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Add C tests
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‎c/tests/test_tables.c

Lines changed: 137 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -8968,6 +8968,28 @@ test_sort_tables_errors(void)
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ret = tsk_table_collection_sort(&tables, &pos, 0);
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CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_SORT_OFFSET_NOT_SUPPORTED);
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8971+
/* Test TSK_ERR_MUTATION_PARENT_INCONSISTENT */
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ret = tsk_table_collection_clear(&tables, 0);
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CU_ASSERT_EQUAL_FATAL(ret, 0);
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tables.sequence_length = 1.0;
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ret = tsk_node_table_add_row(&tables.nodes, 0, 0.0, TSK_NULL, TSK_NULL, NULL, 0);
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CU_ASSERT_FATAL(ret >= 0);
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ret = tsk_site_table_add_row(&tables.sites, 0.0, "x", 1, NULL, 0);
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CU_ASSERT_FATAL(ret >= 0);
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ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, 2, 0.0, "a", 1, NULL, 0);
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CU_ASSERT_FATAL(ret >= 0);
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ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, 3, 0.0, "b", 1, NULL, 0);
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CU_ASSERT_FATAL(ret >= 0);
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ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, 1, 0.0, "c", 1, NULL, 0);
8986+
CU_ASSERT_FATAL(ret >= 0);
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ret = tsk_mutation_table_add_row(&tables.mutations, 0, 0, 2, 0.0, "d", 1, NULL, 0);
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CU_ASSERT_FATAL(ret >= 0);
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8990+
ret = tsk_table_collection_sort(&tables, NULL, 0);
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CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_MUTATION_PARENT_INCONSISTENT);
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89718993
tsk_table_collection_free(&tables);
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tsk_treeseq_free(&ts);
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}
@@ -9032,6 +9054,120 @@ test_sort_tables_mutation_times(void)
90329054
tsk_treeseq_free(&ts);
90339055
}
90349056

9057+
static void
9058+
test_sort_tables_mutations(void)
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{
9060+
int ret;
9061+
tsk_table_collection_t tables;
9062+
9063+
/* Sorting hierarchy:
9064+
* 1. site
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* 2. time (when known)
9066+
* 3. node_time
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* 4. num_descendants: parent mutations first
9068+
* 5. node_id
9069+
* 6. mutation_id
9070+
*/
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9072+
const char *sites = "0.0 A\n"
9073+
"0.5 T\n"
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"0.75 G\n";
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9076+
const char *mutations_unsorted =
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/* Test site criterion (primary) - site 1 should come after site 0 */
9078+
"1 0 X -1 0.0\n" /* mut 0: site 1, will be sorted after site 0 mutations */
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"0 0 Y -1 0.0\n" /* mut 1: site 0, will be sorted before site 1 mutations */
9080+
9081+
/* Test time criterion - within same site, earlier time first */
9082+
"0 4 B -1 2.0\n" /* mut 2: site 0, node 4 (time 1.0), time 2.0 (later time)
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*/
9084+
"0 5 A -1 2.5\n" /* mut 3: site 0, node 5 (time 2.0), time 2.5 (earlier
9085+
relative) */
9086+
9087+
/* Test unknown vs known times - unknown times at site 2, fall back to node_time
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sorting */
9089+
"2 4 U2 -1\n" /* mut 4: site 2, node 4 (time 1.0), unknown time - falls back
9090+
to node_time */
9091+
"2 4 U3 -1\n" /* mut 5: site 2, node 4 (time 1.0), unknown time - should use
9092+
mutation_id as tiebreaker */
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"2 5 U1 -1\n" /* mut 6: site 2, node 5 (time 2.0), unknown time - falls back
9094+
to node_time */
9095+
9096+
/* Test node_time criterion - same site, same mut time, different node times */
9097+
"0 4 D -1 1.5\n" /* mut 7: site 0, node 4 (time 1.0), mut time 1.5 */
9098+
"0 5 C -1 2.5\n" /* mut 8: site 0, node 5 (time 2.0), mut time 2.5 - same
9099+
mut time */
9100+
9101+
/* Test num_descendants criterion with mutation parent-child relationships */
9102+
"0 2 P -1 0.0\n" /* mut 9: site 0, node 2, parent mutation (0 descendants
9103+
initially) */
9104+
"0 1 C1 9 0.0\n" /* mut 10: site 0, node 1, child of mut 9 (parent now has
9105+
1+ descendants) */
9106+
"0 1 C2 9 0.0\n" /* mut 11: site 0, node 1, another child of mut 9 (parent
9107+
now has 2+ descendants) */
9108+
"0 3 Q -1 0.0\n" /* mut 12: site 0, node 3, no children (0 descendants) */
9109+
"0 0 C3 10 0.0\n" /* mut 13: site 0, node 0, child of mut 10 (making mut 9 a
9110+
grandparent) */
9111+
9112+
/* Test node and mutation_id criteria for final tiebreaking */
9113+
"0 0 Z1 -1 0.0\n" /* mut 14: site 0, node 0, no parent, will test node+id
9114+
ordering */
9115+
"0 0 Z2 -1 0.0\n"; /* mut 15: site 0, node 0, no parent, later in input =
9116+
higher ID */
9117+
9118+
const char *mutations_sorted =
9119+
/* Site 0 mutations - known times first, sorted by time */
9120+
"0 5 A -1 2.5\n"
9121+
"0 5 C -1 2.5\n"
9122+
"0 4 B -1 2.0\n"
9123+
"0 4 D -1 1.5\n"
9124+
"0 2 P -1 0.0\n"
9125+
"0 1 C1 4 0.0\n"
9126+
"0 0 Y -1 0.0\n"
9127+
"0 0 C3 5 0.0\n"
9128+
"0 0 Z1 -1 0.0\n"
9129+
"0 0 Z2 -1 0.0\n"
9130+
"0 1 C2 4 0.0\n"
9131+
"0 3 Q -1 0.0\n"
9132+
9133+
/* Site 1 mutations */
9134+
"1 0 X -1 0.0\n"
9135+
9136+
/* Site 2 mutations - unknown times, sorted by node_time then other criteria */
9137+
"2 5 U1 -1\n"
9138+
"2 4 U2 -1\n"
9139+
"2 4 U3 -1\n";
9140+
9141+
ret = tsk_table_collection_init(&tables, 0);
9142+
CU_ASSERT_EQUAL_FATAL(ret, 0);
9143+
tables.sequence_length = 1.0;
9144+
parse_nodes(single_tree_ex_nodes, &tables.nodes);
9145+
parse_edges(single_tree_ex_edges, &tables.edges);
9146+
9147+
parse_sites(sites, &tables.sites);
9148+
CU_ASSERT_EQUAL_FATAL(tables.sites.num_rows, 3);
9149+
9150+
parse_mutations(mutations_unsorted, &tables.mutations);
9151+
CU_ASSERT_EQUAL_FATAL(tables.mutations.num_rows, 16);
9152+
9153+
ret = tsk_table_collection_sort(&tables, NULL, 0);
9154+
CU_ASSERT_EQUAL_FATAL(ret, 0);
9155+
9156+
tsk_table_collection_t expected;
9157+
ret = tsk_table_collection_init(&expected, 0);
9158+
CU_ASSERT_EQUAL_FATAL(ret, 0);
9159+
expected.sequence_length = 1.0;
9160+
parse_nodes(single_tree_ex_nodes, &expected.nodes);
9161+
parse_edges(single_tree_ex_edges, &expected.edges);
9162+
parse_sites(sites, &expected.sites);
9163+
parse_mutations(mutations_sorted, &expected.mutations);
9164+
9165+
CU_ASSERT_TRUE(tsk_mutation_table_equals(&tables.mutations, &expected.mutations, 0));
9166+
9167+
tsk_table_collection_free(&expected);
9168+
tsk_table_collection_free(&tables);
9169+
}
9170+
90359171
static void
90369172
test_sort_tables_canonical_errors(void)
90379173
{
@@ -11608,6 +11744,7 @@ main(int argc, char **argv)
1160811744
{ "test_sort_tables_errors", test_sort_tables_errors },
1160911745
{ "test_sort_tables_individuals", test_sort_tables_individuals },
1161011746
{ "test_sort_tables_mutation_times", test_sort_tables_mutation_times },
11747+
{ "test_sort_tables_mutations", test_sort_tables_mutations },
1161111748
{ "test_sort_tables_migrations", test_sort_tables_migrations },
1161211749
{ "test_sort_tables_no_edge_metadata", test_sort_tables_no_edge_metadata },
1161311750
{ "test_sort_tables_offsets", test_sort_tables_offsets },

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