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Modular incremental trees #2786

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Jul 18, 2023
Merged

Modular incremental trees #2786

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f93e792
Initial version of tsk_tree_position_t and tests
jeromekelleher Jul 7, 2023
63b317c
Convert kc_distance to use tree_position_t
jeromekelleher Jul 12, 2023
2c264be
Convert LS HMM code to use tree_position_t
jeromekelleher Jul 12, 2023
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153 changes: 153 additions & 0 deletions c/tests/test_trees.c
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Original file line number Diff line number Diff line change
Expand Up @@ -175,6 +175,97 @@ verify_individual_nodes(tsk_treeseq_t *ts)
}
}

static void
verify_tree_pos(const tsk_treeseq_t *ts, tsk_size_t num_trees, tsk_id_t *tree_parents)
{
int ret;
const tsk_size_t N = tsk_treeseq_get_num_nodes(ts);
const tsk_id_t *edges_parent = ts->tables->edges.parent;
const tsk_id_t *edges_child = ts->tables->edges.child;
tsk_tree_position_t tree_pos;
tsk_id_t *known_parent;
tsk_id_t *parent = tsk_malloc(N * sizeof(*parent));
tsk_id_t u, index, j, e;
bool valid;

CU_ASSERT_FATAL(parent != NULL);

ret = tsk_tree_position_init(&tree_pos, ts, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);

for (u = 0; u < (tsk_id_t) N; u++) {
parent[u] = TSK_NULL;
}

for (index = 0; index < (tsk_id_t) num_trees; index++) {
known_parent = tree_parents + N * (tsk_size_t) index;

valid = tsk_tree_position_next(&tree_pos);
CU_ASSERT_TRUE(valid);
CU_ASSERT_EQUAL(index, tree_pos.index);

for (j = tree_pos.out.start; j < tree_pos.out.stop; j++) {
e = tree_pos.out.order[j];
parent[edges_child[e]] = TSK_NULL;
}

for (j = tree_pos.in.start; j < tree_pos.in.stop; j++) {
e = tree_pos.in.order[j];
parent[edges_child[e]] = edges_parent[e];
}

for (u = 0; u < (tsk_id_t) N; u++) {
CU_ASSERT_EQUAL(parent[u], known_parent[u]);
}
}

valid = tsk_tree_position_next(&tree_pos);
CU_ASSERT_FALSE(valid);
for (j = tree_pos.out.start; j < tree_pos.out.stop; j++) {
e = tree_pos.out.order[j];
parent[edges_child[e]] = TSK_NULL;
}
for (u = 0; u < (tsk_id_t) N; u++) {
CU_ASSERT_EQUAL(parent[u], TSK_NULL);
}

for (index = (tsk_id_t) num_trees - 1; index >= 0; index--) {
known_parent = tree_parents + N * (tsk_size_t) index;

valid = tsk_tree_position_prev(&tree_pos);
CU_ASSERT_TRUE(valid);
CU_ASSERT_EQUAL(index, tree_pos.index);

for (j = tree_pos.out.start; j > tree_pos.out.stop; j--) {
e = tree_pos.out.order[j];
parent[edges_child[e]] = TSK_NULL;
}

for (j = tree_pos.in.start; j > tree_pos.in.stop; j--) {
CU_ASSERT_FATAL(j >= 0);
e = tree_pos.in.order[j];
parent[edges_child[e]] = edges_parent[e];
}

for (u = 0; u < (tsk_id_t) N; u++) {
CU_ASSERT_EQUAL(parent[u], known_parent[u]);
}
}

valid = tsk_tree_position_prev(&tree_pos);
CU_ASSERT_FALSE(valid);
for (j = tree_pos.out.start; j > tree_pos.out.stop; j--) {
e = tree_pos.out.order[j];
parent[edges_child[e]] = TSK_NULL;
}
for (u = 0; u < (tsk_id_t) N; u++) {
CU_ASSERT_EQUAL(parent[u], TSK_NULL);
}

tsk_tree_position_free(&tree_pos);
tsk_safe_free(parent);
}

static void
verify_trees(tsk_treeseq_t *ts, tsk_size_t num_trees, tsk_id_t *parents)
{
Expand Down Expand Up @@ -233,6 +324,8 @@ verify_trees(tsk_treeseq_t *ts, tsk_size_t num_trees, tsk_id_t *parents)
CU_ASSERT_EQUAL(tsk_treeseq_get_sequence_length(ts), breakpoints[j]);

tsk_tree_free(&tree);

verify_tree_pos(ts, num_trees, parents);
}

static tsk_tree_t *
Expand Down Expand Up @@ -5233,6 +5326,65 @@ test_single_tree_tracked_samples(void)
tsk_tree_free(&tree);
}

static void
test_single_tree_tree_pos(void)
{
tsk_treeseq_t ts;
tsk_tree_position_t tree_pos;
bool valid;
int ret;

tsk_treeseq_from_text(&ts, 1, single_tree_ex_nodes, single_tree_ex_edges, NULL, NULL,
NULL, NULL, NULL, 0);

ret = tsk_tree_position_init(&tree_pos, &ts, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
valid = tsk_tree_position_next(&tree_pos);
CU_ASSERT_FATAL(valid);

CU_ASSERT_EQUAL_FATAL(tree_pos.interval.left, 0);
CU_ASSERT_EQUAL_FATAL(tree_pos.interval.right, 1);
CU_ASSERT_EQUAL_FATAL(tree_pos.in.start, 0);
CU_ASSERT_EQUAL_FATAL(tree_pos.in.stop, 6);
CU_ASSERT_EQUAL_FATAL(tree_pos.in.order, ts.tables->indexes.edge_insertion_order);
CU_ASSERT_EQUAL_FATAL(tree_pos.out.start, 0);
CU_ASSERT_EQUAL_FATAL(tree_pos.out.stop, 0);
CU_ASSERT_EQUAL_FATAL(tree_pos.out.order, ts.tables->indexes.edge_removal_order);

valid = tsk_tree_position_next(&tree_pos);
CU_ASSERT_FATAL(!valid);

tsk_tree_position_print_state(&tree_pos, _devnull);

CU_ASSERT_EQUAL_FATAL(tree_pos.index, -1);
CU_ASSERT_EQUAL_FATAL(tree_pos.out.start, 0);
CU_ASSERT_EQUAL_FATAL(tree_pos.out.stop, 6);
CU_ASSERT_EQUAL_FATAL(tree_pos.out.order, ts.tables->indexes.edge_removal_order);

valid = tsk_tree_position_prev(&tree_pos);
CU_ASSERT_FATAL(valid);

CU_ASSERT_EQUAL_FATAL(tree_pos.interval.left, 0);
CU_ASSERT_EQUAL_FATAL(tree_pos.interval.right, 1);
CU_ASSERT_EQUAL_FATAL(tree_pos.in.start, 5);
CU_ASSERT_EQUAL_FATAL(tree_pos.in.stop, -1);
CU_ASSERT_EQUAL_FATAL(tree_pos.in.order, ts.tables->indexes.edge_removal_order);
CU_ASSERT_EQUAL_FATAL(tree_pos.out.start, 5);
CU_ASSERT_EQUAL_FATAL(tree_pos.out.stop, 5);
CU_ASSERT_EQUAL_FATAL(tree_pos.out.order, ts.tables->indexes.edge_insertion_order);

valid = tsk_tree_position_prev(&tree_pos);
CU_ASSERT_FATAL(!valid);

CU_ASSERT_EQUAL_FATAL(tree_pos.index, -1);
CU_ASSERT_EQUAL_FATAL(tree_pos.out.start, 5);
CU_ASSERT_EQUAL_FATAL(tree_pos.out.stop, -1);
CU_ASSERT_EQUAL_FATAL(tree_pos.out.order, ts.tables->indexes.edge_insertion_order);

tsk_tree_position_free(&tree_pos);
tsk_treeseq_free(&ts);
}

/*=======================================================
* Multi tree tests.
*======================================================*/
Expand Down Expand Up @@ -8185,6 +8337,7 @@ main(int argc, char **argv)
{ "test_single_tree_map_mutations_internal_samples",
test_single_tree_map_mutations_internal_samples },
{ "test_single_tree_tracked_samples", test_single_tree_tracked_samples },
{ "test_single_tree_tree_pos", test_single_tree_tree_pos },

/* Multi tree tests */
{ "test_simple_multi_tree", test_simple_multi_tree },
Expand Down
63 changes: 31 additions & 32 deletions c/tskit/haplotype_matching.c
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Original file line number Diff line number Diff line change
Expand Up @@ -209,7 +209,7 @@ int
tsk_ls_hmm_free(tsk_ls_hmm_t *self)
{
tsk_tree_free(&self->tree);
tsk_diff_iter_free(&self->diffs);
tsk_tree_position_free(&self->tree_pos);
tsk_safe_free(self->recombination_rate);
tsk_safe_free(self->mutation_rate);
tsk_safe_free(self->recombination_rate);
Expand Down Expand Up @@ -248,9 +248,8 @@ tsk_ls_hmm_reset(tsk_ls_hmm_t *self)
tsk_memset(self->transition_parent, 0xff,
self->max_transitions * sizeof(*self->transition_parent));

/* This is safe because we've already zero'd out the memory. */
tsk_diff_iter_free(&self->diffs);
ret = tsk_diff_iter_init_from_ts(&self->diffs, self->tree_sequence, false);
tsk_tree_position_free(&self->tree_pos);
ret = tsk_tree_position_init(&self->tree_pos, self->tree_sequence, 0);
if (ret != 0) {
goto out;
}
Expand Down Expand Up @@ -306,47 +305,48 @@ tsk_ls_hmm_update_tree(tsk_ls_hmm_t *self)
int ret = 0;
tsk_id_t *restrict parent = self->parent;
tsk_id_t *restrict T_index = self->transition_index;
const tsk_id_t *restrict edges_child = self->tree_sequence->tables->edges.child;
const tsk_id_t *restrict edges_parent = self->tree_sequence->tables->edges.parent;
tsk_value_transition_t *restrict T = self->transitions;
tsk_edge_list_node_t *record;
tsk_edge_list_t records_out, records_in;
tsk_edge_t edge;
double left, right;
tsk_id_t u;
tsk_id_t u, c, p, j, e;
tsk_value_transition_t *vt;

ret = tsk_diff_iter_next(&self->diffs, &left, &right, &records_out, &records_in);
if (ret < 0) {
goto out;
}
tsk_tree_position_next(&self->tree_pos);
tsk_bug_assert(self->tree_pos.index != -1);
tsk_bug_assert(self->tree_pos.index == self->tree.index);

for (record = records_out.head; record != NULL; record = record->next) {
u = record->edge.child;
for (j = self->tree_pos.out.start; j < self->tree_pos.out.stop; j++) {
e = self->tree_pos.out.order[j];
c = edges_child[e];
u = c;
if (T_index[u] == TSK_NULL) {
/* Ensure the subtree we're detaching has a transition at the root */
while (T_index[u] == TSK_NULL) {
u = parent[u];
tsk_bug_assert(u != TSK_NULL);
}
tsk_bug_assert(self->num_transitions < self->max_transitions);
T_index[record->edge.child] = (tsk_id_t) self->num_transitions;
T[self->num_transitions].tree_node = record->edge.child;
T_index[c] = (tsk_id_t) self->num_transitions;
T[self->num_transitions].tree_node = c;
T[self->num_transitions].value = T[T_index[u]].value;
self->num_transitions++;
}
parent[record->edge.child] = TSK_NULL;
parent[c] = TSK_NULL;
}

for (record = records_in.head; record != NULL; record = record->next) {
edge = record->edge;
parent[edge.child] = edge.parent;
u = edge.parent;
if (parent[edge.parent] == TSK_NULL) {
for (j = self->tree_pos.in.start; j < self->tree_pos.in.stop; j++) {
e = self->tree_pos.in.order[j];
c = edges_child[e];
p = edges_parent[e];
parent[c] = p;
u = p;
if (parent[p] == TSK_NULL) {
/* Grafting onto a new root. */
if (T_index[record->edge.parent] == TSK_NULL) {
T_index[edge.parent] = (tsk_id_t) self->num_transitions;
if (T_index[p] == TSK_NULL) {
T_index[p] = (tsk_id_t) self->num_transitions;
tsk_bug_assert(self->num_transitions < self->max_transitions);
T[self->num_transitions].tree_node = edge.parent;
T[self->num_transitions].value = T[T_index[edge.child]].value;
T[self->num_transitions].tree_node = p;
T[self->num_transitions].value = T[T_index[c]].value;
self->num_transitions++;
}
} else {
Expand All @@ -356,18 +356,17 @@ tsk_ls_hmm_update_tree(tsk_ls_hmm_t *self)
}
tsk_bug_assert(u != TSK_NULL);
}
tsk_bug_assert(T_index[u] != -1 && T_index[edge.child] != -1);
if (T[T_index[u]].value == T[T_index[edge.child]].value) {
vt = &T[T_index[edge.child]];
tsk_bug_assert(T_index[u] != -1 && T_index[c] != -1);
if (T[T_index[u]].value == T[T_index[c]].value) {
vt = &T[T_index[c]];
/* Mark the value transition as unusued */
vt->value = -1;
vt->tree_node = TSK_NULL;
T_index[edge.child] = TSK_NULL;
T_index[c] = TSK_NULL;
}
}

ret = tsk_ls_hmm_remove_dead_roots(self);
out:
return ret;
}

Expand Down
7 changes: 5 additions & 2 deletions c/tskit/haplotype_matching.h
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
/*
* MIT License
*
* Copyright (c) 2019-2022 Tskit Developers
* Copyright (c) 2019-2023 Tskit Developers
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
Expand Down Expand Up @@ -98,7 +98,10 @@ typedef struct _tsk_ls_hmm_t {
tsk_size_t num_nodes;
/* state */
tsk_tree_t tree;
tsk_diff_iter_t diffs;
/* NOTE: this tree_position will be redundant once we integrate the top-level
* tree class with this.
*/
tsk_tree_position_t tree_pos;
tsk_id_t *parent;
/* The probability value transitions on the tree */
tsk_value_transition_t *transitions;
Expand Down
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