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Fix NPR when CountReadsSpark is run with no output file #1523

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lbergelson opened this issue Feb 25, 2016 · 0 comments · Fixed by #1535
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Fix NPR when CountReadsSpark is run with no output file #1523

lbergelson opened this issue Feb 25, 2016 · 0 comments · Fixed by #1535
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@lbergelson
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alpha-1

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@lbergelson
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Running without an output file causes an NPR. Needs a null check.

./gatk-launch CountReadsSpark -I src/test/resources/org/broadinstitute/hellbender/tools/count_reads_sorted.bam

java.lang.NullPointerException
    at org.broadinstitute.hellbender.utils.gcs.BucketUtils.isCloudStorageUrl(BucketUtils.java:44)
    at org.broadinstitute.hellbender.utils.gcs.BucketUtils.createFile(BucketUtils.java:105)
    at org.broadinstitute.hellbender.tools.spark.pipelines.CountReadsSpark.runTool(CountReadsSpark.java:37)
    at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:310)
    at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:38)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:98)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:146)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:165)
    at org.broadinstitute.hellbender.Main.instanceMain(Main.java:66)
    at org.broadinstitute.hellbender.Main.main(Main.java:81)
@lbergelson lbergelson added the bug label Feb 25, 2016
@lbergelson lbergelson self-assigned this Feb 25, 2016
@lbergelson lbergelson added this to the alpha-1 milestone Feb 25, 2016
lbergelson added a commit that referenced this issue Feb 29, 2016
@lbergelson
fixing nprs in spark tools where no output file was specified
531db69 
adding tests for NPR when there's no output specified
this effects CountBasesSpark, CountReadsSpark, FlagStatSpark, and CountVariantsSpark
fixes #1523

fixing an error in CountVariantsSpark where the vcf input was optional

adding some convinience functions to ArgumentsBuilder
@lbergelson lbergelson mentioned this issue Feb 29, 2016
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fixing nprs in spark tools where no output file was specified broadinstitute/gatk
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