The allele count and variant stats Python bindings now return empty arrow tables

Previously the allele count binding would be return None and the variant stats binding would try to parse the empty buffers returned by the reader, causing a segmentation fault.

Author: alancleary

apis/python/src/tiledbvcf/binding/reader.cc

@@ -516,16 +516,18 @@ py::object Reader::get_variant_stats_results() {
   auto an = BufferInfo::create("an", TILEDB_VCF_INT32, num_rows);
   auto af = BufferInfo::create("af", TILEDB_VCF_FLOAT32, num_rows);
 
-  check_error(
-      reader,
-      tiledb_vcf_reader_read_from_variant_stats(
-          reader,
-          reinterpret_cast<uint32_t*>(pos->data().data()),
-          reinterpret_cast<char*>(allele->data().data()),
-          reinterpret_cast<int32_t*>(allele->offsets().data()),
-          reinterpret_cast<int*>(ac->data().data()),
-          reinterpret_cast<int*>(an->data().data()),
-          reinterpret_cast<float*>(af->data().data())));
+  if (num_rows > 0) {
+    check_error(
+        reader,
+        tiledb_vcf_reader_read_from_variant_stats(
+            reader,
+            reinterpret_cast<uint32_t*>(pos->data().data()),
+            reinterpret_cast<char*>(allele->data().data()),
+            reinterpret_cast<int32_t*>(allele->offsets().data()),
+            reinterpret_cast<int*>(ac->data().data()),
+            reinterpret_cast<int*>(an->data().data()),
+            reinterpret_cast<float*>(af->data().data())));
+  }
 
   build_arrow_array_from_buffer(pos, num_rows, 0, num_rows);
   build_arrow_array_from_buffer(allele, num_rows, 0, alleles_size);
@@ -546,15 +548,16 @@ py::object Reader::get_allele_count_results() {
       reader,
       tiledb_vcf_reader_get_allele_count_buffer_sizes(
           reader, &num_rows, &refs_size, &alts_size, &filters_size, &gts_size));
-  if (num_rows > 0) {
-    auto pos = BufferInfo::create("pos", TILEDB_VCF_INT32, num_rows);
-    auto ref = BufferInfo::create("ref", TILEDB_VCF_CHAR, num_rows, refs_size);
-    auto alt = BufferInfo::create("alt", TILEDB_VCF_CHAR, num_rows, alts_size);
-    auto filter =
-        BufferInfo::create("filter", TILEDB_VCF_CHAR, num_rows, filters_size);
-    auto gt = BufferInfo::create("gt", TILEDB_VCF_CHAR, num_rows, gts_size);
-    auto count = BufferInfo::create("count", TILEDB_VCF_INT32, num_rows);
 
+  auto pos = BufferInfo::create("pos", TILEDB_VCF_INT32, num_rows);
+  auto ref = BufferInfo::create("ref", TILEDB_VCF_CHAR, num_rows, refs_size);
+  auto alt = BufferInfo::create("alt", TILEDB_VCF_CHAR, num_rows, alts_size);
+  auto filter =
+      BufferInfo::create("filter", TILEDB_VCF_CHAR, num_rows, filters_size);
+  auto gt = BufferInfo::create("gt", TILEDB_VCF_CHAR, num_rows, gts_size);
+  auto count = BufferInfo::create("count", TILEDB_VCF_INT32, num_rows);
+
+  if (num_rows > 0) {
     check_error(
         reader,
         tiledb_vcf_reader_read_from_allele_count(
@@ -569,19 +572,18 @@ py::object Reader::get_allele_count_results() {
             reinterpret_cast<char*>(gt->data().data()),
             reinterpret_cast<uint32_t*>(gt->offsets().data()),
             reinterpret_cast<int32_t*>(count->data().data())));
-
-    build_arrow_array_from_buffer(pos, num_rows, 0, num_rows);
-    build_arrow_array_from_buffer(ref, num_rows, 0, num_rows);
-    build_arrow_array_from_buffer(alt, num_rows, 0, num_rows);
-    build_arrow_array_from_buffer(filter, num_rows, 0, num_rows);
-    build_arrow_array_from_buffer(gt, num_rows, 0, num_rows);
-    build_arrow_array_from_buffer(count, num_rows, 0, num_rows);
-
-    std::vector<std::shared_ptr<BufferInfo>> buffers = {
-        pos, ref, alt, filter, gt, count};
-    return buffers_to_table(buffers);
   }
-  return py::cast<py::none> Py_None;
+
+  build_arrow_array_from_buffer(pos, num_rows, 0, num_rows);
+  build_arrow_array_from_buffer(ref, num_rows, 0, num_rows);
+  build_arrow_array_from_buffer(alt, num_rows, 0, num_rows);
+  build_arrow_array_from_buffer(filter, num_rows, 0, num_rows);
+  build_arrow_array_from_buffer(gt, num_rows, 0, num_rows);
+  build_arrow_array_from_buffer(count, num_rows, 0, num_rows);
+
+  std::vector<std::shared_ptr<BufferInfo>> buffers = {
+      pos, ref, alt, filter, gt, count};
+  return buffers_to_table(buffers);
 }
 
 void Reader::deleter(tiledb_vcf_reader_t* r) {