Fix issues with C implm; refactor lowlevel tests; remove nodes mode

tskit-dev · Aug 1, 2024 · 6318fad · 6318fad
1 parent 5d00273
commit 6318fad
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Showing 6 changed files with 321 additions and 252 deletions.
diff --git a/c/tests/test_stats.c b/c/tests/test_stats.c
@@ -306,8 +306,7 @@ verify_divergence_matrix(tsk_treeseq_t *ts, tsk_flags_t options)
 
 /* Check coalescence counts against naive implementation */
 static void
-verify_pair_coalescence_counts(tsk_treeseq_t *ts, tsk_size_t num_time_windows,
-    double *time_windows, tsk_flags_t options)
+verify_pair_coalescence_counts(tsk_treeseq_t *ts, tsk_flags_t options)
 {
     int ret;
     const tsk_size_t n = tsk_treeseq_get_num_samples(ts);
@@ -317,12 +316,17 @@ verify_pair_coalescence_counts(tsk_treeseq_t *ts, tsk_size_t num_time_windows,
     const double *breakpoints = tsk_treeseq_get_breakpoints(ts);
     const tsk_size_t P = 2;
     const tsk_size_t I = P * (P + 1) / 2;
+    tsk_id_t sample_sets[n];
     tsk_size_t sample_set_sizes[P];
     tsk_id_t index_tuples[2 * I];
     tsk_size_t dim = T * N * I;
     double C1[dim]; //, C2[dim];
     tsk_size_t i, j, k;
 
+    for (i = 0; i < n; i++) {
+        sample_sets[i] = samples[i];
+    }
+
     for (i = 0; i < P; i++) {
         sample_set_sizes[i] = 0;
     }
@@ -338,11 +342,52 @@ verify_pair_coalescence_counts(tsk_treeseq_t *ts, tsk_size_t num_time_windows,
         }
     }
 
-    ret = tsk_treeseq_pair_coalescence_stat(ts, P, sample_set_sizes, samples, I,
-        index_tuples, T, breakpoints, num_time_windows, time_windows, options, C1);
+    double max_time = tsk_treeseq_get_max_time(ts);
+    double time_windows[3] = { 0.0, max_time / 2, INFINITY };
+
+    ret = tsk_treeseq_pair_coalescence_stat(ts, P, sample_set_sizes, sample_sets, I,
+        index_tuples, T, breakpoints, 2, time_windows, options, C1);
+    CU_ASSERT_EQUAL_FATAL(ret, 0);
+
+    double trunc_time_windows[3] = { max_time * 0.2, max_time * 0.5, max_time * 0.8 };
+    ret = tsk_treeseq_pair_coalescence_stat(ts, P, sample_set_sizes, sample_sets, I,
+        index_tuples, T, breakpoints, 2, trunc_time_windows, options, C1);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
 
-    /* TODO: check against tree by tree implementation here */
+    /* cover errors */
+    double nil_time_windows[1] = { 0.0 };
+    ret = tsk_treeseq_pair_coalescence_stat(ts, P, sample_set_sizes, sample_sets, I,
+        index_tuples, T, breakpoints, 0, nil_time_windows, options, C1);
+    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_NUM_TIME_WINDOWS);
+
+    double bad_time_windows[2] = { 10.0, 0.0 };
+    ret = tsk_treeseq_pair_coalescence_stat(ts, P, sample_set_sizes, sample_sets, I,
+        index_tuples, T, breakpoints, 1, bad_time_windows, options, C1);
+    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_TIME_WINDOWS);
+
+    double bad_breakpoints[2] = { breakpoints[1], 0.0 };
+    ret = tsk_treeseq_pair_coalescence_stat(ts, P, sample_set_sizes, sample_sets, I,
+        index_tuples, 1, bad_breakpoints, 1, time_windows, options, C1);
+    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_WINDOWS);
+
+    index_tuples[0] = (tsk_id_t) P;
+    ret = tsk_treeseq_pair_coalescence_stat(ts, P, sample_set_sizes, sample_sets, I,
+        index_tuples, 1, breakpoints, 1, time_windows, options, C1);
+    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_SAMPLE_SET_INDEX);
+    index_tuples[0] = 0;
+
+    tsk_size_t tmp = sample_set_sizes[0];
+    sample_set_sizes[0] = 0;
+    ret = tsk_treeseq_pair_coalescence_stat(ts, P, sample_set_sizes, sample_sets, I,
+        index_tuples, 1, breakpoints, 1, time_windows, options, C1);
+    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_EMPTY_SAMPLE_SET);
+    sample_set_sizes[0] = tmp;
+
+    sample_sets[1] = 0;
+    ret = tsk_treeseq_pair_coalescence_stat(ts, P, sample_set_sizes, sample_sets, I,
+        index_tuples, 1, breakpoints, 1, time_windows, options, C1);
+    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_DUPLICATE_SAMPLE);
+    sample_sets[1] = 1;
 }
 
 typedef struct {
@@ -2833,15 +2878,10 @@ test_pair_coalescence_counts(void)
     tsk_treeseq_t ts;
     tsk_treeseq_from_text(&ts, 100, nonbinary_ex_nodes, nonbinary_ex_edges, NULL,
         nonbinary_ex_sites, nonbinary_ex_mutations, NULL, NULL, 0);
-    double max_time = tsk_treeseq_get_max_time(&ts);
-    double time_windows[3] = { 0.0, max_time / 2, INFINITY };
-    double trunc_windows[3] = { max_time * 0.2, max_time * 0.5, max_time * 0.8 };
-    verify_pair_coalescence_counts(&ts, 0, NULL, 0);
-    verify_pair_coalescence_counts(&ts, 0, NULL, TSK_STAT_SPAN_NORMALISE);
-    verify_pair_coalescence_counts(&ts, 2, time_windows, 0);
-    verify_pair_coalescence_counts(&ts, 2, time_windows, TSK_STAT_SPAN_NORMALISE);
-    verify_pair_coalescence_counts(&ts, 2, trunc_windows, 0);
-    verify_pair_coalescence_counts(&ts, 2, trunc_windows, TSK_STAT_SPAN_NORMALISE);
+    verify_pair_coalescence_counts(&ts, TSK_STAT_NODE);
+    verify_pair_coalescence_counts(&ts, TSK_STAT_NODE | TSK_STAT_SPAN_NORMALISE);
+    verify_pair_coalescence_counts(&ts, 0);
+    verify_pair_coalescence_counts(&ts, TSK_STAT_SPAN_NORMALISE);
     tsk_treeseq_free(&ts);
 }