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
GetSampleNameas 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)