Package org.broadinstitute.hellbender.tools.funcotator

Class FuncotatorDataSourceDownloader

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.tools.funcotator.FuncotatorDataSourceDownloader

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@DocumentedFeature
public class FuncotatorDataSourceDownloader
extends CommandLineProgram

FuncotatorDataSourceDownloader is a tool to download the latest data sources for Funcotator.

General Information

This tool can download pre-packaged data sources for both the somatic and germline use cases. The data sources downloaded by this tool correspond to the latest / current maximum of the data sources supported as defined in DataSourceUtils.CURRENT_MAXIMUM_DATA_SOURCE_VERSION.

To download and extract the data sources, you can invoke FuncotatorDataSourceDownloader in the following ways:

• For somatic data sources:
  

  ./gatk FuncotatorDataSourceDownloader --somatic --validate-integrity --extract-after-download

• For germline data sources:
  

  ./gatk FuncotatorDataSourceDownloader --germline --validate-integrity --extract-after-download

Notes

• By default FuncotatorDataSourceDownloader will not overwrite data sources if they already exist locally.
• It is recommended to run the validation step after downloading the data sources to ensure download integrity.
• Using this tool will result in longer download times for data sources than if gsutil were invoked directly to copy down the data sources.
  This is a known issue and is due to the tool printing the progress of the download.

Nested Class Summary

Nested classes/interfaces inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram

CommandLineProgram.AutoCloseableNoCheckedExceptions

Field Summary

Fields

Modifier and Type	Field	Description
static final String	EXTRACT_AFTER_DOWNLOAD
protected boolean	extractDataSourcesAfterDownload
static final String	GERMLINE_ARG_LONG_NAME
protected File	outputFile
static final String	OVERWRITE_ARG_LONG_NAME
static final String	SOMATIC_ARG_LONG_NAME
static final String	SOMATIC_GCLOUD_DATASOURCES_BASEURL
static final Path	SOMATIC_GCLOUD_DATASOURCES_PATH
static final String	VALIDATE_INTEGRITY_ARG_LONG_NAME

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

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

Constructor Summary

Constructors

Constructor	Description
FuncotatorDataSourceDownloader()

Method Summary

Modifier and Type	Method	Description
protected Object	doWork()	Do the work after command line has been parsed.
protected void	onStartup()	Perform initialization/setup after command-line argument parsing but before doWork() is invoked.

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, 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 Details

VALIDATE_INTEGRITY_ARG_LONG_NAME

public static final String VALIDATE_INTEGRITY_ARG_LONG_NAME

See Also:

• Constant Field Values

SOMATIC_ARG_LONG_NAME

public static final String SOMATIC_ARG_LONG_NAME

See Also:

• Constant Field Values

GERMLINE_ARG_LONG_NAME

public static final String GERMLINE_ARG_LONG_NAME

See Also:

• Constant Field Values

OVERWRITE_ARG_LONG_NAME

public static final String OVERWRITE_ARG_LONG_NAME

See Also:

• Constant Field Values

EXTRACT_AFTER_DOWNLOAD

public static final String EXTRACT_AFTER_DOWNLOAD

See Also:

• Constant Field Values

SOMATIC_GCLOUD_DATASOURCES_BASEURL

public static final String SOMATIC_GCLOUD_DATASOURCES_BASEURL

SOMATIC_GCLOUD_DATASOURCES_PATH

public static final Path SOMATIC_GCLOUD_DATASOURCES_PATH

outputFile

@Argument(shortName="O",
          fullName="output",
          doc="Output location for the data sources.",
          optional=true)
protected File outputFile

extractDataSourcesAfterDownload

@Argument(shortName="extract-after-download",
          fullName="extract-after-download",
          doc="Extract the data sources to a sibling folder after they have been downloaded.",
          optional=true)
protected boolean extractDataSourcesAfterDownload

Constructor Details

FuncotatorDataSourceDownloader

public FuncotatorDataSourceDownloader()

Method Details

onStartup

protected void onStartup()

Description copied from class: CommandLineProgram

Perform initialization/setup after command-line argument parsing but before doWork() is invoked. Default implementation does nothing. Subclasses can override to perform initialization.

Overrides:

onStartup in class CommandLineProgram

doWork

protected 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.