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Avoid copy in tsk_treeseq_simplify #2288

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Merged
merged 1 commit into from
May 20, 2022
Merged

Avoid copy in tsk_treeseq_simplify #2288

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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 @@ -40,6 +40,9 @@
- Add ``edge`` attribute to ``mutation_t`` struct make available in tree sequence.
(:user:`jeromekelleher`, :issue:`685`, :pr:`2279`)

- Reduce peak memory usage in ``tsk_treeseq_simplify``.
(:user:`jeromekelleher`, :issue:`2287`, :pr:`2288`)

----------------------
[0.99.15] - 2021-12-07
----------------------
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21 changes: 15 additions & 6 deletions c/tskit/trees.c
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Original file line number Diff line number Diff line change
Expand Up @@ -3227,20 +3227,29 @@ tsk_treeseq_simplify(const tsk_treeseq_t *self, const tsk_id_t *samples,
tsk_id_t *node_map)
{
int ret = 0;
tsk_table_collection_t tables;
tsk_table_collection_t *tables = tsk_malloc(sizeof(*tables));

ret = tsk_treeseq_copy_tables(self, &tables, 0);
if (tables == NULL) {
ret = TSK_ERR_NO_MEMORY;
goto out;
}
ret = tsk_treeseq_copy_tables(self, tables, 0);
if (ret != 0) {
goto out;
}
ret = tsk_table_collection_simplify(
&tables, samples, num_samples, options, node_map);
ret = tsk_table_collection_simplify(tables, samples, num_samples, options, node_map);
if (ret != 0) {
goto out;
}
ret = tsk_treeseq_init(output, &tables, TSK_TS_INIT_BUILD_INDEXES);
ret = tsk_treeseq_init(
output, tables, TSK_TS_INIT_BUILD_INDEXES | TSK_TAKE_OWNERSHIP);
/* Once tsk_tree_init has returned ownership of tables is transferred */
tables = NULL;
out:
tsk_table_collection_free(&tables);
if (tables != NULL) {
tsk_table_collection_free(tables);
tsk_safe_free(tables);
}
return ret;
}

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