Package org.broadinstitute.hellbender.engine

Class MultiplePassVariantWalker

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.GATKTool

org.broadinstitute.hellbender.engine.WalkerBase

org.broadinstitute.hellbender.engine.VariantWalkerBase

org.broadinstitute.hellbender.engine.VariantWalker

org.broadinstitute.hellbender.engine.MultiplePassVariantWalker

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

Direct Known Subclasses:

FilterMutectCalls, LabeledVariantAnnotationsWalker, TwoPassVariantWalker

public abstract class MultiplePassVariantWalker
extends VariantWalker

A VariantWalker that makes multiple passes through the variants. This allows the user to store internal states during early passes, which the user can then process and access during later passes

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.VariantWalker

drivingVariantFile

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

DEFAULT_DRIVING_VARIANTS_LOOKAHEAD_BASES, genomicsDBOptions

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
MultiplePassVariantWalker()

Method Summary

Modifier and Type	Method	Description
protected abstract void	afterNthPass(int n)	Process the data collected during the first pass.
final void	apply(htsjdk.variant.variantcontext.VariantContext variant, ReadsContext readsContext, ReferenceContext referenceContext, FeatureContext featureContext)	Make final to hide it from subclasses
protected abstract void	nthPassApply(htsjdk.variant.variantcontext.VariantContext variant, ReadsContext readsContext, ReferenceContext referenceContext, FeatureContext featureContext, int n)	nth pass through the variants.
protected abstract int	numberOfPasses()
void	traverse()	Implementation of variant-based traversal.

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

getDrivingVariantsFeatureInput, getHeaderForVariants, getSequenceDictionaryForDrivingVariants, getSpliteratorForDrivingVariants, initializeDrivingVariants, onShutdown, onStartup

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

getBestAvailableSequenceDictionary, getDrivingVariantCacheLookAheadBases, getGenomicsDBOptions, getProgressMeterRecordLabel, getTransformedVariantStream, getTransformedVariantStream, makePostVariantFilterTransformer, makePreVariantFilterTransformer, makeVariantFilter, requiresFeatures

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, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultReadFilters, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolName, getTransformedReadStream, getTraversalIntervals, getUserSuppliedIntervals, hasFeatures, hasReads, hasReference, hasUserSuppliedIntervals, initializeProgressMeter, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeSamReaderFactory, 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 Details

MultiplePassVariantWalker

public MultiplePassVariantWalker()

Method Details

numberOfPasses

protected abstract int numberOfPasses()

traverse

public void traverse()

Implementation of variant-based traversal. NOTE: You should only override VariantWalker.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. Implementation of multiple-pass variant traversal. Overrides the default, single-pass traversal framework of VariantWalkerBase allowing for multiple passes. 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.

Overrides:

traverse in class VariantWalker

nthPassApply

protected abstract void nthPassApply(htsjdk.variant.variantcontext.VariantContext variant,
 ReadsContext readsContext,
 ReferenceContext referenceContext,
 FeatureContext featureContext,
 int n)

nth pass through the variants. The user may store data in instance variables of the walker and process them in afterNthPass(int) before making a second pass

Parameters:

variant - A variant record in a vcf

readsContext - Reads overlapping the current variant. Will be empty if a read source (e.g. bam) isn't provided

referenceContext - Reference bases spanning the current variant

featureContext - A record overlapping the current variant from an auxiliary data source (e.g. gnomad)

n - Which pass it is (zero-indexed)

afterNthPass

protected abstract void afterNthPass(int n)

Process the data collected during the first pass. This method is called between the two traversals

apply

public final void apply(htsjdk.variant.variantcontext.VariantContext variant,
 ReadsContext readsContext,
 ReferenceContext referenceContext,
 FeatureContext featureContext)

Make final to hide it from subclasses

Specified by:

apply in class VariantWalker

Parameters:

variant - Current variant being processed.

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

featureContext - Features spanning the current variant. 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).