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@lbergelson lbergelson released this 14 Feb 22:07
· 502 commits to master since this release
2.9.0
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lbergelson Louis Bergelson
GPG key ID: CDB73EA73CD9CF1E
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This release includes some major new functionality as well as minor bug fixes and API updates:

Asynchronous bam decompression If you have an extra core you can speedup bam reading by setting the system property use_async_io_read_samtools=true. Thanks to @d-cameron for this functionality and to all the people who helped review it.

Support for hardware optimized decompression using InflaterFactory: You can use the new InflaterFactory to enable the use of hardware optimized inflaters. An accelerated inflater offering large performance improvements is coming for intel hardware in the near future. Watch https://github.com/Intel-HLS/gkl for updates.

Improved support for java.nio.Path : We're expanding support for using java.nio.Path in addition to the more limited File. You can you now read bams and feature files from a Path. This is exciting for anyone using FileSystem providers to access data in the cloud.

This release removes a number of long deprecated methods and deprecates LazyInitializer. Please update your code accordingly.

Complete change list:

  • Changed parameter names and doc to be consistent in use of "offset" and "position".
  • Make constructors public in CustomGzipOutputStream (#798)
  • Add/improve CRAM roundtripping tests. (#720)
  • updating tribble to support path wrappers (#796)
  • Don't set a custom default InflaterFactory when testing passing in an explicit InflaterFactory (#795)
  • Small patches to custom InflaterFactory support left over from code review (#794)
  • add inflater factory (#771)
  • Add getters for defaults SAMFileWriterFactory fields (#791)
  • wrap both path and index (#785)
  • improve ambiguous documentation in SAMRecord.getAlignmentStart() (#782)
  • Increase Test Coverage, fix tiny bug in Node class (regarding OVERLAPS) (#779)
  • Support use of Path in ParsingUtils, SeekableStreamFactory, AbstractVCFCodec. (#724)
  • fixed unmappable character for encoding ASCII (#784)
  • refactoring Lazy to take a Supplier() (#780)
  • removed deprecated LineReaderUtil (#754)
  • removed gelitext package and usages (#753)
  • removing unused package-specific (visible for testing) deprecated method (#752)
  • Discounts reads that are non-filter-passing in DuplicateScoringStrategy (#745)
  • Async BAM decompression (#576)
  • adding new method SamReaderFactory.setPathWrapper(#775)
  • switching coverage reporting from coveralls to codecov (#764)
  • replacing uses of getRecordAndPositions with getRecordAndOffsets (#715)
  • Methods for default sequence dictionary name (#774)
  • updating the gradle version from 2.13 to 3.2.1 (#727)
  • removed VariantContextWriterFactory (#756)
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