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Merged
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Feb 5, 2021
Merged

Support migrations in sort. #1131

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3 changes: 3 additions & 0 deletions c/CHANGELOG.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,9 @@
- Removed a previous requirement on ``tsk_table_collection_union``, allowing for unioning of
new information both above and below shared history (:user:`petrelharp`, :user:`mufernando`, :pr:`1108`).

- Support migrations in tsk_table_collection_sort. (:user:`jeromekelleher`,
:issue:`22`, :issue:`117`, :pr:`1131`).

**Breaking changes**

- Method ``tsk_individual_table_add_row`` has an extra arguments ``parents`` and ``parents_length``.
Expand Down
119 changes: 101 additions & 18 deletions c/tests/test_tables.c
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,35 @@
#include <unistd.h>
#include <stdlib.h>

static void
reverse_migrations(tsk_table_collection_t *tables)
{
int ret;
tsk_migration_table_t migrations;
tsk_migration_t migration;
tsk_id_t j;

/* Easy way to copy the metadata schema */
ret = tsk_migration_table_copy(&tables->migrations, &migrations, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_migration_table_clear(&migrations);
CU_ASSERT_EQUAL_FATAL(ret, 0);

for (j = (tsk_id_t) tables->migrations.num_rows - 1; j >= 0; j--) {
ret = tsk_migration_table_get_row(&tables->migrations, j, &migration);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_migration_table_add_row(&migrations, migration.left, migration.right,
migration.node, migration.source, migration.dest, migration.time,
migration.metadata, migration.metadata_length);
CU_ASSERT_FATAL(ret >= 0);
}

ret = tsk_migration_table_copy(&migrations, &tables->migrations, TSK_NO_INIT);
CU_ASSERT_EQUAL_FATAL(ret, 0);

tsk_migration_table_free(&migrations);
}

static void
reverse_edges(tsk_table_collection_t *tables)
{
Expand All @@ -37,7 +66,10 @@ reverse_edges(tsk_table_collection_t *tables)
tsk_edge_t edge;
tsk_id_t j;

ret = tsk_edge_table_init(&edges, tables->edges.options);
/* Easy way to copy the metadata schema */
ret = tsk_edge_table_copy(&tables->edges, &edges, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_edge_table_clear(&edges);
CU_ASSERT_EQUAL_FATAL(ret, 0);

for (j = (tsk_id_t) tables->edges.num_rows - 1; j >= 0; j--) {
Expand Down Expand Up @@ -3756,13 +3788,8 @@ test_sort_tables_offsets(void)
ret = tsk_treeseq_copy_tables(ts, &tables, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);

ret = tsk_table_collection_sort(&tables, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_SORT_MIGRATIONS_NOT_SUPPORTED);

tsk_migration_table_clear(&tables.migrations);
ret = tsk_table_collection_sort(&tables, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);

/* Check that setting edge offset = len(edges) does nothing */
reverse_edges(&tables);
ret = tsk_table_collection_copy(&tables, &copy, 0);
Expand All @@ -3773,6 +3800,18 @@ test_sort_tables_offsets(void)
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_FATAL(tsk_table_collection_equals(&tables, &copy, 0));

ret = tsk_table_collection_sort(&tables, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
/* Check that setting migration offset = len(migrations) does nothing */
reverse_migrations(&tables);
ret = tsk_table_collection_copy(&tables, &copy, TSK_NO_INIT);
CU_ASSERT_EQUAL_FATAL(ret, 0);
memset(&bookmark, 0, sizeof(bookmark));
bookmark.migrations = tables.migrations.num_rows;
ret = tsk_table_collection_sort(&tables, &bookmark, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_FATAL(tsk_table_collection_equals(&tables, &copy, 0));

ret = tsk_table_collection_sort(&tables, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_FATAL(tables.sites.num_rows > 2);
Expand Down Expand Up @@ -3942,6 +3981,15 @@ test_sort_tables_errors(void)
ret = tsk_table_collection_sort(&tables, &pos, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_EDGE_OUT_OF_BOUNDS);

memset(&pos, 0, sizeof(pos));
pos.migrations = (tsk_size_t) -1;
ret = tsk_table_collection_sort(&tables, &pos, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_MIGRATION_OUT_OF_BOUNDS);

pos.migrations = tables.migrations.num_rows + 1;
ret = tsk_table_collection_sort(&tables, &pos, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_MIGRATION_OUT_OF_BOUNDS);

/* Individual, node, population and provenance positions are ignored */
memset(&pos, 0, sizeof(pos));
pos.individuals = 1;
Expand All @@ -3963,13 +4011,8 @@ test_sort_tables_errors(void)
ret = tsk_table_collection_sort(&tables, &pos, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);

/* Setting migrations, sites or mutations gives a BAD_PARAM. See
/* Setting sites or mutations gives a BAD_PARAM. See
* github.com/tskit-dev/tskit/issues/101 */
memset(&pos, 0, sizeof(pos));
pos.migrations = 1;
ret = tsk_table_collection_sort(&tables, &pos, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_MIGRATIONS_NOT_SUPPORTED);

memset(&pos, 0, sizeof(pos));
pos.sites = 1;
ret = tsk_table_collection_sort(&tables, &pos, 0);
Expand All @@ -3980,12 +4023,6 @@ test_sort_tables_errors(void)
ret = tsk_table_collection_sort(&tables, &pos, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_SORT_OFFSET_NOT_SUPPORTED);

/* Migrations are not supported */
tsk_migration_table_add_row(&tables.migrations, 0, 1, 0, 0, 0, 0, NULL, 0);
CU_ASSERT_EQUAL_FATAL(tables.migrations.num_rows, 1);
ret = tsk_table_collection_sort(&tables, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_SORT_MIGRATIONS_NOT_SUPPORTED);

tsk_table_collection_free(&tables);
tsk_treeseq_free(&ts);
}
Expand Down Expand Up @@ -4179,6 +4216,51 @@ test_sort_tables_canonical(void)
tsk_table_collection_free(&t1);
}

static void
test_sort_tables_migrations(void)
{
int ret;
tsk_treeseq_t *ts;
tsk_table_collection_t tables, copy;

ts = caterpillar_tree(13, 1, 1);
ret = tsk_treeseq_copy_tables(ts, &tables, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_FATAL(tables.migrations.num_rows > 0);

ret = tsk_table_collection_copy(&tables, &copy, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_FATAL(tsk_table_collection_equals(&tables, &copy, 0));

reverse_migrations(&tables);
CU_ASSERT_FATAL(!tsk_table_collection_equals(&tables, &copy, 0));
ret = tsk_table_collection_sort(&tables, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_FATAL(tsk_migration_table_equals(&tables.migrations, &copy.migrations, 0));
CU_ASSERT_FATAL(tsk_table_collection_equals(&tables, &copy, 0));

/* Make sure we test the deeper comparison keys. The full key is
* (time, source, dest, left, node) */
tsk_migration_table_clear(&tables.migrations);

/* params = left, right, node, source, dest, time */
tsk_migration_table_add_row(&tables.migrations, 0, 1, 0, 0, 1, 0, NULL, 0);
tsk_migration_table_add_row(&tables.migrations, 0, 1, 1, 0, 1, 0, NULL, 0);
ret = tsk_migration_table_copy(&tables.migrations, &copy.migrations, TSK_NO_INIT);
CU_ASSERT_EQUAL_FATAL(ret, 0);

reverse_migrations(&tables);
CU_ASSERT_FATAL(!tsk_table_collection_equals(&tables, &copy, 0));
ret = tsk_table_collection_sort(&tables, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_FATAL(tsk_migration_table_equals(&tables.migrations, &copy.migrations, 0));

tsk_table_collection_free(&tables);
tsk_table_collection_free(&copy);
tsk_treeseq_free(ts);
free(ts);
}

static void
test_sorter_interface(void)
{
Expand Down Expand Up @@ -5942,6 +6024,7 @@ main(int argc, char **argv)
{ "test_sort_tables_edge_metadata", test_sort_tables_edge_metadata },
{ "test_sort_tables_no_edge_metadata", test_sort_tables_no_edge_metadata },
{ "test_sort_tables_mutation_times", test_sort_tables_mutation_times },
{ "test_sort_tables_migrations", test_sort_tables_migrations },
{ "test_edge_update_invalidates_index", test_edge_update_invalidates_index },
{ "test_copy_table_collection", test_copy_table_collection },
{ "test_sort_tables_errors", test_sort_tables_errors },
Expand Down
9 changes: 3 additions & 6 deletions c/tests/testlib.c
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Original file line number Diff line number Diff line change
Expand Up @@ -821,19 +821,16 @@ caterpillar_tree(tsk_size_t n, tsk_size_t num_sites, tsk_size_t num_mutations)
strlen(prov_timestamp), prov_record, strlen(prov_record));
CU_ASSERT_EQUAL_FATAL(ret, 0);

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

/* Add in some mock migrations. Must be done after sort as it doesn't support
* migrations.
* TODO make these consistent with the caterpillar tree topology. */
/* TODO make these consistent with the caterpillar tree topology. */
for (j = 0; j < n - 1; j++) {
m = j % num_metadatas;
ret = tsk_migration_table_add_row(&tables.migrations, 0, 1, j, j, j + 1, j + 1.5,
metadata[m], strlen(metadata[m]));
CU_ASSERT_FATAL(ret >= 0);
}

ret = tsk_table_collection_sort(&tables, 0, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_table_collection_build_index(&tables, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_table_collection_compute_mutation_parents(&tables, 0);
Expand Down
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