Mark samples and index tables

jeromekelleher · Jan 19, 2023 · 5d60e6f · 5d60e6f
1 parent dd99990
commit 5d60e6f
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diff --git a/c/examples/haploid_wright_fisher.c b/c/examples/haploid_wright_fisher.c
@@ -92,6 +92,12 @@ main(int argc, char **argv)
     check_tsk_error(ret);
     srand((unsigned)atoi(argv[5]));
     simulate(&tables, atoi(argv[1]), atoi(argv[2]), atoi(argv[3]));
+
+    /* Sort and index so that the result can be opened as a tree sequence */
+    ret = tsk_table_collection_sort(&tables, NULL, 0);
+    check_tsk_error(ret);
+    ret = tsk_table_collection_build_index(&tables, 0);
+    check_tsk_error(ret);
     ret = tsk_table_collection_dump(&tables, argv[4], 0);
     check_tsk_error(ret);
 

diff --git a/c/examples/multichrom_wright_fisher.c b/c/examples/multichrom_wright_fisher.c
@@ -243,6 +243,10 @@ simulate(
             simplify_tables(tcs, num_chunks, children, N);
         }
     }
+    /* Set the sample flags for final generation */
+    for (j = 0; j < N; j++) {
+        tcs[0].nodes.flags[children[j]] = TSK_NODE_IS_SAMPLE;
+    }
     free(buffer);
 }