Merge pull request #15 from jeromekelleher/buffer-safety

Add paranoia to build options and fix errors

Author: jeromekelleher

lib/meson.build

@@ -4,7 +4,6 @@ project('vcf_encoder', ['c'],
 
 cc = meson.get_compiler('c')
 m_dep = cc.find_library('m', required: false)
-lib_deps = [m_dep]
 
 extra_c_args = [
     '-Wall', '-Wextra', '-Werror', '-Wpedantic', '-W',
@@ -21,4 +20,6 @@ cunit_dep = dependency('cunit')
 tests = executable('tests',
     sources: ['tests.c', 'vcf_encoder.c'],
     dependencies: [cunit_dep, m_dep],
-  )
+    c_args: extra_c_args, 
+)
+test('tests', tests)

lib/tests.c

@@ -11,16 +11,16 @@ FILE *_devnull;
 static void
 test_int_field_1d(void)
 {
-    const int num_rows = 5;
+    const size_t num_rows = 5;
     const int32_t data[] = { 1, 2, 12345789, -1, -100 };
     vcz_field_t field = { .name = "test",
         .type = VCZ_TYPE_INT,
         .item_size = 4,
         .num_columns = 1,
-        .data = data };
+        .data = (const char *) data };
     char buf[1000];
     const char *expected[] = { "1\t", "2\t", "12345789\t", ".\t", "-100\t" };
-    int ret;
+    int64_t ret;
     size_t j;
 
     for (j = 0; j < num_rows; j++) {
@@ -34,16 +34,16 @@ test_int_field_1d(void)
 static void
 test_int_field_2d(void)
 {
-    const int num_rows = 4;
+    const size_t num_rows = 4;
     const int32_t data[] = { 1, 2, 3, 1234, 5678, -2, -1, -2, -2, -2, -2, -2 };
     vcz_field_t field = { .name = "test",
         .type = VCZ_TYPE_INT,
         .item_size = 4,
         .num_columns = 3,
-        .data = data };
+        .data = (const char *) data };
     char buf[1000];
     const char *expected[] = { "1,2,3\t", "1234,5678\t", ".\t", "\t" };
-    int ret;
+    int64_t ret;
     size_t j;
 
     for (j = 0; j < num_rows; j++) {
@@ -58,7 +58,7 @@ static void
 test_string_field_1d(void)
 {
     /* item_size=3, rows=3, cols=1 */
-    const int num_rows = 3;
+    const size_t num_rows = 3;
     const char data[] = "X\0\0" /* X */
                         "XX\0"  /* XX*/
                         "XXX";  /* XXX, */
@@ -70,7 +70,7 @@ test_string_field_1d(void)
         .data = data };
     char buf[1000];
     const char *expected[] = { "X\t", "XX\t", "XXX\t" };
-    int ret;
+    int64_t ret;
     size_t j;
 
     CU_ASSERT_EQUAL_FATAL(sizeof(data), 10);
@@ -85,7 +85,7 @@ static void
 test_string_field_2d(void)
 {
     /* item_size=3, rows=3, cols=3 */
-    const int num_rows = 3;
+    const size_t num_rows = 3;
     const char data[] = "X\0\0Y\0\0\0\0\0" /* [X, Y] */
                         "XX\0YY\0Z\0\0"    /* [XX, YY, Z], */
                         "XXX\0\0\0\0\0";   /* [XXX], */
@@ -97,7 +97,7 @@ test_string_field_2d(void)
         .data = data };
     char buf[1000];
     const char *expected[] = { "X,Y\t", "XX,YY,Z\t", "XXX\t" };
-    int ret;
+    int64_t ret;
     size_t j;
 
     CU_ASSERT_EQUAL_FATAL(sizeof(data), 27);
@@ -113,22 +113,23 @@ static void
 test_variant_encoder_minimal(void)
 {
     // Two rows, one column in each field, two samples
-    const int num_rows = 2;
+    const size_t num_rows = 2;
     const char contig_data[] = "X\0YY";
     const int32_t pos_data[] = { 123, 45678 };
     const char id_data[] = "RS1RS2";
     const char ref_data[] = "AG";
     const char alt_data[] = "T";
-    const float qual_data[] = { 9, 12.1 };
+    const float qual_data[] = { 9, 12.1f };
     const char filter_id_data[] = "PASS\0FILT1";
-    const int8_t filter_data[] = {1, 0, 0, 1};
+    const int8_t filter_data[] = { 1, 0, 0, 1 };
     const int32_t an_data[] = { -1, 9 };
-    const char* aa_data = "G.";
-    const int8_t flag_data[] = {0, 1};
+    const char *aa_data = "G.";
+    const int8_t flag_data[] = { 0, 1 };
     const int32_t gt_data[] = { 0, 0, 0, 1, 1, 1, 1, 0 };
     const int8_t gt_phased_data[] = { 0, 1, 1, 0 };
-    const int32_t hq_data[] = { 10, 15, 7, 12, -1, -1, -1, -1};
-    int ret, j;
+    const int32_t hq_data[] = { 10, 15, 7, 12, -1, -1, -1, -1 };
+    int64_t ret;
+    size_t j;
     vcz_variant_encoder_t writer;
     const char *expected[] = {
         "X\t123\tRS1\tA\tT\t9\tPASS\tAA=G\tGT:HQ\t0/0:10,15\t0|1:7,12",
@@ -137,30 +138,31 @@ test_variant_encoder_minimal(void)
     char buf[1000];
 
     ret = vcz_variant_encoder_init(&writer, 2, 2, contig_data, 2, pos_data, id_data, 3,
-        1, ref_data, 1, alt_data, 1, 1, qual_data,
-        filter_id_data, 5, 2, filter_data);
+        1, ref_data, 1, alt_data, 1, 1, qual_data, filter_id_data, 5, 2, filter_data);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     ret = vcz_variant_encoder_add_gt_field(&writer, gt_data, 4, 2, gt_phased_data);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     ret = vcz_variant_encoder_add_info_field(&writer, "AN", VCZ_TYPE_INT, 4, 1, an_data);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
-    ret = vcz_variant_encoder_add_info_field(&writer, "AA", VCZ_TYPE_STRING, 1, 1, aa_data);
+    ret = vcz_variant_encoder_add_info_field(
+        &writer, "AA", VCZ_TYPE_STRING, 1, 1, aa_data);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
-    ret = vcz_variant_encoder_add_info_field(&writer, "FLAG", VCZ_TYPE_BOOL, 1, 1, flag_data);
+    ret = vcz_variant_encoder_add_info_field(
+        &writer, "FLAG", VCZ_TYPE_BOOL, 1, 1, flag_data);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     ret = vcz_variant_encoder_add_format_field(
         &writer, "HQ", VCZ_TYPE_INT, 4, 2, hq_data);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
 
     vcz_variant_encoder_print_state(&writer, _devnull);
-    printf("\n");
+    /* printf("\n"); */
     /* vcz_variant_encoder_print_state(&writer, stdout); */
 
     for (j = 0; j < num_rows; j++) {
         ret = vcz_variant_encoder_write_row(&writer, j, buf, 1000);
         /* printf("ret = %d\n", ret); */
-        printf("GOT:%s\n", buf);
-        printf("EXP:%s\n", expected[j]);
+        /* printf("GOT:%s\n", buf); */
+        /* printf("EXP:%s\n", expected[j]); */
         /* printf("GOT:%d\n", (int) strlen(buf)); */
         /* printf("EXP:%d\n", (int) strlen(expected[j])); */
         CU_ASSERT_EQUAL(ret, strlen(expected[j]));
@@ -186,37 +188,37 @@ test_itoa_small(void)
     }
 }
 
-
 static void
 test_ftoa(void)
 {
     struct test_case {
         float val;
         const char *expected;
     };
+    // clang-format off
     struct test_case cases[] = {
-        {0.0, "0"},
-        {0.0001, "0"},
-        {0.0005, "0.001"},
-        {0.3, "0.3"},
-        {0.32, "0.32"},
-        {0.329, "0.329"},
-        {0.3217, "0.322"},
-        {8.0, "8"},
-        {8.0001, "8"},
-        {8.3, "8.3"},
-        {8.32, "8.32"},
-        {8.329, "8.329"},
-        {8.3217, "8.322"},
-        {443.998, "443.998"},
-        {1028.0, "1028"},
-        {1028.0001, "1028"},
-        {1028.3, "1028.3"},
-        {1028.32, "1028.32"},
-        {1028.329, "1028.329"},
-        {1028.3217, "1028.322"},
+        {0.0f, "0"},
+        {0.0001f, "0"},
+        {0.0005f, "0.001"},
+        {0.3f, "0.3"},
+        {0.32f, "0.32"},
+        {0.329f, "0.329"},
+        {0.3217f, "0.322"},
+        {8.0f, "8"},
+        {8.0001f, "8"},
+        {8.3f, "8.3"},
+        {8.32f, "8.32"},
+        {8.329f, "8.329"},
+        {8.3217f, "8.322"},
+        {443.998f, "443.998"},
+        {1028.0f, "1028"},
+        {1028.0001f, "1028"},
+        {1028.3f, "1028.3"},
+        {1028.32f, "1028.32"},
+        {1028.329f, "1028.329"},
+        {1028.3217f, "1028.322"},
         {1000000, "1000000"},
-        {-100.0, "-100"},
+        {-100.0f, "-100"},
         {NAN, "nan"},
         {INFINITY, "inf"},
         {-INFINITY, "-inf"},
@@ -225,7 +227,9 @@ test_ftoa(void)
         {-16777216, "-16777216"},
         /* TODO test extreme value here, that push against the limits of f32 */
     };
-    int j, len;
+    // clang-format on
+    int len;
+    size_t j;
     char buf[1024];
 
     for (j = 0; j < sizeof(cases) / sizeof(*cases); j++) {
@@ -267,7 +271,7 @@ handle_cunit_error(void)
     exit(EXIT_FAILURE);
 }
 
-int
+static int
 test_main(CU_TestInfo *tests, int argc, char **argv)
 {
     int ret;