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
broadinstitute · Oct 8, 2018 · bd0247d · bd0247d
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Showing 13 changed files with 7 additions and 1,052 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/engine/spark/AddContextDataToReadSpark.java b/src/main/java/org/broadinstitute/hellbender/engine/spark/AddContextDataToReadSpark.java
diff --git a/src/main/java/org/broadinstitute/hellbender/engine/spark/BroadcastJoinReadsWithRefBases.java b/src/main/java/org/broadinstitute/hellbender/engine/spark/BroadcastJoinReadsWithRefBases.java
diff --git a/src/main/java/org/broadinstitute/hellbender/engine/spark/BroadcastJoinReadsWithVariants.java b/src/main/java/org/broadinstitute/hellbender/engine/spark/BroadcastJoinReadsWithVariants.java
diff --git a/src/main/java/org/broadinstitute/hellbender/engine/spark/JoinStrategy.java b/src/main/java/org/broadinstitute/hellbender/engine/spark/JoinStrategy.java
diff --git a/src/main/java/org/broadinstitute/hellbender/engine/spark/KnownSitesCache.java b/src/main/java/org/broadinstitute/hellbender/engine/spark/KnownSitesCache.java