v0.2.2

0.2.2 (2024-05-31)

Bug Fixes

• start with empty files without throwing an error (d407b92)

v0.2.1

0.2.1 (2024-05-28)

Bug Fixes

• allow insertions that start at 0 (#449) (f427137)

v0.2.0

0.2.0 (2024-05-23)

⚠ BREAKING CHANGES

• old database_config files might be invalid if they contained insertion columns. Also, we are more prohibitive for ndjson input files, which now MUST contain nucleotide/amino acid insertions for all respective sequences. The insertions action and filter do no longer require a column field.

Features

• insertions no longer in metadata or databaseConfig, instead expected for all aligned sequences #372 (1f3680c)

v0.1.1

0.1.1 (2024-05-23)

Features

• add number of partitions to /info (1e780b5)
• add serializationVersion to SILO output for smoother transitioning to new formats (d3badb6)

v0.1.0

0.1.0 (2024-05-10)

⚠ BREAKING CHANGES

• return data as NDJSON instead of JSON

Features

• AAMutations with multiple sequences (0def8b2)
• Action for amino acid distribution (a0a4cf1)
• add limit orderBy and offset to all query actions (13b7e01)
• add log statements to loadDatabaseState (46a0421)
• add more tests, make less flaky and viable with large dataset (7772ae3)
• add unit test for findIllegalNucleotideChar, unique test case name for insertion contains invalid pattern tests (99c9c4b)
• added amino acid insertion search, added many test cases and fixed various bugs (d1e4b2b)
• allow default preprocessing config along with user defined preprocessing config (ee9f20e)
• allow reading fasta files with missing segments and genes #220 (8ea9893)
• allow reading segments and genes that are null from ndjson file #220 (d0a3a7e)
• also get Runtime Config options from environment variables (33bdd65)
• also log to stdout (54b8a47)
• also return mutation destructed that does not need to be reparsed (a93abbf)
• Alternative templating of symbol classes (6b61985)
• automatically detect file endings for fasta files (75bd14e)
• be more lenient on input data, ignore superfluous sequences and fill missing sequences with Ns (ee12186)
• Better test coverage for SymbolEquals filter (42c685c)
• boolean columns, resolves #384: const declaration (685db9f)
• boolean columns: actions/tuple: update assignTupleField() (b020109)
• boolean columns: add and use JsonValueType (2ad1268)
• boolean columns: add bool to JsonValueType, update tuple (3c990e2)
• boolean columns: add expression_type "BooleanEquals" (b82ec69)
• boolean columns: add filter_expressions/bool_equals (ff2a138)
• boolean columns: add optional_bool (a2e47f8)
• boolean columns: add storage/column/bool_column (5eb3430)
• boolean columns: column_group: update ColumnPartitionGroup (d7adecf)
• boolean columns: column_group.h: add {ColumnPartitionGroup,ColumnGroup}::bool_columns fields (af44f1a)
• boolean columns: database (c555a68)
• boolean columns: database_config: add "bool" case to DatabaseConfigReader::readConfig() (12fc7b8)
• boolean columns: database_config: add "boolean" case to de/serialisation (e6d5363)
• boolean columns: database_config: add BOOL to ValueType (0b47b82)
• boolean columns: database_config: update DatabaseMetadata::getColumnType() (30febdd)
• boolean columns: database_partition (0aef8f0)
• boolean columns: optional_bool: add == (f0aa3e8)
• boolean columns: selection (e52f2dc)
• build metadata in parallel to sequences. Do not create unaligned sequence tables in preprocessing, rather hive-partition them directly to disk. Better (debug-)logging (c1cdfeb)
• bulk Tuple allocations now possible (902ec04)
• clearer Operator::negate and Expression::toString, logical Equivalents for debug printing/logging for the Leaf Operators IndexScan and BitmapSelection (026b639)
• consistent behavior of configs when starting SILO with both --preprocessing and --api (847ec7e)
• declutter README.md from linting option, which is now disabled by default and enforced in the CI for the Linter (9220435)
• details no longer shows insertions (#354) (473cd98)
• display database info after loading new database state (0249416)
• display preprocessing duration in logs in human-readable format (not in microseconds) #296 (a2499af)
• do not enforce building with clang-tidy by default. Linter will still be enforced (7134e45)
• FastaAligned action (50776c8)
• faster builds by copying @corneliusroemer image caching for our dependency images, which rarely change (#374) (7867bc7)
• filter for amino acids (b52aabd)
• fix sorting (1ed18ae)
• flipped bitmap can now be set before insertion (f61c803)
• format DatabaseConfig (4fb8f1b)
• format PreprocessingConfig (ee35207)
• generalize mutations action to have consistent behavior for different symbols (9834aea)
• generalizing symbol and mutation filters. Clear handling of ambiguous symbols (aa9ad4d)
• Generalizing the config for multiple nucleotide sequences and multiple genes (9a80204)
• have structured and destructured insertion in insertions response (0a7e46a)
• hide intermediate results of the preprocessing - don't put it in the output (44327b0)
• implement basic request id to trace requests #303 ([4defb59](https...