill_lower_triangle(result, n, num_windows);

out:
tsk_safe_free(sample_index_map);
return ret;
}
Loading