WIP

Author: benjeffery

c/tskit/tables.c

@@ -160,6 +160,7 @@ cast_offset_array(read_table_ragged_col_t *col, uint32_t *source, tsk_size_t num
     for (j = 0; j < len; j++) {
         dest[j] = source[j];
     }
+    tsk_safe_free(source);
 out:
     return ret;
 }
@@ -328,18 +329,19 @@ read_table(kastore_t *store, tsk_size_t *num_rows, read_table_col_t *cols,
     return ret;
 }
 
-static void
-free_read_table_mem(read_table_col_t *TSK_UNUSED(cols),
-    read_table_ragged_col_t *ragged_cols, read_table_property_t *TSK_UNUSED(properties))
-{
-    read_table_ragged_col_t *ragged_col;
+// static void
+// free_read_table_mem(read_table_col_t *TSK_UNUSED(cols),
+//     read_table_ragged_col_t *ragged_cols, read_table_property_t
+//     *TSK_UNUSED(properties))
+// {
+//     read_table_ragged_col_t *ragged_col;
 
-    if (ragged_cols != NULL) {
-        for (ragged_col = ragged_cols; ragged_col->name != NULL; ragged_col++) {
-            tsk_safe_free(ragged_col->offset_array_mem);
-        }
-    }
-}
+//     if (ragged_cols != NULL) {
+//         for (ragged_col = ragged_cols; ragged_col->name != NULL; ragged_col++) {
+//             tsk_safe_free(ragged_col->offset_array_mem);
+//         }
+//     }
+// }
 
 static int
 write_offset_col(
@@ -1681,7 +1683,7 @@ tsk_individual_table_load(tsk_individual_table_t *self, kastore_t *store)
     if (ret != 0) {
         goto out;
     }
-    ret = tsk_individual_table_set_columns(self, num_rows, flags, location,
+    ret = tsk_individual_table_takeset_columns(self, num_rows, flags, location,
         location_offset, parents, parents_offset, metadata, metadata_offset);
     if (ret != 0) {
         goto out;
@@ -1694,7 +1696,7 @@ tsk_individual_table_load(tsk_individual_table_t *self, kastore_t *store)
         }
     }
 out:
-    free_read_table_mem(cols, ragged_cols, properties);
+    // free_read_table_mem(cols, ragged_cols, properties);
     return ret;
 }
 
@@ -2317,7 +2319,7 @@ tsk_node_table_load(tsk_node_table_t *self, kastore_t *store)
     if (ret != 0) {
         goto out;
     }
-    ret = tsk_node_table_set_columns(
+    ret = tsk_node_table_takeset_columns(
         self, num_rows, flags, time, population, individual, metadata, metadata_offset);
     if (ret != 0) {
         goto out;
@@ -2330,7 +2332,7 @@ tsk_node_table_load(tsk_node_table_t *self, kastore_t *store)
         }
     }
 out:
-    free_read_table_mem(cols, ragged_cols, properties);
+    // free_read_table_mem(cols, ragged_cols, properties);
     return ret;
 }
 
@@ -2990,7 +2992,7 @@ tsk_edge_table_load(tsk_edge_table_t *self, kastore_t *store)
     if (ret != 0) {
         goto out;
     }
-    ret = tsk_edge_table_set_columns(
+    ret = tsk_edge_table_takeset_columns(
         self, num_rows, left, right, parent, child, metadata, metadata_offset);
     if (ret != 0) {
         goto out;
@@ -3003,7 +3005,7 @@ tsk_edge_table_load(tsk_edge_table_t *self, kastore_t *store)
         }
     }
 out:
-    free_read_table_mem(cols, ragged_cols, properties);
+    // free_read_table_mem(cols, ragged_cols, properties);
     return ret;
 }
 
@@ -3702,7 +3704,7 @@ tsk_site_table_load(tsk_site_table_t *self, kastore_t *store)
     if (ret != 0) {
         goto out;
     }
-    ret = tsk_site_table_set_columns(self, num_rows, position, ancestral_state,
+    ret = tsk_site_table_takeset_columns(self, num_rows, position, ancestral_state,
         ancestral_state_offset, metadata, metadata_offset);
     if (ret != 0) {
         goto out;
@@ -3715,7 +3717,7 @@ tsk_site_table_load(tsk_site_table_t *self, kastore_t *store)
         }
     }
 out:
-    free_read_table_mem(cols, ragged_cols, properties);
+    // free_read_table_mem(cols, ragged_cols, properties);
     return ret;
 }
 
@@ -4450,7 +4452,7 @@ tsk_mutation_table_load(tsk_mutation_table_t *self, kastore_t *store)
     if (ret != 0) {
         goto out;
     }
-    ret = tsk_mutation_table_set_columns(self, num_rows, site, node, parent, time,
+    ret = tsk_mutation_table_takeset_columns(self, num_rows, site, node, parent, time,
         derived_state, derived_state_offset, metadata, metadata_offset);
     if (ret != 0) {
         goto out;
@@ -4463,7 +4465,7 @@ tsk_mutation_table_load(tsk_mutation_table_t *self, kastore_t *store)
         }
     }
 out:
-    free_read_table_mem(cols, ragged_cols, properties);
+    // free_read_table_mem(cols, ragged_cols, properties);
     return ret;
 }
 
@@ -5085,7 +5087,7 @@ tsk_migration_table_load(tsk_migration_table_t *self, kastore_t *store)
     if (ret != 0) {
         goto out;
     }
-    ret = tsk_migration_table_set_columns(self, num_rows, left, right, node, source,
+    ret = tsk_migration_table_takeset_columns(self, num_rows, left, right, node, source,
         dest, time, metadata, metadata_offset);
     if (ret != 0) {
         goto out;
@@ -5098,7 +5100,7 @@ tsk_migration_table_load(tsk_migration_table_t *self, kastore_t *store)
         }
     }
 out:
-    free_read_table_mem(cols, ragged_cols, properties);
+    // free_read_table_mem(cols, ragged_cols, properties);
     return ret;
 }
 
@@ -5623,7 +5625,8 @@ tsk_population_table_load(tsk_population_table_t *self, kastore_t *store)
     if (ret != 0) {
         goto out;
     }
-    ret = tsk_population_table_set_columns(self, num_rows, metadata, metadata_offset);
+    ret = tsk_population_table_takeset_columns(
+        self, num_rows, metadata, metadata_offset);
     if (ret != 0) {
         goto out;
     }
@@ -5635,7 +5638,7 @@ tsk_population_table_load(tsk_population_table_t *self, kastore_t *store)
         }
     }
 out:
-    free_read_table_mem(NULL, ragged_cols, properties);
+    // free_read_table_mem(NULL, ragged_cols, properties);
     return ret;
 }
 
@@ -6226,13 +6229,13 @@ tsk_provenance_table_load(tsk_provenance_table_t *self, kastore_t *store)
     if (ret != 0) {
         goto out;
     }
-    ret = tsk_provenance_table_set_columns(
+    ret = tsk_provenance_table_takeset_columns(
         self, num_rows, timestamp, timestamp_offset, record, record_offset);
     if (ret != 0) {
         goto out;
     }
 out:
-    free_read_table_mem(NULL, ragged_cols, NULL);
+    // free_read_table_mem(NULL, ragged_cols, NULL);
     return ret;
 }
 
@@ -11042,11 +11045,12 @@ tsk_table_collection_loadf_inited(
     int ret = 0;
     kastore_t store;
 
-    int kas_flags = KAS_READ_ALL;
+    int kas_flags = KAS_READ_ALL | KAS_GET_TAKES_OWNERSHIP;
     if ((options & TSK_LOAD_SKIP_TABLES)
         || (options & TSK_LOAD_SKIP_REFERENCE_SEQUENCE)) {
         kas_flags = 0;
     }
+    printf("WTF");
     ret = kastore_openf(&store, file, "r", kas_flags);
 
     if (ret != 0) {