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Remove unused classes following #5127. #5292

Merged
merged 1 commit into from
Jan 11, 2019
Merged

Remove unused classes following #5127. #5292

merged 1 commit into from
Jan 11, 2019

Commits on Jan 11, 2019

  1. Remove unused classes following #5127. 

    * AddContextDataToReadSpark (and AddContextDataToReadSparkUnitTest) implemented the different JoinStrategy options for
  BQSR; has been replaced with the Spark Files mecahnism (see #5127)
* BroadcastJoinReadsWithRefBases and JoinReadsWithRefBasesSparkUnitTest were only used by AddContextDataToReadSpark
* BroadcastJoinReadsWithVariants and JoinReadsWithVariantsSparkUnitTest were only used by AddContextDataToReadSpark
* ShuffleJoinReadsWithRefBases and ShuffleJoinReadsWithVariants were only used by AddContextDataToReadSpark
* JoinStrategy was only used for BQSR (HC always uses overlaps partitioner), but is no longer used since #5127
* KnownSitesCache was replaced with Spark Files
* ReferenceMultiSourceAdapter in HaplotypeCallerSpark was replaced with the regular ReferenceDataSource
* BaseRecalibratorEngineSparkWrapper was only used by BaseRecalibratorSparkSharded, which was removed in #5192
    @tomwhite @jamesemery
    tomwhite authored and jamesemery committed Jan 11, 2019
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