Skip to content

make subset and canonicalise deal with individual parents #1226

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 2 commits into from
Mar 16, 2021
Merged

make subset and canonicalise deal with individual parents #1226

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
85297db
subset does not reorder individuals
petrelharp Feb 28, 2021
f48a9ee
union consistency check and py_union fix: closes #1243
petrelharp Mar 15, 2021
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
97 changes: 77 additions & 20 deletions c/tests/test_tables.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4122,6 +4122,9 @@ test_sort_tables_canonical_errors(void)
ret = tsk_table_collection_init(&tables, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
tables.sequence_length = 1;
tsk_id_t null_p[] = { -1 };
tsk_id_t zero_p[] = { 0 };
tsk_id_t one_p[] = { 1 };

ret = tsk_node_table_add_row(&tables.nodes, 0, 0.0, TSK_NULL, TSK_NULL, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
Expand All @@ -4140,7 +4143,7 @@ test_sort_tables_canonical_errors(void)
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_MUTATION_PARENT_INCONSISTENT);

ret = tsk_mutation_table_clear(&tables.mutations);
CU_ASSERT_FATAL(ret >= 0);
CU_ASSERT_FATAL(ret == 0);
ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, 2, 0.0, "a", 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, 3, 0.0, "b", 1, NULL, 0);
Expand All @@ -4153,6 +4156,44 @@ test_sort_tables_canonical_errors(void)
ret = tsk_table_collection_canonicalise(&tables, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);

ret = tsk_node_table_add_row(&tables.nodes, 0, 0.0, TSK_NULL, 0, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_node_table_add_row(&tables.nodes, 0, 0.0, TSK_NULL, 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_individual_table_add_row(
&tables.individuals, 0, NULL, 0, one_p, 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_individual_table_add_row(
&tables.individuals, 0, NULL, 0, zero_p, 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);

ret = tsk_table_collection_canonicalise(&tables, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_INDIVIDUAL_PARENT_CYCLE);

ret = tsk_individual_table_clear(&tables.individuals);
CU_ASSERT_FATAL(ret == 0);
ret = tsk_individual_table_add_row(
&tables.individuals, 0, NULL, 0, zero_p, 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_individual_table_add_row(
&tables.individuals, 0, NULL, 0, zero_p, 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);

ret = tsk_table_collection_canonicalise(&tables, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_INDIVIDUAL_SELF_PARENT);

ret = tsk_individual_table_clear(&tables.individuals);
CU_ASSERT_FATAL(ret == 0);
ret = tsk_individual_table_add_row(
&tables.individuals, 0, NULL, 0, null_p, 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_individual_table_add_row(
&tables.individuals, 0, NULL, 0, zero_p, 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);

ret = tsk_table_collection_canonicalise(&tables, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);

tsk_table_collection_free(&tables);
}

Expand All @@ -4169,10 +4210,10 @@ test_sort_tables_canonical(void)
"0 1 2 -1\n"
"0 2 -1 2\n"
"0 3 -1 -1\n";
const char *individuals = "0 0.0\n"
"0 1.0\n"
"0 2.0\n"
"0 3.0\n";
const char *individuals = "0 0.0 1\n"
"0 1.0 -1\n"
"0 2.0 1,3\n"
"0 3.0 -1,1\n";
const char *sites = "0 0\n"
"0.2 0\n"
"0.1 0\n";
Expand All @@ -4192,9 +4233,9 @@ test_sort_tables_canonical(void)
"0 1 0 -1\n"
"0 2 -1 2\n"
"0 3 -1 -1\n";
const char *individuals_sorted = "0 1.0\n"
"0 3.0\n"
"0 2.0\n";
const char *individuals_sorted = "0 1.0 -1\n"
"0 3.0 -1,0\n"
"0 2.0 0,1\n";
const char *sites_sorted = "0 0\n"
"0.1 0\n"
"0.2 0\n";
Expand All @@ -4207,10 +4248,10 @@ test_sort_tables_canonical(void)
"2 1 4 4 0.5\n"
"2 1 5 6 0.5\n"
"2 1 6 6 0.5\n";
const char *individuals_sorted_kept = "0 1.0\n"
"0 3.0\n"
"0 2.0\n"
"0 0.0\n";
const char *individuals_sorted_kept = "0 1.0 -1\n"
"0 3.0 -1,0\n"
"0 2.0 0,1\n"
"0 0.0 0\n";

ret = tsk_table_collection_init(&t1, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
Expand Down Expand Up @@ -5338,6 +5379,8 @@ test_table_collection_subset_with_options(tsk_flags_t options)
tsk_table_collection_t tables_copy;
int k;
tsk_id_t nodes[4];
tsk_id_t zero_p[] = { 0 };
tsk_id_t one_p[] = { 1 };

ret = tsk_table_collection_init(&tables, options);
CU_ASSERT_EQUAL_FATAL(ret, 0);
Expand All @@ -5360,15 +5403,18 @@ test_table_collection_subset_with_options(tsk_flags_t options)
ret = tsk_node_table_add_row(
&tables.nodes, TSK_NODE_IS_SAMPLE, 0.0, TSK_NULL, 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
// unused individual who is the parent of others
ret = tsk_individual_table_add_row(
&tables.individuals, 0, NULL, 0, NULL, 0, NULL, 0);
ret = tsk_individual_table_add_row(
&tables.individuals, 0, NULL, 0, zero_p, 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_individual_table_add_row(
&tables.individuals, 0, NULL, 0, NULL, 0, NULL, 0);
&tables.individuals, 0, NULL, 0, one_p, 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
// unused individual
ret = tsk_individual_table_add_row(
&tables.individuals, 0, NULL, 0, NULL, 0, NULL, 0);
&tables.individuals, 0, NULL, 0, one_p, 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_population_table_add_row(&tables.populations, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
Expand Down Expand Up @@ -5425,7 +5471,8 @@ test_table_collection_subset_with_options(tsk_flags_t options)
ret = tsk_table_collection_subset(&tables_copy, NULL, 0, TSK_KEEP_UNREFERENCED);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_EQUAL_FATAL(tables_copy.nodes.num_rows, 0);
CU_ASSERT_EQUAL_FATAL(tables_copy.individuals.num_rows, 3);
CU_ASSERT_FATAL(
tsk_individual_table_equals(&tables.individuals, &tables_copy.individuals, 0));
CU_ASSERT_EQUAL_FATAL(tables_copy.populations.num_rows, 2);
CU_ASSERT_EQUAL_FATAL(tables_copy.mutations.num_rows, 0);
CU_ASSERT_FATAL(tsk_site_table_equals(&tables.sites, &tables_copy.sites, 0));
Expand All @@ -5437,13 +5484,14 @@ test_table_collection_subset_with_options(tsk_flags_t options)
&tables_copy, NULL, 0, TSK_KEEP_UNREFERENCED | TSK_NO_CHANGE_POPULATIONS);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_EQUAL_FATAL(tables_copy.nodes.num_rows, 0);
CU_ASSERT_EQUAL_FATAL(tables_copy.individuals.num_rows, 3);
CU_ASSERT_FATAL(
tsk_individual_table_equals(&tables.individuals, &tables_copy.individuals, 0));
CU_ASSERT_EQUAL_FATAL(tables_copy.mutations.num_rows, 0);
CU_ASSERT_FATAL(
tsk_population_table_equals(&tables.populations, &tables_copy.populations, 0));
CU_ASSERT_FATAL(tsk_site_table_equals(&tables.sites, &tables_copy.sites, 0));

// the identity transformation, since unused inds/pops are at the end
// the identity transformation, since unused pops are at the end
for (k = 0; k < 4; k++) {
nodes[k] = k;
}
Expand All @@ -5458,14 +5506,16 @@ test_table_collection_subset_with_options(tsk_flags_t options)
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_table_collection_subset(&tables_copy, nodes, 4, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_table_collection_check_integrity(&tables_copy, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_FATAL(tsk_node_table_equals(&tables.nodes, &tables_copy.nodes, 0));
CU_ASSERT_EQUAL_FATAL(tables_copy.individuals.num_rows, 2);
CU_ASSERT_EQUAL_FATAL(tables_copy.populations.num_rows, 1);
CU_ASSERT_EQUAL_FATAL(tables_copy.sites.num_rows, 2);
CU_ASSERT_FATAL(
tsk_mutation_table_equals(&tables.mutations, &tables_copy.mutations, 0));

// reverse twice should get back to the start, since unused inds/pops are at the end
// reverse twice should get back to the start, since unused pops are at the end
for (k = 0; k < 4; k++) {
nodes[k] = 3 - k;
}
Expand All @@ -5475,6 +5525,8 @@ test_table_collection_subset_with_options(tsk_flags_t options)
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_table_collection_subset(&tables_copy, nodes, 4, TSK_KEEP_UNREFERENCED);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_table_collection_check_integrity(&tables_copy, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_FATAL(tsk_table_collection_equals(&tables, &tables_copy, 0));

tsk_table_collection_free(&tables_copy);
Expand All @@ -5496,6 +5548,7 @@ test_table_collection_subset_unsorted(void)
tsk_table_collection_t tables_copy;
int k;
tsk_id_t nodes[3];
tsk_id_t one_p[] = { 1 };

ret = tsk_table_collection_init(&tables, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
Expand All @@ -5508,10 +5561,14 @@ test_table_collection_subset_unsorted(void)
&tables.nodes, TSK_NODE_IS_SAMPLE, 0.0, TSK_NULL, TSK_NULL, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_node_table_add_row(
&tables.nodes, TSK_NODE_IS_SAMPLE, 0.5, TSK_NULL, TSK_NULL, NULL, 0);
&tables.nodes, TSK_NODE_IS_SAMPLE, 0.5, TSK_NULL, 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_node_table_add_row(&tables.nodes, 0, 1.0, TSK_NULL, TSK_NULL, NULL, 0);
ret = tsk_node_table_add_row(&tables.nodes, 0, 1.0, TSK_NULL, 0, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_individual_table_add_row(
&tables.individuals, 0, NULL, 0, one_p, 1, NULL, 0);
ret = tsk_individual_table_add_row(
&tables.individuals, 0, NULL, 0, NULL, 0, NULL, 0);
ret = tsk_edge_table_add_row(&tables.edges, 0.0, 0.5, 2, 1, NULL, 0);
CU_ASSERT_FATAL(ret >= 0);
ret = tsk_edge_table_add_row(&tables.edges, 0.0, 1.0, 1, 0, NULL, 0);
Expand Down
Loading