Releases: TileDB-Inc/TileDB-VCF
Releases · TileDB-Inc/TileDB-VCF
0.11.0
0.10.1
0.10.0
Changes
Added
- Add support for time traveling (#357)
- Support for merging contigs into single fragments (#330)
- Introduce spdlog for finer grain log verbosity (#353)
Changed
- Update pylint CI script (#355)
- Run clang-format on api code (#352)
- Increase bedfile region parsing timeout to 5 minutes (#345)
- Add option for cmake build type in spark/java (#343)
Fixed
- Fix incomplete VCF export for v4 arrays (#360)
- Block until safe to close arrays in vacuum operations (#359)
- Fix spdlog cmake and remove nested namespaces (#358)
- Remove extra tab in TSV export (#354)
- Remove duplicate sample field in TSV header (#351)
- Fix typo in setting compute levels (#350)
- Check async query future is valid before getting (#341)
0.9.0
Changes:
- 1f15266 Merge pull request #339 from TileDB-Inc/ss/update-tiledb-2.3.1
- 40f0b02 Merge pull request #338 from TileDB-Inc/ss/update-tiledb-2.3.0
- cadae0b Update minimum cmake version
- ae530ce Update to TileDB 2.3.1 and add MacOS arm64 prebuilt
- 63b38a1 Update to TileDB 2.3.0
This list of changes was auto generated.
0.8.9
0.8.8
Changes:
- 26bfaaa Merge pull request #332 from TileDB-Inc/ss/native-lib-building-should-not-run-check
- 883f3d9 No need to run tests when building libs for jars
- 2119fb5 Merge pull request #316 from TileDB-Inc/sethshelnutt/ch6900/add-support-for-resume-of-storing-a-sample
- a9d0062 Merge pull request #331 from TileDB-Inc/ss/tiledb-2.2.9
- da052f0 Support resuming a partial ingestion with --resume
- ed3e9af Merge pull request #326 from TileDB-Inc/ss/switch-progress-disabled-by-default
- 280543f Merge pull request #329 from TileDB-Inc/sethshelnutt/ch7287/concurrency-issues-with-destructor-of-tiledbvcfdataset
- 8552d7b Update to TileDB 2.2.9
- 662965e Merge pull request #324 from TileDB-Inc/sethshelnutt/ch7272/print-spark-options-to-log
- 01b9f3e Merge pull request #320 from TileDB-Inc/sethshelnutt/ch7217/exit-early-if-sample-partition-is-empty
See More
- e3f05f1 Merge pull request #328 from TileDB-Inc/ss/cmake-super-build-set-build-type-once
- fea2273 Fix concurrent issues with dataset destructor
- 94b0c96 Only set CMAKE_BUILD_TYPE on in FindTileDB_EP
- 99909d8 Merge pull request #327 from TileDB-Inc/sethshelnutt/ch4840/add-support-for-bedfile-row-id-in-output
- 34c52e7 Add support for query bed file line number export
- d1467c0 Merge pull request #325 from TileDB-Inc/ss/fix-java-version-printing
- 574c4fc Switch progress estimate to off by default
- 5d4dac2 Adjust where Java verion info is printed
- d64099e Print spark options at info level in log
- c37b430 Merge pull request #322 from TileDB-Inc/sethshelnutt/ch7254/add-option-to-disable-estimated-result-size
- 03bbf70 Support disabling progress estimation w/verbose
- 41cd66f Merge pull request #323 from TileDB-Inc/ss/update-java-spark-version-0.8.8
- 7cfa859 Merge pull request #321 from TileDB-Inc/aaronwolen/ch6998/add-version-output-to-spark-logging-by-default
- 4b0b357 Update java/spark version to 0.8.8
- de4c96e Merge pull request #318 from TileDB-Inc/sethshelnutt/ch7184/invalid-partition-created
- 506cbfa Add version function to c-api/python/java/spark
- 4cf4d4f Another partitioning logic update for uneven division
- d7ebbb5 Add CLI test for sample partition uniqueness
- 0eb51cc Add CLI test for empty partitions
- 9d6e491 Fix partitioning logic for uneven division
- 107c609 Fix C API: Reader submit (partitioned)
- 0b9f589 If a sample partition is empty exit early [ #318 ]
- 2bf9f54 Merge pull request #306 from TileDB-Inc/ihn/test_macos10.15
- c2c7c81 Merge pull request #317 from TileDB-Inc/sethshelnutt/ch7151/properly-check-header-for-parsing-error-in
- 140d3fa Add error checking to v4 header parsing on fetch
- f3cb859 Make macos 10.15 test stage name unique
- a5ab713 Add test on macOS 10.15
This list of changes was auto generated.
0.8.7
Changes:
- 0b81352 Update Java/Spark version to 0.8.7
- b3c7e7f Merge pull request #309 from TileDB-Inc/sethshelnutt/ch6461/attribute-is-fixed-len-reports-true-for-v4
- 846182e Fix attribute_is_fixed_len for v4 sample
- ef18689 Merge pull request #311 from TileDB-Inc/sethshelnutt/ch6997/update-to-tiledb-2-2-8
- e4ea521 Merge pull request #310 from TileDB-Inc/sethshelnutt/ch6996/always-set-sm-skip-est-size-partitioning
- ae6a840 Update to TileDB 2.2.8
- 7983591 Set core sm.skip_est_size_partitioning config to 'true' by default
- c257e55 Patch htslib 1.10 to fix build with autoconf 2.70+ (#314)
- 813d422 Symlink pyarrow libraries to build python wheels
This list of changes was auto generated.
0.8.6
Changes include:
- Update to TileDB 2.2.6 #303
- Load non-empty domain async on dataset open #300
- Optimize when headers are fetched #301
- Add heuristic to query buffer to better optimize buffer usage #299
- TileDB Cloud arrays do not need memory reserved for core library or caches #297
- Fix issue with materialized attributes failing to load intermittently #298
- Fix verbose mode in python #296
0.8.5
Changes:
- 4d2a074 Merge pull request #295 from TileDB-Inc/ss/java-spark-verison-0.8.5
- f2a84ff Update version to 0.8.5
- 2032ad1 Merge pull request #294 from TileDB-Inc/ss/remote-unused-pybind11-variable
- 690da91 Merge pull request #293 from TileDB-Inc/ss/metadata-always-reset-buffers
- 0692e5e Revert queryable attributes back to vector of char
- d4774c6 Revert "Use fixed buffer budget for VCF headers"
- 975eb60 Always reset metadata array buffers on reads
- 891b150 Update .gitignore for newer htslib
- e19c1d4 Remove unused variable in pybind11
- b1bf5ea Merge pull request #292 from TileDB-Inc/ss/improve-materialized-attribute-detection
See More
- ca49d9e Merge pull request #291 from TileDB-Inc/ss/fix-gcc-4.8.5-build
- c08f3ed Improve materialized attribute detection
- a52845b Fix GCC 4.8.5 build issue
- 549e80a Merge pull request #290 from TileDB-Inc/ss/update-conda-env-pyarrow-3.0
- 6e0fb15 Update conda env for pyarrow 3.0
This list of changes was auto generated.
0.8.4
Changes:
- 325cb74 Merge pull request #288 from TileDB-Inc/sethshelnutt/ch5628/switch-python-api-to-build-arrow-table-directly
- e316ea8 Merge pull request #286 from TileDB-Inc/sethshelnutt/ch5625/don-t-fetch-sample-names-when-using-all-samples
- da55c3e Merge pull request #289 from TileDB-Inc/ss/update-version-0.8.4
- d899056 Avoid unnecessary fetching of sample list for v4
- 9688a90 Merge pull request #285 from TileDB-Inc/sethshelnutt/ch5606/don-t-fetch-header-unless-they-are-needed
- 1ec8028 Update spark/java version for 0.8.4
- 770e20d Only fetch headers if needed
- 4d374af Cleanup
- f4e261a Build arrow table in pybind11
- 3fd4d9d Python: Replace numpy arrays with array buffers
This list of changes was auto generated.