Fix missing checks on GT

Author: jeromekelleher

lib/tests.c

@@ -280,13 +280,13 @@ test_variant_encoder_minimal(void)
     const int32_t hq_data[] = { 10, 15, 7, 12, -1, -1, -1, -1 };
     const float gl_data[] = { 1, 2, 3, 4, 1.1f, 1.2f, 1.3f, 1.4f };
     int64_t ret;
-    size_t j;
+    size_t j, buflen;
     vcz_variant_encoder_t writer;
     const char *expected[] = {
         "X\t123\tRS1\tA\tT\t9\tPASS\tAA=G\tGT:HQ:GL\t0/0:10,15:1,2\t0|1:7,12:3,4",
         "YY\t45678\tRS2\tG\t.\t12.1\tFILT1\tAN=9;FLAG\tGT:GL\t1|1:1.1,1.2\t1/0:1.3,1.4",
     };
-    char buf[1000];
+    char *buf;
 
     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);
@@ -313,14 +313,27 @@ test_variant_encoder_minimal(void)
     /* vcz_variant_encoder_print_state(&writer, stdout); */
 
     for (j = 0; j < num_rows; j++) {
-        ret = vcz_variant_encoder_write_row(&writer, j, buf, 1000);
+        for (buflen = 0;; buflen++) {
+            /* printf("buflen = %d\n", (int) buflen); */
+            buf = malloc(buflen);
+            CU_ASSERT_FATAL(buf != NULL);
+            ret = vcz_variant_encoder_write_row(&writer, j, buf, buflen);
+            if (ret < 0) {
+                free(buf);
+                CU_ASSERT_EQUAL_FATAL(ret, VCZ_ERR_BUFFER_OVERFLOW);
+            } else {
+                break;
+            }
+        }
+        CU_ASSERT_FATAL(buflen >= strlen(expected[j]));
         /* printf("ret = %d\n", (int) ret); */
         /* 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]));
         CU_ASSERT_STRING_EQUAL(buf, expected[j]);
+        free(buf);
     }
     vcz_variant_encoder_free(&writer);
 }

lib/vcf_encoder.c

@@ -144,8 +144,8 @@ append_int(char *restrict buf, int32_t value, int64_t offset, int64_t buflen)
 }
 
 static inline int64_t
-append_float(char *restrict buf, int32_t int32_value, float value, int64_t offset,
-    int64_t buflen)
+append_float(
+    char *restrict buf, int32_t int32_value, float value, int64_t offset, int64_t buflen)
 {
     if (int32_value == VCZ_FLOAT32_MISSING_AS_INT32) {
         return append_char(buf, '.', offset, buflen);
@@ -204,8 +204,8 @@ string_all_missing(const char *restrict data, size_t item_size, size_t n)
 }
 
 static int64_t
-string_field_write_entry(const vcz_field_t *self, const void *data, char *buf,
-    int64_t buflen, int64_t offset)
+string_field_write_entry(
+    const vcz_field_t *self, const void *data, char *buf, int64_t buflen, int64_t offset)
 {
     const char *source = (const char *) data;
     size_t column, byte;
@@ -297,8 +297,8 @@ float32_field_write_entry(const vcz_field_t *self, const void *restrict data,
 }
 
 static int64_t
-vcz_field_write_entry(const vcz_field_t *self, const void *data, char *buf,
-    int64_t buflen, int64_t offset)
+vcz_field_write_entry(
+    const vcz_field_t *self, const void *data, char *buf, int64_t buflen, int64_t offset)
 {
     if (self->type == VCZ_TYPE_INT) {
         if (self->item_size == 4) {
@@ -403,7 +403,7 @@ vcz_field_init(vcz_field_t *self, const char *name, int type, size_t item_size,
 
 static int64_t
 vcz_variant_encoder_write_sample_gt(const vcz_variant_encoder_t *self, size_t variant,
-    size_t sample, char *buf, int64_t VCZ_UNUSED(buflen), int64_t offset)
+    size_t sample, char *buf, int64_t buflen, int64_t offset)
 {
     const size_t ploidy = self->gt.num_columns;
     size_t source_offset = variant * self->num_samples * ploidy + sample * ploidy;
@@ -420,18 +420,19 @@ vcz_variant_encoder_write_sample_gt(const vcz_variant_encoder_t *self, size_t va
 
     for (ploid = 0; ploid < ploidy; ploid++) {
         value = source[ploid];
-        if (value != VCZ_INT_FILL) {
-            if (ploid > 0) {
-                buf[offset] = sep;
-                offset++;
-            }
-            if (value == VCZ_INT_MISSING) {
-                buf[offset] = '.';
-                offset++;
-            } else {
-                offset += vcz_itoa(buf + offset, value);
+        if (value == VCZ_INT_FILL) {
+            break;
+        }
+        if (ploid > 0) {
+            offset = append_char(buf, sep, offset, buflen);
+            if (offset < 0) {
+                goto out;
             }
         }
+        offset = append_int(buf, value, offset, buflen);
+        if (offset < 0) {
+            goto out;
+        }
     }
 out:
     return offset;
@@ -543,7 +544,6 @@ vcz_variant_encoder_write_format_fields(const vcz_variant_encoder_t *self,
             }
         }
     } else {
-
         if (!gt_missing) {
             offset = append_string(buf, "GT:", 3, offset, buflen);
             if (offset < 0) {