Merge pull request #30 from Intel-HLS/workaround

Workaround BCF2 limitations in htsjdk - bcf_str_missing is defined to be

include/query_operations/variant_operations.h

@@ -181,7 +181,8 @@ class VariantFieldHandlerBase
     virtual bool compute_valid_element_wise_sum(const Variant& variant, const VariantQueryConfig& query_config,
         unsigned query_idx, void* output_ptr, unsigned num_elements) = 0;
     virtual bool collect_and_extend_fields(const Variant& variant, const VariantQueryConfig& query_config, 
-        unsigned query_idx, const void ** output_ptr, unsigned& num_elements, const bool use_missing_values_only_not_vector_end=false) = 0;
+        unsigned query_idx, const void ** output_ptr, unsigned& num_elements,
+        const bool use_missing_values_only_not_vector_end=false, const bool use_vector_end_only=false) = 0;
 };
 
 //Big bag handler functions useful for handling different types of fields (int, char etc)
@@ -225,7 +226,8 @@ class VariantFieldHandler : public VariantFieldHandlerBase
      * Create an extended vector for use in BCF format fields, return result in output_ptr and num_elements
      */
     bool collect_and_extend_fields(const Variant& variant, const VariantQueryConfig& query_config, 
-        unsigned query_idx, const void ** output_ptr, unsigned& num_elements, const bool use_missing_values_only_not_vector_end=false);
+        unsigned query_idx, const void ** output_ptr, unsigned& num_elements,
+        const bool use_missing_values_only_not_vector_end=false, const bool use_vector_end_only=false);
   private:
     std::vector<uint64_t> m_num_calls_with_valid_data;
     DataType m_bcf_missing_value;

src/genomicsdb/variant_field_handler.cc

@@ -262,7 +262,8 @@ bool VariantFieldHandler<DataType>::compute_valid_element_wise_sum(const Variant
 
 template<class DataType>
 bool VariantFieldHandler<DataType>::collect_and_extend_fields(const Variant& variant, const VariantQueryConfig& query_config, 
-        unsigned query_idx, const void ** output_ptr, unsigned& num_elements, const bool use_missing_values_only_not_vector_end)
+        unsigned query_idx, const void ** output_ptr, unsigned& num_elements,
+        const bool use_missing_values_only_not_vector_end, const bool use_vector_end_only)
 {
   auto max_elements_per_call = 0u;
   auto valid_idx = 0u;
@@ -301,7 +302,8 @@ bool VariantFieldHandler<DataType>::collect_and_extend_fields(const Variant& var
     }
     if(num_elements_inserted == 0u) //no elements inserted, insert missing value first
     {
-      m_extended_field_vector[extended_field_vector_idx] = get_bcf_missing_value<DataType>();
+      m_extended_field_vector[extended_field_vector_idx] = use_vector_end_only ? get_bcf_vector_end_value<DataType>()
+        : get_bcf_missing_value<DataType>();
       ++num_elements_inserted;
       ++extended_field_vector_idx;
     }

src/query_operations/broad_combined_gvcf.cc

@@ -243,14 +243,16 @@ void BroadCombinedGVCFOperator::handle_FORMAT_fields(const Variant& variant)
     auto known_field_enum = BCF_FORMAT_GET_KNOWN_FIELD_ENUM(curr_tuple);
     assert(known_field_enum < g_known_variant_field_names.size());
     auto variant_type_enum = BCF_FORMAT_GET_VARIANT_FIELD_TYPE_ENUM(curr_tuple);
+    auto is_char_type = (variant_type_enum == VARIANT_FIELD_CHAR);
     //valid field handler
     assert(variant_type_enum < m_field_handlers.size() && m_field_handlers[variant_type_enum].get());
     //Check if this is a field that was remapped - for remapped fields, we must use field objects from m_remapped_variant
     //else we should use field objects from the original variant
     auto query_field_idx = m_query_config->get_query_idx_for_known_field_enum(known_field_enum);
     auto& src_variant = (m_remapping_needed && KnownFieldInfo::is_length_allele_dependent(known_field_enum)) ? m_remapped_variant : variant;
     auto valid_field_found = m_field_handlers[variant_type_enum]->collect_and_extend_fields(src_variant, *m_query_config,
-        query_field_idx, &ptr, num_elements, m_use_missing_values_not_vector_end);
+        query_field_idx, &ptr, num_elements,
+        m_use_missing_values_not_vector_end && !is_char_type, m_use_missing_values_not_vector_end && is_char_type);
     if(valid_field_found)
     {
       auto j=0u;
@@ -326,10 +328,12 @@ void BroadCombinedGVCFOperator::handle_FORMAT_fields(const Variant& variant)
     auto& curr_tuple = m_unknown_FORMAT_fields_vec[i];
     auto query_field_idx = BCF_FORMAT_GET_QUERY_FIELD_IDX(curr_tuple);
     auto variant_type_enum = BCF_FORMAT_GET_VARIANT_FIELD_TYPE_ENUM(curr_tuple);
+    auto is_char_type = (variant_type_enum == VARIANT_FIELD_CHAR);
     //valid field handler
     assert(variant_type_enum < m_field_handlers.size() && m_field_handlers[variant_type_enum].get());
     auto valid_field_found = m_field_handlers[variant_type_enum]->collect_and_extend_fields(variant, *m_query_config,
-        query_field_idx, &ptr, num_elements, m_use_missing_values_not_vector_end);
+        query_field_idx, &ptr, num_elements,
+        m_use_missing_values_not_vector_end && !is_char_type, m_use_missing_values_not_vector_end && is_char_type);
     if(valid_field_found)
       bcf_update_format(m_vcf_hdr, m_bcf_out, m_query_config->get_query_attribute_name(query_field_idx).c_str(), ptr, num_elements,
           BCF_FORMAT_GET_BCF_HT_TYPE(curr_tuple));