org.broadinstitute.hellbender.engine

Class FeatureWalker<F extends htsjdk.tribble.Feature>

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.GATKTool

org.broadinstitute.hellbender.engine.WalkerBase

org.broadinstitute.hellbender.engine.FeatureWalker<F>

Type Parameters:

F - the driving feature type.

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

Direct Known Subclasses:

ExampleFeatureWalker, FuncotateSegments

public abstract class FeatureWalker<F extends htsjdk.tribble.Feature>
extends WalkerBase

A FeatureWalker is a tool that processes a Feature at a time from a source of Features, with optional contextual information from a reference, sets of reads, and/or supplementary sources of Features. Subclasses must implement the apply(Feature, ReadsContext, ReferenceContext, FeatureContext) method to process each Feature, as well as isAcceptableFeatureType(Class) and getDrivingFeatureFile(), and may optionally implement GATKTool.onTraversalStart(), GATKTool.onTraversalSuccess(), and/or GATKTool.closeTool().

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
FeatureWalker()

Method Summary

Modifier and Type	Method and Description
abstract void	apply(F feature, ReadsContext readsContext, ReferenceContext referenceContext, FeatureContext featureContext) Process an individual feature.
abstract java.io.File	getDrivingFeatureFile() Returns the file that contains the driving features.
java.lang.String	getProgressMeterRecordLabel()
protected abstract boolean	isAcceptableFeatureType(java.lang.Class<? extends htsjdk.tribble.Feature> featureType) Returns whether the given class of features is acceptable for this walker.
protected <T extends htsjdk.tribble.Feature> SimpleInterval	makeFeatureInterval(T feature) This method can be overridden if you need to customize the interval for a given feature.
protected void	onShutdown() Close the reads and reference data sources.
protected void	onStartup() Set the intervals for traversal in the driving features.
boolean	requiresFeatures() Does this tool require features? 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, createSAMWriter, 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, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeVariantAnnotations, onTraversalStart, onTraversalSuccess, requiresIntervals, requiresReads, 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

Constructor Detail

FeatureWalker

public FeatureWalker()

Method Detail

requiresFeatures

public boolean requiresFeatures()

Description copied from class: GATKTool

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

Overrides:

requiresFeatures in class GATKTool

Returns:

true if this tool requires reads, otherwise false

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")

onStartup

protected final void onStartup()

Set the intervals for traversal in the driving features. Marked final so that subclasses don't override it. Subclasses should override GATKTool.onTraversalStart() instead.

Overrides:

onStartup in class GATKTool

isAcceptableFeatureType

protected abstract boolean isAcceptableFeatureType(java.lang.Class<? extends htsjdk.tribble.Feature> featureType)

Returns whether the given class of features is acceptable for this walker.

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 Feature-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

makeFeatureInterval

protected <T extends htsjdk.tribble.Feature> SimpleInterval makeFeatureInterval(T feature)

This method can be overridden if you need to customize the interval for a given feature.

Type Parameters:

T - Class that extends feature.

Parameters:

feature - Feature to derive the interval.

Returns:

Interval for the given feature. Typically, this is just the extents of the feature itself. Never null

apply

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

Process an individual feature. In general, subclasses should simply stream their output from apply(), and maintain as little internal state as possible.

Parameters:

feature - Current Feature being processed.

readsContext - Reads overlapping the current feature. Will be an empty, but non-null, context object if there is no backing source of reads data (in which case all queries on it will return an empty array/iterator)

referenceContext - Reference bases spanning the current feature. Will be an empty, but non-null, context object if there is no backing source of reference data (in which case all queries on it will return an empty array/iterator). Can request extra bases of context around the current feature's interval by invoking ReferenceContext.setWindow(int, int) on this object before calling ReferenceContext.getBases()

featureContext - Features spanning the current feature. 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()

Close the reads and reference data sources. Marked final so that subclasses don't override it. Subclasses should override GATKTool.onTraversalSuccess() instead.

Overrides:

onShutdown in class GATKTool

getDrivingFeatureFile

public abstract java.io.File getDrivingFeatureFile()

Returns the file that contains the driving features.

Returns:

never null.