org.broadinstitute.hellbender.tools

Class GetSampleName

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.GATKTool

org.broadinstitute.hellbender.tools.GetSampleName

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@DocumentedFeature
public final class GetSampleName
extends GATKTool

Emit a single sample name from the bam header into an output file. The sample name is that in the read group (RG) sample (SM) field

Note: If the bam has zero or more than one sample names in the header, this tool will error, by design. This tool has not been tested extensively. Most options supported by the GATK are irrelevant for this tool.

Input

• A BAM file with a single sample name in the header

Output

• A file with a single sample name in it

Example Usage

   gatk GetSampleName \
     -I input.bam \
     -O sample_name.txt
 

Field Summary

Fields

Modifier and Type	Field and Description
protected java.io.File	outputSampleNameFile
static java.lang.String	STANDARD_ENCODING
static java.lang.String	URL_ENCODING_LONG_NAME
static java.lang.String	URL_ENCODING_SHORT_NAME
protected boolean	urlEncode

Fields inherited from class org.broadinstitute.hellbender.engine.GATKTool

addOutputSAMProgramRecord, addOutputVCFCommandLine, cloudIndexPrefetchBuffer, cloudPrefetchBuffer, createOutputBamIndex, createOutputBamMD5, createOutputVariantIndex, createOutputVariantMD5, disableBamIndexCaching, features, intervalArgumentCollection, lenientVCFProcessing, outputSitesOnlyVCFs, progressMeter, readArguments, referenceArguments, SECONDS_BETWEEN_PROGRESS_UPDATES_NAME, seqValidationArguments

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
GetSampleName()

Method Summary

Modifier and Type	Method and Description
void	onTraversalStart() Operations performed just prior to the start of traversal.
boolean	requiresReads() Does this tool require reads? Traversals types and/or tools that do should override to return true.
void	traverse() A complete traversal from start to finish.

Methods inherited from class org.broadinstitute.hellbender.engine.GATKTool

addFeatureInputsAfterInitialization, closeTool, createSAMWriter, createSAMWriter, createVCFWriter, createVCFWriter, directlyAccessEngineFeatureManager, directlyAccessEngineReadsDataSource, directlyAccessEngineReferenceDataSource, doWork, getBestAvailableSequenceDictionary, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultReadFilters, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getGenomicsDBOptions, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getProgressMeterRecordLabel, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolName, getTransformedReadStream, getTraversalIntervals, hasFeatures, hasReads, hasReference, hasUserSuppliedIntervals, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeVariantAnnotations, onShutdown, onStartup, onTraversalSuccess, requiresFeatures, requiresIntervals, requiresReference, transformTraversalIntervals, useVariantAnnotations

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

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getSupportInformation, getToolkitName, getToolkitShortName, getToolStatusWarning, getUsage, getVersion, instanceMain, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, 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

STANDARD_ENCODING

public static final java.lang.String STANDARD_ENCODING

See Also:

Constant Field Values

outputSampleNameFile

@Argument(doc="Output file with only the sample name in it.",
          fullName="output",
          shortName="O")
protected java.io.File outputSampleNameFile

URL_ENCODING_LONG_NAME

public static final java.lang.String URL_ENCODING_LONG_NAME

See Also:

Constant Field Values

URL_ENCODING_SHORT_NAME

public static final java.lang.String URL_ENCODING_SHORT_NAME

See Also:

Constant Field Values

urlEncode

@Argument(doc="Apply URL encoding to convert spaces and other special characters in sample name.",
          fullName="use-url-encoding",
          shortName="encode")
protected boolean urlEncode

Constructor Detail

GetSampleName

public GetSampleName()

Method Detail

traverse

public void traverse()

Description copied from class: GATKTool

A complete traversal from start to finish. Tool authors who wish to "roll their own" traversal from scratch can extend this class directly and implement this method. Walker authors should instead extend a Walker class and implement the Walker-appropriate apply() method, since the Walker base classes implement the various kinds of traversals for you.

Specified by:

traverse in class GATKTool

requiresReads

public boolean requiresReads()

Description copied from class: GATKTool

Does this tool require reads? Traversals types and/or tools that do should override to return true.

Overrides:

requiresReads in class GATKTool

Returns:

true if this tool requires reads, otherwise false

onTraversalStart

public void onTraversalStart()

Description copied from class: GATKTool

Operations performed just prior to the start of traversal. Should be overridden by tool authors who need to process arguments local to their tool or perform other kinds of local initialization. Default implementation does nothing.

Overrides:

onTraversalStart in class GATKTool