ASAN fixes

libtiledbvcf/src/read/reader.cc

@@ -47,6 +47,8 @@ Reader::~Reader() {
     ctx_->cancel_tasks();
     read_state_.async_query.wait();
   }
+
+  utils::free_htslib_tiledb_context();
 }
 
 void Reader::open_dataset(const std::string& dataset_uri) {
@@ -1399,7 +1401,7 @@ void Reader::prepare_regions_v4(
         query_region_contig = &query_regions->back().second;
       }
       // Start a new query region.
-      query_region_contig->push_back({});
+      query_region_contig->emplace_back();
       query_region_contig->back().col_min = widened_reg_min;
       query_region_contig->back().col_max = reg_max;
       query_region_contig->back().contig = r.seq_name;
@@ -1414,7 +1416,7 @@ void Reader::prepare_regions_v4(
     size_t query_regions_size = query_region_pair.second.size();
     for (size_t i = 0; i < query_regions_size; i++) {
       auto& query_region = query_region_pair.second[i];
-      for (size_t j = i + 1; j < query_regions->size(); j++) {
+      for (size_t j = i + 1; j < query_region_pair.second.size(); j++) {
         auto& query_region_to_check = query_region_pair.second[j];
         if (query_region.col_min <= query_region_to_check.col_max &&
             query_region.col_max >= query_region_to_check.col_min) {

libtiledbvcf/src/utils/utils.cc

@@ -354,6 +354,15 @@ void set_htslib_tiledb_context(const std::vector<std::string>& tiledb_config) {
   }
 }
 
+void free_htslib_tiledb_context() {
+  const std::lock_guard<std::mutex> lock(cfg_mutex);
+  last_set_config.clear();
+  if (hfile_tiledb_vfs_ctx != nullptr)
+    tiledb_ctx_free(&hfile_tiledb_vfs_ctx);
+  if (hfile_tiledb_vfs_config != nullptr)
+    tiledb_config_free(&hfile_tiledb_vfs_config);
+}
+
 void init_htslib() {
   const std::lock_guard<std::mutex> lock(init_mutex);
   // trick to init some of htslib's internal data structures for plugins

libtiledbvcf/src/utils/utils.h

@@ -331,6 +331,13 @@ void set_tiledb_config(
  */
 void set_htslib_tiledb_context(const std::vector<std::string>& tiledb_config);
 
+/**
+ * Free the htslib plugin context
+ * a thread-safe implementation
+ *
+ */
+void free_htslib_tiledb_context();
+
 /**
  * Help function to initialize the htslib plugin
  */

libtiledbvcf/src/write/writer.cc

@@ -41,6 +41,10 @@ namespace vcf {
 Writer::Writer() {
 }
 
+Writer::~Writer() {
+  utils::free_htslib_tiledb_context();
+}
+
 void Writer::init(const std::string& uri, const std::string& config_str) {
   if (!config_str.empty())
     set_tiledb_config(config_str);

libtiledbvcf/src/write/writer.h

@@ -99,6 +99,8 @@ class Writer {
   /** Constructor. */
   Writer();
 
+  ~Writer();
+
   /**
    * Initializes the writer for storing to the given dataset. Opens the array,
    * creates the TileDB query, etc.