Commits on Nov 19, 2015

1. [ADAM-883] Add caching to Transform pipeline. …

   The Transform pipeline in the CLI has several stages (e.g., sort, indel
   realignment, BQSR) that trigger recomputation. If you are running a single
   stage off of local storage/HDFS/Tachyon, this is OK. However, if you're running
   multiple stages, or you are loading data from S3/etc, this can lead to serious
   performance degradation. To address this, I've added the proper caching
   statements. Additionally, I've added a hook so that the user can specify the
   storage level to use for caching. Resolves bigdatagenomics#883.

   

   fnothaft committed Nov 19, 2015
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