Merge branch 'develop'

tskit-dev · Nov 27, 2015 · 7a1b4e0 · 7a1b4e0
2 parents cc9eec5 + 5d766cc
commit 7a1b4e0
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Showing 7 changed files with 202 additions and 137 deletions.
diff --git a/lib/dev.cfg b/lib/dev.cfg
@@ -1,5 +1,5 @@
 # Development config file
-sample_size = 20;
+sample_size = 9;
 num_loci = 57;
 random_seed = 878638576;
 # The scaled recombination rate, 4 Ne rho. Note that unlike ms

diff --git a/lib/main.c b/lib/main.c
@@ -406,41 +406,46 @@ run_simulate(char *conf_file)
     if (ret != 0) {
         goto out;
     }
-    result = msp_run(msp, DBL_MAX, ULONG_MAX);
-    if (result < 0) {
-        ret = result;
-        goto out;
+    result = 1;
+    while (result == 1) {
+        result = msp_run(msp, DBL_MAX, 1);
+        if (result < 0) {
+            ret = result;
+            goto out;
+        }
+        msp_verify(msp);
+        /* ret = msp_print_state(msp); */
     }
     ret = msp_print_state(msp);
     if (ret != 0) {
         goto out;
     }
-    /* Create the tree_sequence from the state of the simulator. */
-    ret = tree_sequence_create(tree_seq, msp);
-    if (ret != 0) {
-        goto out;
-    }
-    ret = tree_sequence_generate_mutations(tree_seq,
-            mutation_params.mutation_rate, mutation_params.random_seed);
-    if (ret != 0) {
-        goto out;
-    }
-    int j;
-    for (j = 0; j < 1; j++) {
-        ret = tree_sequence_dump(tree_seq, output_file, 0);
+    if (0) {
+        /* Create the tree_sequence from the state of the simulator. */
+        ret = tree_sequence_create(tree_seq, msp);
         if (ret != 0) {
             goto out;
         }
-        tree_sequence_free(tree_seq);
-        memset(tree_seq, 0, sizeof(tree_sequence_t));
-        ret = tree_sequence_load(tree_seq, output_file, 0);
+        ret = tree_sequence_generate_mutations(tree_seq,
+                mutation_params.mutation_rate, mutation_params.random_seed);
         if (ret != 0) {
             goto out;
         }
-    }
-    print_tree_sequence(tree_seq);
-    print_haplotypes(tree_seq);
-    if (0) {
+        int j;
+        for (j = 0; j < 1; j++) {
+            ret = tree_sequence_dump(tree_seq, output_file, 0);
+            if (ret != 0) {
+                goto out;
+            }
+            tree_sequence_free(tree_seq);
+            memset(tree_seq, 0, sizeof(tree_sequence_t));
+            ret = tree_sequence_load(tree_seq, output_file, 0);
+            if (ret != 0) {
+                goto out;
+            }
+        }
+        print_tree_sequence(tree_seq);
+        print_haplotypes(tree_seq);
         tree_sequence_print_state(tree_seq);
         print_newick_trees(tree_seq);
         tree_sequence_print_state(tree_seq);