2849
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Ran 06 Oct 2015 08:56PM UTC

Jobs 2

Files 533

Run time 12min

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Build # 2849

Build Type

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.

Run Details

22296 of 27531 relevant lines covered (80.99%)

0.98 hits per line

Jobs

ID	Job ID	Ran	Files	Coverage
1	2849.1 (CLOUD=mandatory)	06 Oct 2015 09:08PM UTC	0	18.86	Travis Job 2849.1
3	2849.3 (CLOUD=false)	06 Oct 2015 08:56PM UTC	0	78.71	Travis Job 2849.3

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