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@lbergelson lbergelson released this 06 Sep 18:06
· 1839 commits to master since this release
4.beta.5
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lbergelson Louis Bergelson
GPG key ID: CDB73EA73CD9CF1E
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Small release, includes highlights include an update to our BWA-MEM version, an experimental PythonScriptExecutor and an important bugfix for ValidateVariants -gvcf mode

Note: this still includes snapshot dependencies that prevent us from releasing to Maven central.

Complete change list:

  • Make directory name unique for BucketUtilsTest#testDirSizeGCS to avoid unwanted test interaction. (#3547)
  • Simple PythonScriptExecutor. #3501 (#3536)
  • Fix BucketUtils#dirSize on GCS. #3437 (#3539)
  • code duplication in read pos rank sum and its allele-specific version #1882 (#2657)
  • validatevariants -gvcf fix (#3530)
  • Added GetSampleName as stopgap until we have named parameters (#3538)
  • Pair HMM docs (#3433)
  • Fix MissingReferenceDictFile exception constructor. #3492 #2922 (#3524)
  • Extend ReadsPipelineSpark to run HaplotypeCallerSpark (#3452)
  • Updates bwamem-jni depedency to 1.0.2 and adds the possibility of aligning singletons to BwaEngine classes. (#3474)
  • Structural Variant Context (#3476)
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