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Refseq update #1944

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merged 1 commit into from
Dec 2, 2021
Merged

Refseq update #1944

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56 changes: 56 additions & 0 deletions c/tests/test_file_format.c
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Original file line number Diff line number Diff line change
Expand Up @@ -636,6 +636,47 @@ test_malformed_indexes(void)
free(ts);
}

static void
test_missing_reference_sequence(void)
{
int ret;
tsk_treeseq_t *ts = caterpillar_tree(5, 3, 3);
tsk_table_collection_t t1, t2;
const char *cols[] = { "reference_sequence/data", "reference_sequence/url",
"reference_sequence/metadata_schema", "reference_sequence/metadata" };

CU_ASSERT_TRUE(tsk_treeseq_has_reference_sequence(ts));

ret = tsk_treeseq_copy_tables(ts, &t1, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);

copy_store_drop_columns(ts, 1, cols, _tmp_file_name);
ret = tsk_table_collection_load(&t2, _tmp_file_name, 0);
CU_ASSERT_TRUE(tsk_table_collection_has_reference_sequence(&t2));
tsk_table_collection_free(&t2);

copy_store_drop_columns(ts, 2, cols, _tmp_file_name);
ret = tsk_table_collection_load(&t2, _tmp_file_name, 0);
CU_ASSERT_TRUE(tsk_table_collection_has_reference_sequence(&t2));
tsk_table_collection_free(&t2);

copy_store_drop_columns(ts, 3, cols, _tmp_file_name);
ret = tsk_table_collection_load(&t2, _tmp_file_name, 0);
CU_ASSERT_TRUE(tsk_table_collection_has_reference_sequence(&t2));
tsk_table_collection_free(&t2);

/* Dropping all the columns gives us a NULL reference_sequence, though */
copy_store_drop_columns(ts, 4, cols, _tmp_file_name);
ret = tsk_table_collection_load(&t2, _tmp_file_name, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_FALSE(tsk_table_collection_has_reference_sequence(&t2));
tsk_table_collection_free(&t2);

tsk_table_collection_free(&t1);
tsk_treeseq_free(ts);
free(ts);
}

static void
test_bad_column_types(void)
{
Expand Down Expand Up @@ -699,6 +740,18 @@ test_bad_column_types(void)
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_COLUMN_TYPE);
tsk_table_collection_free(&tables);

cols[0] = "reference_sequence/metadata";
copy_store_drop_columns(ts, 1, cols, _tmp_file_name);
ret = kastore_open(&store, _tmp_file_name, "a", 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = kastore_puts(&store, cols[0], NULL, 0, KAS_FLOAT32, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = kastore_close(&store);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_table_collection_load(&tables, _tmp_file_name, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_COLUMN_TYPE);
tsk_table_collection_free(&tables);

free(col_memory);
tsk_treeseq_free(ts);
free(ts);
Expand Down Expand Up @@ -760,6 +813,8 @@ test_metadata_schemas_optional(void)
const char *cols[] = {
"metadata",
"metadata_schema",
"reference_sequence/metadata",
"reference_sequence/metadata_schema",
"individuals/metadata_schema",
"populations/metadata_schema",
"nodes/metadata_schema",
Expand Down Expand Up @@ -1290,6 +1345,7 @@ main(int argc, char **argv)
{ "test_format_data_load_errors", test_format_data_load_errors },
{ "test_missing_indexes", test_missing_indexes },
{ "test_malformed_indexes", test_malformed_indexes },
{ "test_missing_reference_sequence", test_missing_reference_sequence },
{ "test_bad_column_types", test_bad_column_types },
{ "test_missing_required_columns", test_missing_required_columns },
{ "test_missing_optional_column_pairs", test_missing_optional_column_pairs },
Expand Down
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