org.broadinstitute.hellbender.engine

Class MultiVariantWalker

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.MultiVariantWalker

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

Direct Known Subclasses:

ApplyVQSR, MultiVariantWalkerGroupedOnStart, VariantEval, VariantRecalibrator

public abstract class MultiVariantWalker
extends VariantWalkerBase

A MultiVariantWalker is a tool that processes one variant at a time, in position order, from multiple sources of variants, with optional contextual information from a reference, sets of reads, and/or supplementary sources of Features. VariantWalker authors must implement the apply(htsjdk.variant.variantcontext.VariantContext, org.broadinstitute.hellbender.engine.ReadsContext, org.broadinstitute.hellbender.engine.ReferenceContext, org.broadinstitute.hellbender.engine.FeatureContext) method to process each variant, and may optionally implement GATKTool.onTraversalStart(), GATKTool.onTraversalSuccess() and/or GATKTool.closeTool().

Field Summary

Fields

Modifier and Type	Field and Description
protected MultiVariantInputArgumentCollection	multiVariantInputArgumentCollection

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 and Description
MultiVariantWalker()

Method Summary

Modifier and Type	Method and Description
abstract void	apply(htsjdk.variant.variantcontext.VariantContext variant, ReadsContext readsContext, ReferenceContext referenceContext, FeatureContext featureContext) Process an individual variant.
boolean	doDictionaryCrossValidation() Should this tool cross-validate the sequence dictionaries for input feature files? If a large number of inputs are expected, the tools should override to return false and require a reference.
protected java.util.List<FeatureInput<htsjdk.variant.variantcontext.VariantContext>>	getDrivingVariantsFeatureInputs() Returns a list of feature inputs used for the driving variants for this source.
htsjdk.variant.vcf.VCFHeader	getHeaderForVariants() Gets the header associated with our driving source of variants as a VCFHeader.
protected MultiVariantInputArgumentCollection	getMultiVariantInputArgumentCollection() Return an argument collection that provides the driving variants.
java.util.SortedSet<java.lang.String>	getSamplesForVariants() Get in name-sorted order a list of samples merged from the driving variants files.
protected htsjdk.samtools.SAMSequenceDictionary	getSequenceDictionaryForDrivingVariants() Return the primary sequence dictionary to be used for the driving variants for this tool.
protected java.util.Spliterator<htsjdk.variant.variantcontext.VariantContext>	getSpliteratorForDrivingVariants() Return a spliterator to be used to iterate over the elements of the driving variants.
protected void	initializeDrivingVariants() Process the feature inputs that represent the primary driving source(s) of variants for this tool, and perform any necessary header and sequence dictionary validation.
protected void	onShutdown() Close all data sources.
protected void	onStartup() Marked final so that tool authors don't override it.
void	traverse() A complete traversal from start to finish.

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, closeTool, createSAMWriter, createVCFWriter, createVCFWriter, createVCFWriter, doWork, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultReadFilters, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolName, getTransformedReadStream, getTraversalIntervals, hasFeatures, hasReads, hasReference, hasUserSuppliedIntervals, initializeProgressMeter, 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

Field Detail

multiVariantInputArgumentCollection

@ArgumentCollection
protected MultiVariantInputArgumentCollection multiVariantInputArgumentCollection

Constructor Detail

MultiVariantWalker

public MultiVariantWalker()

Method Detail

getSequenceDictionaryForDrivingVariants

protected htsjdk.samtools.SAMSequenceDictionary getSequenceDictionaryForDrivingVariants()

Description copied from class: VariantWalkerBase

Return the primary sequence dictionary to be used for the driving variants for this tool. The value returned will usually have been prepared in VariantWalkerBase.initializeDrivingVariants()

Specified by:

getSequenceDictionaryForDrivingVariants in class VariantWalkerBase

getSpliteratorForDrivingVariants

protected java.util.Spliterator<htsjdk.variant.variantcontext.VariantContext> getSpliteratorForDrivingVariants()

Description copied from class: VariantWalkerBase

Return a spliterator to be used to iterate over the elements of the driving variants.

Specified by:

getSpliteratorForDrivingVariants in class VariantWalkerBase

onStartup

protected final void onStartup()

Marked final so that tool authors don't override it. Tool authors should override GATKTool.onTraversalStart() instead.

Overrides:

onStartup in class GATKTool

getMultiVariantInputArgumentCollection

protected MultiVariantInputArgumentCollection getMultiVariantInputArgumentCollection()

Return an argument collection that provides the driving variants. This allows subclasses to override and use a different argument pattern besides the default -V

doDictionaryCrossValidation

public boolean doDictionaryCrossValidation()

Should this tool cross-validate the sequence dictionaries for input feature files? If a large number of inputs are expected, the tools should override to return false and require a reference.

Returns:

true if this tool should check all input feature files' contigs against each other, otherwise false

initializeDrivingVariants

protected void initializeDrivingVariants()

Description copied from class: VariantWalkerBase

Process the feature inputs that represent the primary driving source(s) of variants for this tool, and perform any necessary header and sequence dictionary validation. Called by the framework during feature initialization.

Specified by:

initializeDrivingVariants in class VariantWalkerBase

getDrivingVariantsFeatureInputs

protected final java.util.List<FeatureInput<htsjdk.variant.variantcontext.VariantContext>> getDrivingVariantsFeatureInputs()

Returns a list of feature inputs used for the driving variants for this source.

getHeaderForVariants

public final htsjdk.variant.vcf.VCFHeader getHeaderForVariants()

Gets the header associated with our driving source of variants as a VCFHeader.

Specified by:

getHeaderForVariants in class VariantWalkerBase

Returns:

VCFHeader for our driving source of variants

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 multi-variant 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(htsjdk.variant.variantcontext.VariantContext variant,
                           ReadsContext readsContext,
                           ReferenceContext referenceContext,
                           FeatureContext featureContext)

Process an individual variant. 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:

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).

onShutdown

protected final void onShutdown()

Close all data sources. Marked final so that tool authors don't override it. Tool authors should override GATKTool.onTraversalSuccess() and/or GATKTool.closeTool() instead.

Overrides:

onShutdown in class GATKTool

getSamplesForVariants

public final java.util.SortedSet<java.lang.String> getSamplesForVariants()

Get in name-sorted order a list of samples merged from the driving variants files.

Returns:

SampleSet merged requiring unique names from the drivingVariants