2861
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Ran 07 Oct 2015 04:25PM UTC

Jobs 2

Files 537

Run time 9min

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Build # 2861

Build Type

Pull #955

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.

Pull Request Pull Request #955: GATKSparkTool: first step towards unifying handling of standard tool inputs in Spark

Run Details

22319 of 27562 relevant lines covered (80.98%)

0.98 hits per line

Uncovered Existing Lines

Lines	Coverage	File
1	100.0	src/main/java/org/broadinstitute/hellbender/tools/spark/BaseRecalibratorSpark.java
1	100.0	src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/CountBasesSpark.java
1	100.0	src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/CountReadsSpark.java
1	100.0	src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/FlagStatSpark.java
2	100.0	src/main/java/org/broadinstitute/hellbender/tools/spark/ApplyBQSRSpark.java
2	100.0	src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/PrintReadsSpark.java
3	100.0	src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/SortBamSpark.java
3	100.0	src/main/java/org/broadinstitute/hellbender/tools/spark/transforms/markduplicates/MarkDuplicatesSpark.java
12	100.0	src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/ReadsPipelineSpark.java

Jobs

ID	Job ID	Ran	Files	Coverage
1	2861.1 (CLOUD=mandatory)	07 Oct 2015 04:25PM UTC	0	18.78	Travis Job 2861.1
3	2861.3 (CLOUD=false)	07 Oct 2015 04:34PM UTC	0	78.91	Travis Job 2861.3

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