org.broadinstitute.hellbender.engine

Class ReferenceWalker

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.GATKTool

org.broadinstitute.hellbender.engine.WalkerBase

org.broadinstitute.hellbender.engine.ReferenceWalker

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

Direct Known Subclasses:

CountBasesInReference, ExampleReferenceWalker, FastaReferenceMaker

public abstract class ReferenceWalker
extends WalkerBase

A reference walker is a tool which processes each base in a given reference. Each base can be processed individually or in a context of multiple bases in a window. Reads and Feature tracks can optionally be included as well. The reference bases to process can be subset to a given set of intervals. ReferenceWalker authors must implement the apply() method to process each position, and may optionally implement GATKTool.onTraversalStart() and/or GATKTool.onTraversalSuccess(). Tool authors may also implement getReferenceWindow(SimpleInterval) to provide additional bases of context around each position. See the ExampleReferenceWalker walker for an example.

Field Summary

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
ReferenceWalker()

Method Summary

Modifier and Type	Method and Description
abstract void	apply(ReferenceContext referenceContext, ReadsContext readsContext, FeatureContext featureContext) Process an individual reference locus (with optional contextual information).
java.lang.String	getProgressMeterRecordLabel()
protected SimpleInterval	getReferenceWindow(SimpleInterval locus) Determine the window to use when creating the ReferenceContext in apply.
protected void	onShutdown() Shutdown data sources.
protected void	onStartup() Initialize data sources for traversal.
boolean	requiresReference() Does this tool require reference data? 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.WalkerBase

directlyAccessEngineFeatureManager, directlyAccessEngineReadsDataSource, directlyAccessEngineReferenceDataSource

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

addFeatureInputsAfterInitialization, closeTool, createSAMWriter, createVCFWriter, createVCFWriter, createVCFWriter, doWork, getBestAvailableSequenceDictionary, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultReadFilters, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getGenomicsDBOptions, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolName, getTransformedReadStream, getTraversalIntervals, hasFeatures, hasReads, hasReference, hasUserSuppliedIntervals, initializeProgressMeter, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeVariantAnnotations, onTraversalStart, onTraversalSuccess, requiresFeatures, requiresIntervals, requiresReads, 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

Constructor Detail

ReferenceWalker

public ReferenceWalker()

Method Detail

getProgressMeterRecordLabel

public java.lang.String getProgressMeterRecordLabel()

Overrides:

getProgressMeterRecordLabel in class GATKTool

Returns:

String label to use for records in progress meter output. Defaults to ProgressMeter.DEFAULT_RECORD_LABEL, but tools may override to provide a more appropriate label (like "reads" or "regions")

requiresReference

public final boolean requiresReference()

Description copied from class: GATKTool

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

Overrides:

requiresReference in class GATKTool

Returns:

true if this tool requires a reference, otherwise false

onStartup

protected final void onStartup()

Initialize data sources for traversal. Marked final so that tool authors don't override it. Tool authors should override onTraversalStart() instead.

Overrides:

onStartup in class GATKTool

traverse

public void traverse()

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. Implementation of reference-locus-based traversal. NOTE: You should only override traverse() if you are writing a new walker base class in the engine package that extends this class. It is not meant to be overridden by tools outside of the engine package.

Specified by:

traverse in class GATKTool

getReferenceWindow

protected SimpleInterval getReferenceWindow(SimpleInterval locus)

Determine the window to use when creating the ReferenceContext in apply. This determines which reference bases are seen at each position, as well as which reads / features are considered to overlap the reference site. The default implementation returns the single reference locus passed that is passed in, but subclasses may override this method in order to change the window size.

Parameters:

locus - the current locus being processed in the traversal

Returns:

the window to use when creating the ReferenceContext that is passed into apply(ReferenceContext, ReadsContext, FeatureContext)

apply

public abstract void apply(ReferenceContext referenceContext,
                           ReadsContext readsContext,
                           FeatureContext featureContext)

Process an individual reference locus (with optional contextual information). Must be implemented by tool authors. In general, tool authors should simply stream their output from apply(), and maintain as little internal state as possible.

Parameters:

referenceContext - Reference bases at the current locus. The window around the single locus is provided by getReferenceWindow(SimpleInterval) Additional bases my be retrieved by invoking the by invoking ReferenceContext.setWindow(int, int) on this object before calling ReferenceContext.getBases(), however this will not effect the set of reads and features that are considered overlapping which are based on the preset window passed in.

readsContext - Reads spanning the current reference window. Will be an empty, but non-null, context object if there is no backing source of Read data (in which case all queries on it will return an empty List).

featureContext - Features spanning the current reference window. Will be an empty, but non-null, context object if there is no backing source of Feature data (in which case all queries on it will return an empty List).

onShutdown

protected final void onShutdown()

Shutdown data sources. Marked final so that tool authors don't override it. Tool authors should override GATKTool.onTraversalSuccess() instead.

Overrides:

onShutdown in class GATKTool