More tests for C side

Author: benjeffery

c/tests/test_genotypes.c

@@ -1367,6 +1367,64 @@ test_alignments_discrete_genome_required(void)
     tsk_treeseq_free(&ts);
 }
 
+static void
+test_alignments_null_reference(void)
+{
+    int ret = 0;
+    tsk_treeseq_t ts;
+    const tsk_id_t *samples;
+    tsk_size_t n;
+    char buf[10];
+
+    build_balanced_three_example_align(&ts);
+    samples = tsk_treeseq_get_samples(&ts);
+    n = tsk_treeseq_get_num_samples(&ts);
+
+    ret = tsk_treeseq_decode_alignments(&ts, NULL, 10, samples, n, 0, 10, 'N', buf, 0);
+    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_PARAM_VALUE);
+    tsk_treeseq_free(&ts);
+}
+
+static void
+test_alignments_null_nodes_or_buf(void)
+{
+    int ret = 0;
+    tsk_treeseq_t ts;
+    const char *ref = "NNNNNNNNNN";
+    const tsk_id_t *samples;
+    tsk_size_t n;
+    char buf[30];
+
+    build_balanced_three_example_align(&ts);
+    samples = tsk_treeseq_get_samples(&ts);
+    n = tsk_treeseq_get_num_samples(&ts);
+
+    ret = tsk_treeseq_decode_alignments(&ts, ref, 10, NULL, n, 0, 10, 'N', buf, 0);
+    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_PARAM_VALUE);
+
+    ret = tsk_treeseq_decode_alignments(&ts, ref, 10, samples, n, 0, 10, 'N', NULL, 0);
+    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_PARAM_VALUE);
+
+    tsk_treeseq_free(&ts);
+}
+
+static void
+test_alignments_node_out_of_bounds(void)
+{
+    int ret = 0;
+    tsk_treeseq_t ts;
+    const char *ref = "NNNNNNNNNN";
+    tsk_id_t bad_node;
+    char buf[10];
+
+    build_balanced_three_example_align(&ts);
+    bad_node = (tsk_id_t) tsk_treeseq_get_num_nodes(&ts);
+
+    ret = tsk_treeseq_decode_alignments(&ts, ref, 10, &bad_node, 1, 0, 10, 'N', buf, 0);
+    CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_NODE_OUT_OF_BOUNDS);
+    tsk_treeseq_free(&ts);
+}
+
 static void
 test_alignments_isolated_as_not_missing(void)
 {
@@ -1612,6 +1670,9 @@ main(int argc, char **argv)
         { "test_alignments_non_integer_bounds", test_alignments_non_integer_bounds },
         { "test_alignments_discrete_genome_required",
             test_alignments_discrete_genome_required },
+        { "test_alignments_null_reference", test_alignments_null_reference },
+        { "test_alignments_null_nodes_or_buf", test_alignments_null_nodes_or_buf },
+        { "test_alignments_node_out_of_bounds", test_alignments_node_out_of_bounds },
         { "test_alignments_missing_char_collision",
             test_alignments_missing_char_collision },
         { "test_alignments_zero_nodes_ok", test_alignments_zero_nodes_ok },

python/tests/test_lowlevel.py

@@ -3348,6 +3348,61 @@ def test_missing_char_validation(self):
         with pytest.raises(TypeError, match="single character"):
             ts.decode_alignments(ref, nodes, 0, ts.get_sequence_length(), "NN", True)
 
+    def test_argument_parsing_error(self):
+        ts = self.get_simple_example()
+        ref = b"NNNNNNNNNN"
+        nodes = np.array(ts.get_samples(), dtype=np.int32)
+        # left must be a float-like value
+        with pytest.raises(TypeError):
+            ts.decode_alignments(
+                ref, nodes, "bad_left", ts.get_sequence_length(), "N", True
+            )
+
+    def test_reference_sequence_type_validation(self):
+        ts = self.get_simple_example()
+        ref = "NNNNNNNNNN"
+        nodes = np.array(ts.get_samples(), dtype=np.int32)
+        with pytest.raises(TypeError, match="must be bytes"):
+            ts.decode_alignments(ref, nodes, 0, ts.get_sequence_length(), "N", True)
+
+    def test_missing_char_type_validation(self):
+        ts = self.get_simple_example()
+        ref = b"NNNNNNNNNN"
+        nodes = np.array(ts.get_samples(), dtype=np.int32)
+        with pytest.raises(TypeError, match="length 1"):
+            ts.decode_alignments(ref, nodes, 0, ts.get_sequence_length(), b"N", True)
+
+    def test_missing_char_unicode_error(self):
+        ts = self.get_simple_example()
+        ref = b"NNNNNNNNNN"
+        nodes = np.array(ts.get_samples(), dtype=np.int32)
+        with pytest.raises(UnicodeEncodeError):
+            ts.decode_alignments(
+                ref,
+                nodes,
+                0,
+                ts.get_sequence_length(),
+                NON_UTF8_STRING,
+                True,
+            )
+
+    def test_isolated_as_missing_flag_false(self):
+        ts = self.get_simple_example()
+        ref = b"NNNNNNNNNN"
+        nodes = np.array(ts.get_samples(), dtype=np.int32)
+        buf = ts.decode_alignments(
+            ref,
+            nodes,
+            0,
+            ts.get_sequence_length(),
+            "N",
+            False,
+        )
+        assert isinstance(buf, (bytes, bytearray))
+        L = int(ts.get_sequence_length())
+        rows = [buf[i * L : (i + 1) * L].decode("ascii") for i in range(nodes.shape[0])]
+        assert rows == ["NNGNNNNNNT", "NNANNNNNNC", "NNANNNNNNC"]
+
     def test_length_and_interval_validation(self):
         ts = self.get_simple_example()
         nodes = np.array(ts.get_samples(), dtype=np.int32)