org.broadinstitute.hellbender.tools

Class IndexFeatureFile

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.tools.IndexFeatureFile

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@DocumentedFeature
public final class IndexFeatureFile
extends CommandLineProgram

This tool creates an index file for the various kinds of feature-containing files supported by GATK (such as VCF and BED files). An index allows querying features by a genomic interval.

Usage example

 gatk IndexFeatureFile \
     -I cohort.vcf.gz
 

This produces the corresponding index, cohort.vcf.gz.tbi.

Field Summary

Fields

Modifier and Type	Field and Description
GATKPath	featurePath
static java.lang.String	GVCF_FILE_EXTENSION
static int	OPTIMAL_GVCF_INDEX_BIN_SIZE
GATKPath	outputPath

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 and Description
IndexFeatureFile()

Method Summary

Modifier and Type	Method and Description
protected 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

Field Detail

featurePath

@Argument(shortName="I",
          fullName="input",
          doc="Feature file (eg., VCF or BED file) to index. Must be in a tribble-supported format")
public GATKPath featurePath

outputPath

@Argument(shortName="O",
          fullName="output",
          doc="The output index file. If missing, the tool will create an index file in the same directory as the input file.",
          optional=true)
public GATKPath outputPath

OPTIMAL_GVCF_INDEX_BIN_SIZE

public static final int OPTIMAL_GVCF_INDEX_BIN_SIZE

See Also:

Constant Field Values

GVCF_FILE_EXTENSION

public static final java.lang.String GVCF_FILE_EXTENSION

See Also:

Constant Field Values

Constructor Detail

IndexFeatureFile

public IndexFeatureFile()

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.