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@gsvic gsvic released this 01 Sep 19:28
0.5.1
1e37e36
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Learn about vigilant mode.

Notable

Compressed BED files are now supported for exports.

Core

Added

  • htslib is now used for parsing BED files (#130).
  • CI now builds cross-platform JAR files (#148) .

Changed

  • Docker images are now built in a separate CI stage (#158).

CLI

Added

  • export gains a --sorted flag to skip BED file sorting when the file is already known to be sorted (#147)

Python

Fixed

  • Fix buffer memory leak (#152)

Java/Spark

Added

  • Additional tests for decoding attributes from info/fmt byte blobs (#140)

Changed

  • getRanges()'s option for specifying genomic regions has been renamed from ranges to regions in order to be consistent with the other APIs (#151).

All Changes

  • 4bb70cd Add stage for building docker images
  • df78833 Merge pull request #157 from TileDB-Inc/ss/log-on-error-java-native-loading
  • ce46126 Log all errors for java native lib loading
  • cc4b8a1 Merge pull request #156 from TileDB-Inc/aw/ch3038/fix-var-len-filters
  • 9994517 Merge pull request #155 from TileDB-Inc/sethshelnutt/ch3038/incorrect-values-in-filter-field
  • f5bdb58 fix pytest for varable length filter
  • 36b09a3 Filter/Allele index should be based on list_offset
  • 5fd6fe9 Add pytest for querying variable length filters
  • 6eebc7d Use correct post-condition for limit_partitions
  • e1022c7 Add docstring and test for read_dask(limit_partitions=) kwarg
  • d58a9a3 Add limit_partitions kwarg option for read_dask/map_dask
  • 9a92107 Fix buffer memory leak
  • 7c949d9 Add support for regions spark option
  • 04f4437 Merge pull request #149 from TileDB-Inc/aw/ch2942/v3-example-array
  • 0c0275e Merge pull request #150 from TileDB-Inc/sethshelnutt/ch2994/setting-memory-budget-and-tbb-config-causes
  • b9930e4 Delay creating contexts for read
  • f4011c8 Pin badge to master branch
  • 6269ee8 Don't use deprecated python class in README
  • 0409ac7 Use URI for v3 of vcf-samples-20 array
  • ad59d23 Added CI step that builds a cross-platform jar
  • c401bc5 Make clang-format happy
  • dab62cb Update CLI description for no-duplicates arg
  • 68803e5 Add CLI flag to skip region sorting
  • 7b93018 Update to Gradle 6.6
  • a12a147 Reader validity test
  • 2398f30 Add parsing of bedfile via htslib
  • e504249 Report diffs in run-cli-tests.sh
  • efef9e2 Enable trace logging in cli tests
  • b31d17f Add htslib plugin for reading files via VFS
  • a3d0569 Merge pull request #145 from TileDB-Inc/ss/spark-java-version-0.5.1-snapshot
  • c70da3e Update spark/java version to 0.5.1-SNAPSHOT
  • ebd7905 Add unit tests which compares VCFInfoFmtDecoder [ch2819]
Assets 6
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