diff --git a/include/silo/storage/sequence_store.h b/include/silo/storage/sequence_store.h index d8fa6e29b..094e46ad5 100644 --- a/include/silo/storage/sequence_store.h +++ b/include/silo/storage/sequence_store.h @@ -34,8 +34,8 @@ class NucPosition { template void serialize(Archive& archive, [[maybe_unused]] const uint32_t version) { // clang-format off - archive & symbol_whose_bitmap_is_flipped; archive & bitmaps; + archive & symbol_whose_bitmap_is_flipped; // clang-format on } @@ -46,7 +46,7 @@ class NucPosition { explicit NucPosition(std::optional symbol); SymbolMap bitmaps; - std::optional symbol_whose_bitmap_is_flipped = std::nullopt; + std::optional symbol_whose_bitmap_is_flipped; std::optional flipMostNumerousBitmap(uint32_t sequence_count); }; @@ -63,8 +63,8 @@ class SequenceStorePartition { template void serialize(Archive& archive, [[maybe_unused]] const uint32_t version) { // clang-format off - archive & positions; archive & indexing_differences_to_reference_genome; + archive & positions; archive & nucleotide_symbol_n_bitmaps; archive & sequence_count; // clang-format on diff --git a/src/silo/storage/aa_store.cpp b/src/silo/storage/aa_store.cpp index db7d45c84..c1e4ec27f 100644 --- a/src/silo/storage/aa_store.cpp +++ b/src/silo/storage/aa_store.cpp @@ -56,15 +56,15 @@ std::optional silo::AAPosition::flipMostNumerousBitmap(uint32_t } silo::AAStorePartition::AAStorePartition(const std::vector& reference_sequence) - : reference_sequence(reference_sequence) { - for (const AA_SYMBOL symbol : reference_sequence) { - positions.emplace_back(symbol); - } -} + : reference_sequence(reference_sequence) {} size_t silo::AAStorePartition::fill(silo::ZstdFastaReader& input_file) { static constexpr size_t BUFFER_SIZE = 1024; + for (const AA_SYMBOL symbol : reference_sequence) { + positions.emplace_back(symbol); + } + size_t read_sequences_count = 0; std::vector sequence_buffer; diff --git a/src/silo/storage/sequence_store.cpp b/src/silo/storage/sequence_store.cpp index 3eef973b1..0d5e92367 100644 --- a/src/silo/storage/sequence_store.cpp +++ b/src/silo/storage/sequence_store.cpp @@ -61,15 +61,15 @@ std::optional silo::NucPosition::flipMostNumerousBitmap silo::SequenceStorePartition::SequenceStorePartition( const std::vector& reference_genome ) - : reference_genome(reference_genome) { - for (const NUCLEOTIDE_SYMBOL symbol : reference_genome) { - positions.emplace_back(symbol); - } -} + : reference_genome(reference_genome) {} size_t silo::SequenceStorePartition::fill(silo::ZstdFastaReader& input_file) { static constexpr size_t BUFFER_SIZE = 1024; + for (const NUCLEOTIDE_SYMBOL symbol : reference_genome) { + positions.emplace_back(symbol); + } + size_t read_sequences_count = 0; std::vector genome_buffer; diff --git a/src/silo_api/database_directory_watcher.cpp b/src/silo_api/database_directory_watcher.cpp index 12209ae8b..16ce7e0cd 100644 --- a/src/silo_api/database_directory_watcher.cpp +++ b/src/silo_api/database_directory_watcher.cpp @@ -126,4 +126,8 @@ void silo_api::DatabaseDirectoryWatcher::checkDirectoryForData(Poco::Timer& /*ti SPDLOG_INFO("New data version detected: {}", most_recent_database_state->first.string()); database_mutex.setDatabase(silo::Database::loadDatabaseState(most_recent_database_state->first)); + SPDLOG_INFO( + "New database with version {} successfully loaded.", + most_recent_database_state->first.string() + ); } \ No newline at end of file