org.broadinstitute.hellbender.engine.spark

Class SparkCommandLineProgram

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram

All Implemented Interfaces:

java.io.Serializable, org.broadinstitute.barclay.argparser.CommandLinePluginProvider

Direct Known Subclasses:

CreateReadCountPanelOfNormals, GATKSparkTool

public abstract class SparkCommandLineProgram
extends CommandLineProgram
implements java.io.Serializable

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String	programName
static java.lang.String	SPARK_PROGRAM_NAME_LONG_NAME
SparkCommandLineArgumentCollection	sparkArgs

Fields inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram

GATK_CONFIG_FILE, logger, NIO_MAX_REOPENS, NIO_PROJECT_FOR_REQUESTER_PAYS, QUIET, specialArgumentsCollection, tmpDir, useJdkDeflater, useJdkInflater, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
SparkCommandLineProgram()

Method Summary

Modifier and Type	Method and Description
protected void	afterPipeline(org.apache.spark.api.java.JavaSparkContext ctx) Extend this method to run code after the pipeline returns.
protected java.lang.Object	doWork() Do the work after command line has been parsed.
protected java.lang.String	getProgramName() Returns the program's name.
protected abstract void	runPipeline(org.apache.spark.api.java.JavaSparkContext ctx) Runs the pipeline.

Methods inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getPluginDescriptors, getSupportInformation, getToolkitName, getToolkitShortName, getToolStatusWarning, getUsage, getVersion, instanceMain, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, onShutdown, onStartup, parseArgs, printLibraryVersions, printSettings, printStartupMessage, runTool, setDefaultHeaders, warnOnToolStatus

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

SPARK_PROGRAM_NAME_LONG_NAME

public static final java.lang.String SPARK_PROGRAM_NAME_LONG_NAME

See Also:

Constant Field Values

programName

@Argument(doc="Name of the program running",
          fullName="program-name",
          optional=true)
public java.lang.String programName

sparkArgs

@ArgumentCollection
public SparkCommandLineArgumentCollection sparkArgs

Constructor Detail

SparkCommandLineProgram

public SparkCommandLineProgram()

Method Detail

doWork

protected java.lang.Object doWork()

Description copied from class: CommandLineProgram

Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.

Specified by:

doWork in class CommandLineProgram

Returns:

the return value or null is there is none.

runPipeline

protected abstract void runPipeline(org.apache.spark.api.java.JavaSparkContext ctx)

Runs the pipeline.

afterPipeline

protected void afterPipeline(org.apache.spark.api.java.JavaSparkContext ctx)

Extend this method to run code after the pipeline returns. This method is called whether or not the runPipeline call succeeded.

getProgramName

protected java.lang.String getProgramName()

Returns the program's name. If programName argument is provided, returns that. Otherwise, returns the simple name of the class. Subclasses can override if desired.