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@lbergelson lbergelson released this 01 Jun 19:43
· 463 commits to master since this release
2.10.0
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lbergelson Louis Bergelson
GPG key ID: CDB73EA73CD9CF1E
Learn about vigilant mode.
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This release includes useful new features and a lot of bug fixes:

  • Expanded support for Path to more of the api (#846, #810, #814)
  • There's now support for creating fasta.fai indexes (#842)
  • HTSJDK tests can now be written in scala as well as java (#789)

This release includes changes to the htsjdk.tribble.Index API. Anyone who has implemented a subclass of Index will have to update their class See #841 and #810 for more details.

Detailed Changes:

  • Revert "The existing code was throwing a NPE when using a CRAMFileReader for … (#879)" (#885)
  • The existing code was throwing a NPE when using a CRAMFileReader for … (#879)
  • Index.writeBasedOnFeaturePath throws instead of silently failing (#841)
  • fixed a small NPE in MD5CalculatingOutputStream (#881)
  • Fix ordering of assignments in FastQReader constructor. (#878)
  • Adding OpenJDK8 to travis configuration (#875)
  • Defensive programming around test case race condition to address #776 (#790)
  • Obey the tmpDir setting in several constructors that currently ignore it (#826)
  • add UNKNOWN sort order(#862)
  • More informative IO error for FASTQ reader (#865)
  • Add .fai index creation support (#842)
  • Add fromPath to IntervalList. (#846)
  • Count the number of warnings and errors during SAM file validation (#855)
  • Added the ability to query the length of the line terminator to AsciiLineReader. (#843)
  • removing scripts/release_picard.sh (#858)
  • Adding a pre-test check that looks for java files in the test/scala d… (#857)
  • Expose a couple of protected methods and replace hard coded strings with an enum. (#854)
  • check for negative length in CigarElement ctor (#839)
  • replace method getRefPos() into abstract class EdgingRecordAndOffset and delete constructor in AbstractRecordAndOffset (#849)
  • Enabling writing and running of tests with scalatest. (#789)
  • Maintain ordering of header in smartMergeHeader #847 (#848)
  • Fix DateParserTest unit tests that were failing in my locale. (#832)
  • Make exception message informative in SAMUtils.charToCompressedBase (#836)
  • Adding getSAMString to AbstractSAMHeaderRecord (#827)
  • Update javadoc for Feature (#818)
  • Tribble/Tabix index path support (#810)
  • Fix for issue #513: NPE in ValidateSamFile with CRAM (#735)
  • fixing vararg warnings on test compilation (#809)
  • support Path in Md5CalculatingOutputStream(#814)
  • Fixed bug where calling IntervalList.uniqued(false) would fail if the interval names were null. (#815)
  • Refactoring FastqRecord (#572)
  • automatically adding @OverRide annotations (#729)
  • add a coverage drop threshold to limit codecov failure spam (#803)
  • fixes for issue #547
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