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Ran 07 Oct 2015 04:13PM UTC

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Committed 07 Oct 2015 03:36PM UTC coverage: 18.783% (-0.08%) from 18.862%

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push

travis-ci

Committed by

droazen

Commit Message

GATKSparkTool: first step towards unifying handling of standard tool inputs in Spark

-Created a new base class for Spark tools, GATKSparkTool, that centrally manages
 and validates standard tool inputs (reads, reference, and intervals). This allows
 us to enforce consistency across tools, delete duplicated boilerplate code from tools
 to load inputs, and perform standard kinds of validation (eg., sequence dictionary
 validation) in one place.

-Tools that don't fit into the pattern established by GATKSparkTool can still extend
 SparkCommandLineProgram directly.

-This is just a first step -- there is still much work to be done to unify our data source
 classes and transparently handle inputs from different sources (GCS, hdfs, files), but
 having inputs centrally managed should make the remaining tasks much easier.

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