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Merge pull request #1226 from petrelharp/subset_indivs
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make subset and canonicalise deal with individual parents
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@mergify
mergify[bot] authored Mar 16, 2021
2 parents fbba717 + f48a9ee commit d911160
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Showing 8 changed files with 707 additions and 157 deletions.
97 changes: 77 additions & 20 deletions c/tests/test_tables.c
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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
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