[ADAM-883] Add caching to Transform pipeline. #884
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Test PASSed. |
| @@ -105,6 +106,10 @@ class TransformArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs { | |||
| var mdTagsFragmentSize: Long = 1000000L | |||
| @Args4jOption(required = false, name = "-md_tag_overwrite", usage = "When adding MD tags to reads, overwrite existing incorrect tags.") | |||
| var mdTagsOverwrite: Boolean = false | |||
| @Args4jOption(required = false, name = "-cache", usage = "Cache data to avoid recomputing between stages.") | |||
| var cache: Boolean = false | |||
| @Args4jOption(required = false, name = "-storageLevel", usage = "Set the storage level to use for caching.") | |||
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-storageLevel → -storage_level?
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Good catch; will fix. Thanks!
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.
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Fixed nit and rebased. |
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Test PASSed. |
heuermh
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Nov 19, 2015
[ADAM-883] Add caching to Transform pipeline.
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Thanks! |
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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 #883.