org.broadinstitute.hellbender.tools.walkers.mutect

Class MergeMutectStats

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.tools.walkers.mutect.MergeMutectStats

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

public class MergeMutectStats
extends CommandLineProgram

Merge the stats output by scatters of a single Mutect2 job.

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
MergeMutectStats()

Method Summary

Modifier and Type	Method and Description
java.lang.Object	doWork() Do the work after command line has been parsed.

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

Constructor Detail

MergeMutectStats

public MergeMutectStats()

Method Detail

doWork

public 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.