Package org.broadinstitute.hellbender.engine

Class IntervalWalker

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.GATKTool

org.broadinstitute.hellbender.engine.WalkerBase

org.broadinstitute.hellbender.engine.IntervalWalker

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

Direct Known Subclasses:

ExampleIntervalWalker

public abstract class IntervalWalker
extends WalkerBase

An IntervalWalker is a tool that processes a single interval at a time, with the ability to query optional overlapping sources of reads, reference data, and/or variants/features. The current implementation uses no caching, and so will likely only provide acceptable performance if intervals are spaced sufficiently far apart that few records (reads, etc.) will overlap more than one interval. Performance will likely be poor given a large set of small, nearby intervals, but we will address this issue when porting this traversal to dataflow. IntervalWalker authors must implement the apply() method to process each interval, and may optionally implement onTraversalStart() and/or onTraversalSuccess(). See the ExampleIntervalWalker tool for an example.

Nested Class Summary

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

CommandLineProgram.AutoCloseableNoCheckedExceptions

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	Description
IntervalWalker()

Method Summary

Modifier and Type	Method	Description
abstract void	apply(SimpleInterval interval, ReadsContext readsContext, ReferenceContext referenceContext, FeatureContext featureContext)	Process an individual interval.
String	getProgressMeterRecordLabel()
protected final void	onShutdown()	Close data sources.
protected final void	onStartup()	Initialize data sources.
boolean	requiresIntervals()	Does this tool require intervals? 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, bamIndexCachingShouldBeEnabled, closeTool, createSAMWriter, createVCFWriter, createVCFWriter, createVCFWriter, disableProgressMeter, doWork, getBestAvailableSequenceDictionary, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultReadFilters, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getGenomicsDBOptions, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolName, getTransformedReadStream, getTraversalIntervals, getUserSuppliedIntervals, hasFeatures, hasReads, hasReference, hasUserSuppliedIntervals, initializeProgressMeter, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeSamReaderFactory, makeVariantAnnotations, onTraversalStart, onTraversalSuccess, requiresFeatures, 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 Details

IntervalWalker

public IntervalWalker()

Method Details

requiresIntervals

public boolean requiresIntervals()

Description copied from class: GATKTool

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

Overrides:

requiresIntervals in class GATKTool

Returns:

true if this tool requires intervals, otherwise false

getProgressMeterRecordLabel

public 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()

Initialize data sources. Marked final so that tool authors don't override it. Tool authors should override onTraversalSuccess() 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 interval-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

apply

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

Process an individual interval. 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:

interval - Current interval being processed.

readsContext - Reads overlapping the current interval. 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 interval. 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 interval by invoking ReferenceContext.setWindow(int, int) on this object before calling ReferenceContext.getBases()

featureContext - Features spanning the current interval. 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 data sources. Marked final so that tool authors don't override it. Tool authors should override onTraversalSuccess() instead.

Overrides:

onShutdown in class GATKTool