Check mutation parents on tree sequence init

c/CHANGELOG.rst

@@ -1,3 +1,35 @@
+--------------------
+[1.2.0] - 2025-XX-XX
+--------------------
+
+**Breaking changes**
+
+- ``tsk_treeseq_init`` now requires that mutation parents in the table collection
+  are correct and consistent with the topology of the tree at each mutation site.
+  Returns ``TSK_ERR_BAD_MUTATION_PARENT`` if this is not the case, or 
+  ``TSK_ERR_MUTATION_PARENT_AFTER_CHILD`` if the mutations are not in an order
+  compatible with the correct mutation parent.
+  (:user:`benjeffery`, :issue:`2729`, :issue:`2732`, :pr:`3212`).
+
+**Features**
+
+- Add ``TSK_TS_INIT_COMPUTE_MUTATION_PARENTS`` to ``tsk_treeseq_init``
+  to compute mutation parents from the tree sequence topology.
+  Note that the mutations must be in the correct order.
+  (:user:`benjeffery`, :issue:`2757`, :pr:`3212`).
+
+- Add ``TSK_CHECK_MUTATION_PARENTS`` option to ``tsk_table_collection_check_integrity``
+  to check that mutation parents are consistent with the tree sequence topology.
+  This option implies ``TSK_CHECK_TREES``.
+  (:user:`benjeffery`, :issue:`2729`, :issue:`2732`, :pr:`3212`).
+
+- Add the ``TSK_NO_CHECK_INTEGRITY`` option to ``tsk_table_collection_compute_mutation_parents``
+  to skip the integrity checks that are normally run when computing mutation parents.
+  This is useful for speeding up the computation of mutation parents when the
+  tree sequence is certainly known to be valid.
+  (:user:`benjeffery`, :pr:`3212`).
+
+
 --------------------
 [1.1.4] - 2025-03-31
 --------------------

c/tests/test_tables.c

@@ -9011,7 +9011,7 @@ test_sort_tables_mutation_times(void)
     CU_ASSERT_EQUAL_FATAL(ret, 0);
 
     /* Check to make sure we have legal mutations */
-    ret = tsk_treeseq_init(&ts, &tables, 0);
+    ret = tsk_treeseq_init(&ts, &tables, TSK_TS_INIT_COMPUTE_MUTATION_PARENTS);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
 
     ret = tsk_treeseq_copy_tables(&ts, &t1, 0);
@@ -10576,6 +10576,64 @@ test_table_collection_check_integrity_bad_indexes(void)
     tsk_table_collection_free(&tables);
 }
 
+static void
+test_check_integrity_bad_mutation_parent_topology(void)
+{
+    int ret;
+    tsk_id_t ret_trees;
+    tsk_table_collection_t tables;
+    const char *sites = "0       0\n";
+    /* Make a mutation on a parallel branch the parent*/
+    const char *bad_mutations = "0   0  1  -1\n"
+                                "0   1  1  0\n";
+
+    /* A mutation above is set as child*/
+    const char *reverse_mutations = "0   0  1  -1\n"
+                                    "0   4  1  0\n";
+
+    const char *reverse_sites = "0.5       0\n"
+                                "0       0\n";
+
+    ret = tsk_table_collection_init(&tables, 0);
+    CU_ASSERT_EQUAL_FATAL(ret, 0);
+
+    tables.sequence_length = 1;
+    parse_nodes(single_tree_ex_nodes, &tables.nodes);
+    CU_ASSERT_EQUAL_FATAL(tables.nodes.num_rows, 7);
+    parse_edges(single_tree_ex_edges, &tables.edges);
+    CU_ASSERT_EQUAL_FATAL(tables.edges.num_rows, 6);
+    parse_sites(sites, &tables.sites);
+    CU_ASSERT_EQUAL_FATAL(tables.sites.num_rows, 1);
+    parse_mutations(bad_mutations, &tables.mutations);
+    CU_ASSERT_EQUAL_FATAL(tables.mutations.num_rows, 2);
+    tables.sequence_length = 1.0;
+
+    ret = tsk_table_collection_build_index(&tables, 0);
+    CU_ASSERT_EQUAL_FATAL(ret, 0);
+
+    ret_trees = tsk_table_collection_check_integrity(&tables, TSK_CHECK_TREES);
+    CU_ASSERT_EQUAL_FATAL(ret_trees, 1);
+    ret_trees
+        = tsk_table_collection_check_integrity(&tables, TSK_CHECK_MUTATION_PARENTS);
+    CU_ASSERT_EQUAL_FATAL(ret_trees, TSK_ERR_BAD_MUTATION_PARENT);
+
+    parse_mutations(reverse_mutations, &tables.mutations);
+    ret_trees = tsk_table_collection_check_integrity(&tables, TSK_CHECK_TREES);
+    CU_ASSERT_EQUAL_FATAL(ret_trees, 1);
+    ret_trees
+        = tsk_table_collection_check_integrity(&tables, TSK_CHECK_MUTATION_PARENTS);
+    CU_ASSERT_EQUAL_FATAL(ret_trees, TSK_ERR_MUTATION_PARENT_AFTER_CHILD);
+
+    /* Now check that TSK_CHECK_MUTATION_PARENTS implies TSK_CHECK_TREES
+       by triggering an error with reversed sites */
+    parse_sites(reverse_sites, &tables.sites);
+    ret_trees
+        = tsk_table_collection_check_integrity(&tables, TSK_CHECK_MUTATION_PARENTS);
+    CU_ASSERT_EQUAL_FATAL(ret_trees, TSK_ERR_UNSORTED_SITES);
+
+    tsk_table_collection_free(&tables);
+}
+
 static void
 test_table_collection_subset_with_options(tsk_flags_t options)
 {
@@ -11658,6 +11716,8 @@ main(int argc, char **argv)
             test_table_collection_check_integrity_bad_indexes_example },
         { "test_table_collection_check_integrity_bad_indexes",
             test_table_collection_check_integrity_bad_indexes },
+        { "test_check_integrity_bad_mutation_parent_topology",
+            test_check_integrity_bad_mutation_parent_topology },
         { "test_table_collection_subset", test_table_collection_subset },
         { "test_table_collection_subset_unsorted",
             test_table_collection_subset_unsorted },

c/tests/test_trees.c

@@ -3886,16 +3886,16 @@ test_simplest_mutation_edges(void)
                         "1  2   2   0\n";
     const char *sites = "0.5  0\n"
                         "1.5  0\n";
-    const char *mutations = "0    1     1\n"
+    const char *mutations = "0    2     1\n"
+                            "0    1     1\n"
                             "0    0     1\n"
-                            "0    2     1\n"
-                            "1    0     1\n"
+                            "1    2     1\n"
                             "1    1     1\n"
-                            "1    2     1\n";
+                            "1    0     1\n";
     tsk_treeseq_t ts;
     tsk_tree_t tree;
     /* We have mutations over roots, samples and just isolated nodes */
-    tsk_id_t mutation_edges[] = { -1, 0, -1, 1, -1, -1 };
+    tsk_id_t mutation_edges[] = { -1, -1, 0, -1, -1, 1 };
     tsk_size_t i, j, k, t;
     tsk_mutation_t mut;
     tsk_site_t site;
@@ -4238,7 +4238,7 @@ test_single_tree_bad_mutations(void)
     ret = tsk_treeseq_init(&ts, &tables, load_flags);
     CU_ASSERT_EQUAL(ret, TSK_ERR_MUTATION_PARENT_AFTER_CHILD);
     tsk_treeseq_free(&ts);
-    tables.mutations.parent[3] = TSK_NULL;
+    tables.mutations.parent[3] = 2;
 
     /* time < node time */
     tables.mutations.time[2] = 0;
@@ -8715,6 +8715,112 @@ test_init_take_ownership_no_edge_metadata(void)
     tsk_treeseq_free(&ts);
 }
 
+static void
+test_init_compute_mutation_parents(void)
+{
+    int ret;
+    tsk_table_collection_t *tables, *tables2;
+    tsk_treeseq_t ts;
+    const char *sites = "0       0\n";
+    /* Make a mutation on a parallel branch the parent*/
+    const char *bad_mutations = "0   0  1  -1\n"
+                                "0   1  1  0\n";
+
+    tables = tsk_malloc(sizeof(tsk_table_collection_t));
+    CU_ASSERT_NOT_EQUAL_FATAL(tables, NULL);
+    tables2 = tsk_malloc(sizeof(tsk_table_collection_t));
+    CU_ASSERT_NOT_EQUAL_FATAL(tables2, NULL);
+
+    CU_ASSERT_FATAL(tables != NULL);
+    ret = tsk_table_collection_init(tables, 0);
+    CU_ASSERT_EQUAL_FATAL(ret, 0);
+
+    tables->sequence_length = 1;
+    parse_nodes(single_tree_ex_nodes, &tables->nodes);
+    CU_ASSERT_EQUAL_FATAL(tables->nodes.num_rows, 7);
+    parse_edges(single_tree_ex_edges, &tables->edges);
+    CU_ASSERT_EQUAL_FATAL(tables->edges.num_rows, 6);
+    parse_sites(sites, &tables->sites);
+    CU_ASSERT_EQUAL_FATAL(tables->sites.num_rows, 1);
+    parse_mutations(bad_mutations, &tables->mutations);
+    CU_ASSERT_EQUAL_FATAL(tables->mutations.num_rows, 2);
+    tables->sequence_length = 1.0;
+    ret = tsk_table_collection_copy(tables, tables2, 0);
+    CU_ASSERT_EQUAL_FATAL(ret, 0);
+
+    ret = tsk_treeseq_init(&ts, tables, TSK_TS_INIT_BUILD_INDEXES);
+    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_MUTATION_PARENT);
+    tsk_treeseq_free(&ts);
+
+    ret = tsk_treeseq_init(
+        &ts, tables, TSK_TS_INIT_BUILD_INDEXES | TSK_TS_INIT_COMPUTE_MUTATION_PARENTS);
+    CU_ASSERT_EQUAL_FATAL(ret, 0);
+    tsk_treeseq_free(&ts);
+
+    /* When we use take ownership, the check of parents shouldn't overwrite them*/
+    ret = tsk_treeseq_init(&ts, tables, TSK_TAKE_OWNERSHIP | TSK_TS_INIT_BUILD_INDEXES);
+    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_MUTATION_PARENT);
+    CU_ASSERT_EQUAL(tables->mutations.parent[0], -1);
+    CU_ASSERT_EQUAL(tables->mutations.parent[1], 0);
+    tsk_treeseq_free(&ts);
+
+    /* When we use take ownership and compute, the tables are overwritten*/
+    ret = tsk_treeseq_init(&ts, tables2,
+        TSK_TAKE_OWNERSHIP | TSK_TS_INIT_BUILD_INDEXES
+            | TSK_TS_INIT_COMPUTE_MUTATION_PARENTS);
+    CU_ASSERT_EQUAL_FATAL(ret, 0);
+    CU_ASSERT_EQUAL(tables2->mutations.parent[0], -1);
+    CU_ASSERT_EQUAL(tables2->mutations.parent[1], -1);
+
+    /* Don't need to free tables as we took ownership */
+    tsk_treeseq_free(&ts);
+}
+
+static void
+test_init_compute_mutation_parents_errors(void)
+{
+    int ret;
+    tsk_id_t row_ret;
+    tsk_table_collection_t tables;
+    tsk_treeseq_t ts;
+    const char *sites = "0.5       0\n"
+                        "0         0\n";
+
+    ret = tsk_table_collection_init(&tables, 0);
+    CU_ASSERT_EQUAL_FATAL(ret, 0);
+
+    tables.sequence_length = 1;
+    parse_nodes(single_tree_ex_nodes, &tables.nodes);
+    CU_ASSERT_EQUAL_FATAL(tables.nodes.num_rows, 7);
+    parse_edges(single_tree_ex_edges, &tables.edges);
+    CU_ASSERT_EQUAL_FATAL(tables.edges.num_rows, 6);
+    parse_sites(sites, &tables.sites);
+    CU_ASSERT_EQUAL_FATAL(tables.sites.num_rows, 2);
+    tables.sequence_length = 1.0;
+
+    ret = tsk_treeseq_init(
+        &ts, &tables, TSK_TS_INIT_BUILD_INDEXES | TSK_TS_INIT_COMPUTE_MUTATION_PARENTS);
+    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_UNSORTED_SITES);
+    tsk_treeseq_free(&ts);
+
+    tsk_site_table_clear(&tables.sites);
+    row_ret = tsk_site_table_add_row(&tables.sites, 0.5, "A", 1, NULL, 0);
+    CU_ASSERT_EQUAL_FATAL(row_ret, 0);
+    row_ret = tsk_mutation_table_add_row(
+        &tables.mutations, 0, 0, TSK_NULL, TSK_UNKNOWN_TIME, "A", 1, NULL, 0);
+    CU_ASSERT_EQUAL_FATAL(row_ret, 0);
+    row_ret = tsk_mutation_table_add_row(
+        &tables.mutations, 0, 4, TSK_NULL, TSK_UNKNOWN_TIME, "A", 1, NULL, 0);
+    CU_ASSERT_EQUAL_FATAL(row_ret, 1);
+
+    ret = tsk_treeseq_init(
+        &ts, &tables, TSK_TS_INIT_BUILD_INDEXES | TSK_TS_INIT_COMPUTE_MUTATION_PARENTS);
+    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_MUTATION_PARENT_AFTER_CHILD);
+    tsk_treeseq_free(&ts);
+
+    tsk_table_collection_free(&tables);
+}
+
 int
 main(int argc, char **argv)
 {
@@ -8923,6 +9029,9 @@ main(int argc, char **argv)
             test_extend_haplotypes_conflicting_times },
         { "test_init_take_ownership_no_edge_metadata",
             test_init_take_ownership_no_edge_metadata },
+        { "test_init_compute_mutation_parents", test_init_compute_mutation_parents },
+        { "test_init_compute_mutation_parents_errors",
+            test_init_compute_mutation_parents_errors },
         { NULL, NULL },
     };
 

c/tests/testlib.c

@@ -767,6 +767,8 @@ tsk_treeseq_from_text(tsk_treeseq_t *ts, double sequence_length, const char *nod
     tsk_table_collection_t tables;
     tsk_id_t max_population_id;
     tsk_size_t j;
+    tsk_flags_t ts_flags;
+    bool all_parents_null;
 
     CU_ASSERT_FATAL(ts != NULL);
     CU_ASSERT_FATAL(nodes != NULL);
@@ -807,7 +809,21 @@ tsk_treeseq_from_text(tsk_treeseq_t *ts, double sequence_length, const char *nod
         }
     }
 
-    ret = tsk_treeseq_init(ts, &tables, TSK_TS_INIT_BUILD_INDEXES);
+    /* If all mutation.parent are TSK_NULL, use TSK_TS_COMPUTE_MUTATION_PARENTS flag too
+     */
+    ts_flags = TSK_TS_INIT_BUILD_INDEXES;
+    all_parents_null = true;
+    for (j = 0; j < tables.mutations.num_rows; j++) {
+        if (tables.mutations.parent[j] != TSK_NULL) {
+            all_parents_null = false;
+            break;
+        }
+    }
+    if (all_parents_null) {
+        ts_flags |= TSK_TS_INIT_COMPUTE_MUTATION_PARENTS;
+    }
+
+    ret = tsk_treeseq_init(ts, &tables, ts_flags);
     /* tsk_treeseq_print_state(ts, stdout); */
     if (ret != 0) {
         printf("\nret = %s\n", tsk_strerror(ret));

c/tskit/core.c

@@ -347,6 +347,12 @@ tsk_strerror_internal(int err)
                   "(TSK_ERR_DISALLOWED_UNKNOWN_MUTATION_TIME)";
             break;
 
+        case TSK_ERR_BAD_MUTATION_PARENT:
+            ret = "A mutation's parent is not consistent with the topology of the tree. "
+                  "Use compute_mutation_parents to set the parents correctly."
+                  "(TSK_ERR_BAD_MUTATION_PARENT)";
+            break;
+
         /* Migration errors */
         case TSK_ERR_UNSORTED_MIGRATIONS:
             ret = "Migrations must be sorted by time. (TSK_ERR_UNSORTED_MIGRATIONS)";

c/tskit/core.h

@@ -510,6 +510,12 @@ Some mutations have TSK_UNKNOWN_TIME in an algorithm where that's
 disallowed (use compute_mutation_times?).
 */
 #define TSK_ERR_DISALLOWED_UNKNOWN_MUTATION_TIME                    -510
+
+/** 
+A mutation's parent was not consistent with the topology of the tree.
+ */
+#define TSK_ERR_BAD_MUTATION_PARENT                                 -511
+
 /** @} */
 
 /**