org.broadinstitute.hellbender.cmdline

Class PicardCommandLineProgramExecutor

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

public class PicardCommandLineProgramExecutor
extends CommandLineProgram

Adapter shim for use within GATK to run Picard tools. Note that this class does not have it's own CommandLineProgramProperties annotation, and isn't intended to be run from the command line.

Field Summary

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
PicardCommandLineProgramExecutor(CommandLineProgram picardCommandLineProgram)

Method Summary

Modifier and Type	Method and Description
protected java.lang.Object	doWork() Do the work after command line has been parsed.
java.lang.Object	instanceMain(java.lang.String[] argv) Entry point for Picard tools that are called from GATK.

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

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getPluginDescriptors, getSupportInformation, getToolkitName, getToolkitShortName, getToolStatusWarning, getUsage, getVersion, 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

Constructor Detail

PicardCommandLineProgramExecutor

public PicardCommandLineProgramExecutor(CommandLineProgram picardCommandLineProgram)

Method Detail

instanceMain

public java.lang.Object instanceMain(java.lang.String[] argv)

Entry point for Picard tools that are called from GATK.

Overrides:

instanceMain in class CommandLineProgram

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.