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Merged
merged 2 commits into from
Sep 11, 2020
Merged

Add include_terminal param #787

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f677e36
Change diff iter types to tsk_ equivalents
hyanwong Aug 21, 2020
e91b436
Add include_terminal param to edge diff iterator
hyanwong Aug 21, 2020
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2 changes: 2 additions & 0 deletions c/CHANGELOG.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,8 @@
[0.99.7] - 2020-XX-XX
---------------------

- Added ``TSK_INCLUDE_TERMINAL`` option to ``tsk_diff_iter_init`` to output the last edges
at the end of a tree sequence (:user:`hyanwong`, :issue:`783`, :pr:`787`)

---------------------
[0.99.6] - 2020-09-04
Expand Down
111 changes: 81 additions & 30 deletions c/tests/test_trees.c
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Original file line number Diff line number Diff line change
Expand Up @@ -175,7 +175,7 @@ verify_individual_nodes(tsk_treeseq_t *ts)
}

static void
verify_trees(tsk_treeseq_t *ts, uint32_t num_trees, tsk_id_t *parents)
verify_trees(tsk_treeseq_t *ts, tsk_size_t num_trees, tsk_id_t *parents)
{
int ret;
tsk_id_t u, j, v;
Expand Down Expand Up @@ -378,16 +378,16 @@ verify_tree_next_prev(tsk_treeseq_t *ts)
}

static void
verify_tree_diffs(tsk_treeseq_t *ts)
verify_tree_diffs(tsk_treeseq_t *ts, tsk_flags_t options)
{
int ret;
int ret, valid_tree;
tsk_diff_iter_t iter;
tsk_tree_t tree;
tsk_edge_list_node_t *record;
tsk_edge_list_t records_out, records_in;
size_t num_nodes = tsk_treeseq_get_num_nodes(ts);
size_t j, num_trees;
double left, right;
tsk_size_t num_nodes = tsk_treeseq_get_num_nodes(ts);
tsk_size_t j, num_trees;
double lft, rgt;
tsk_id_t *parent = malloc(num_nodes * sizeof(tsk_id_t));
tsk_id_t *child = malloc(num_nodes * sizeof(tsk_id_t));
tsk_id_t *sib = malloc(num_nodes * sizeof(tsk_id_t));
Expand All @@ -400,17 +400,17 @@ verify_tree_diffs(tsk_treeseq_t *ts)
child[j] = TSK_NULL;
sib[j] = TSK_NULL;
}
ret = tsk_diff_iter_init(&iter, ts);
ret = tsk_diff_iter_init(&iter, ts, options);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_tree_init(&tree, ts, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_tree_first(&tree);
CU_ASSERT_EQUAL_FATAL(ret, 1);
valid_tree = tsk_tree_first(&tree);
CU_ASSERT_EQUAL_FATAL(valid_tree, 1);
tsk_diff_iter_print_state(&iter, _devnull);

num_trees = 0;
while ((ret = tsk_diff_iter_next(&iter, &left, &right, &records_out, &records_in))
== 1) {
while (
(ret = tsk_diff_iter_next(&iter, &lft, &rgt, &records_out, &records_in)) == 1) {
tsk_diff_iter_print_state(&iter, _devnull);
num_trees++;
/* Update forwards */
Expand All @@ -420,9 +420,11 @@ verify_tree_diffs(tsk_treeseq_t *ts)
for (record = records_in.head; record != NULL; record = record->next) {
parent[record->edge.child] = record->edge.parent;
}
/* Now check against the sparse tree iterator. */
for (j = 0; j < num_nodes; j++) {
CU_ASSERT_EQUAL(parent[j], tree.parent[j]);
if (valid_tree) {
/* Now check against the sparse tree iterator. */
for (j = 0; j < num_nodes; j++) {
CU_ASSERT_EQUAL(parent[j], tree.parent[j]);
}
}
/* Update backwards */
for (record = records_out.tail; record != NULL; record = record->prev) {
Expand All @@ -431,21 +433,34 @@ verify_tree_diffs(tsk_treeseq_t *ts)
for (record = records_in.tail; record != NULL; record = record->prev) {
parent[record->edge.child] = record->edge.parent;
}
/* Now check against the sparse tree iterator. */
for (j = 0; j < num_nodes; j++) {
CU_ASSERT_EQUAL(parent[j], tree.parent[j]);
}
CU_ASSERT_EQUAL(tree.left, left);
CU_ASSERT_EQUAL(tree.right, right);
ret = tsk_tree_next(&tree);
if (num_trees < tsk_treeseq_get_num_trees(ts)) {
CU_ASSERT_EQUAL(ret, 1);
if (valid_tree) {
/* Now check against the sparse tree iterator. */
for (j = 0; j < num_nodes; j++) {
CU_ASSERT_EQUAL(parent[j], tree.parent[j]);
}
CU_ASSERT_EQUAL(tree.left, lft);
CU_ASSERT_EQUAL(tree.right, rgt);
valid_tree = tsk_tree_next(&tree);
if (num_trees < tsk_treeseq_get_num_trees(ts)) {
CU_ASSERT_EQUAL(valid_tree, 1);
} else {
CU_ASSERT_EQUAL(valid_tree, 0);
}
} else {
CU_ASSERT_EQUAL(ret, 0);
CU_ASSERT_TRUE_FATAL(options & TSK_INCLUDE_TERMINAL);
for (j = 0; j < num_nodes; j++) {
CU_ASSERT_EQUAL(parent[j], -1);
}
CU_ASSERT_EQUAL(lft, tsk_treeseq_get_sequence_length(ts));
CU_ASSERT_EQUAL(rgt, tsk_treeseq_get_sequence_length(ts));
}
}
CU_ASSERT_EQUAL(num_trees, tsk_treeseq_get_num_trees(ts));
CU_ASSERT_EQUAL_FATAL(ret, 0);
if (options & TSK_INCLUDE_TERMINAL) {
CU_ASSERT_EQUAL(num_trees, tsk_treeseq_get_num_trees(ts) + 1);
} else {
CU_ASSERT_EQUAL(num_trees, tsk_treeseq_get_num_trees(ts));
}
CU_ASSERT_EQUAL_FATAL(valid_tree, 0);
ret = tsk_diff_iter_free(&iter);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_tree_free(&tree);
Expand Down Expand Up @@ -4597,7 +4612,8 @@ test_simple_diff_iter(void)
tsk_treeseq_from_text(&ts, 10, paper_ex_nodes, paper_ex_edges, NULL, NULL, NULL,
paper_ex_individuals, NULL, 0);

verify_tree_diffs(&ts);
verify_tree_diffs(&ts, 0);
verify_tree_diffs(&ts, TSK_INCLUDE_TERMINAL);

ret = tsk_treeseq_free(&ts);
CU_ASSERT_EQUAL(ret, 0);
Expand All @@ -4611,7 +4627,8 @@ test_nonbinary_diff_iter(void)

tsk_treeseq_from_text(&ts, 100, nonbinary_ex_nodes, nonbinary_ex_edges, NULL, NULL,
NULL, NULL, NULL, 0);
verify_tree_diffs(&ts);
verify_tree_diffs(&ts, 0);
verify_tree_diffs(&ts, TSK_INCLUDE_TERMINAL);

ret = tsk_treeseq_free(&ts);
CU_ASSERT_EQUAL(ret, 0);
Expand All @@ -4625,7 +4642,8 @@ test_unary_diff_iter(void)

tsk_treeseq_from_text(
&ts, 10, unary_ex_nodes, unary_ex_edges, NULL, NULL, NULL, NULL, NULL, 0);
verify_tree_diffs(&ts);
verify_tree_diffs(&ts, 0);
verify_tree_diffs(&ts, TSK_INCLUDE_TERMINAL);

ret = tsk_treeseq_free(&ts);
CU_ASSERT_EQUAL(ret, 0);
Expand All @@ -4639,7 +4657,38 @@ test_internal_sample_diff_iter(void)

tsk_treeseq_from_text(&ts, 10, internal_sample_ex_nodes, internal_sample_ex_edges,
NULL, NULL, NULL, NULL, NULL, 0);
verify_tree_diffs(&ts);
verify_tree_diffs(&ts, 0);
verify_tree_diffs(&ts, TSK_INCLUDE_TERMINAL);

ret = tsk_treeseq_free(&ts);
CU_ASSERT_EQUAL(ret, 0);
}

static void
test_multiroot_diff_iter(void)
{
int ret;
tsk_treeseq_t ts;

tsk_treeseq_from_text(&ts, 10, multiroot_ex_nodes, multiroot_ex_edges, NULL, NULL,
NULL, NULL, NULL, 0);
verify_tree_diffs(&ts, 0);
verify_tree_diffs(&ts, TSK_INCLUDE_TERMINAL);

ret = tsk_treeseq_free(&ts);
CU_ASSERT_EQUAL(ret, 0);
}

static void
test_empty_diff_iter(void)
{
int ret;
tsk_treeseq_t ts;

tsk_treeseq_from_text(
&ts, 10, empty_ex_nodes, empty_ex_edges, NULL, NULL, NULL, NULL, NULL, 0);
verify_tree_diffs(&ts, 0);
verify_tree_diffs(&ts, TSK_INCLUDE_TERMINAL);

ret = tsk_treeseq_free(&ts);
CU_ASSERT_EQUAL(ret, 0);
Expand Down Expand Up @@ -6041,6 +6090,8 @@ main(int argc, char **argv)
{ "test_nonbinary_diff_iter", test_nonbinary_diff_iter },
{ "test_unary_diff_iter", test_unary_diff_iter },
{ "test_internal_sample_diff_iter", test_internal_sample_diff_iter },
{ "test_multiroot_diff_iter", test_multiroot_diff_iter },
{ "test_empty_diff_iter", test_empty_diff_iter },

/* Sample sets */
{ "test_simple_sample_sets", test_simple_sample_sets },
Expand Down
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