org.broadinstitute.hellbender.engine

Class VariantLocusWalker

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.VariantLocusWalker

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

Direct Known Subclasses:

GenotypeGVCFs

public abstract class VariantLocusWalker
extends VariantWalkerBase

VariantLocusWalker processes variants from a single source, grouped by locus overlap, or optionally one at a time in order, with optional contextual information from a reference, sets of reads, and/or supplementary sources of Features. By-variant traversal is opt in, via changeTraversalModeToByVariant(), otherwise only loci with overlapping variants are traversed. VariantLocusWalker authors must implement the apply(htsjdk.samtools.util.Locatable, java.util.List<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
java.lang.String	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 and Description
VariantLocusWalker()

Method Summary

Modifier and Type	Method and Description
abstract void	apply(htsjdk.samtools.util.Locatable loc, java.util.List<htsjdk.variant.variantcontext.VariantContext> variants, ReadsContext readsContext, ReferenceContext referenceContext, FeatureContext featureContext) Process by locus, with all variants overlapping the current locus, or by individual variant when in by-variants traversal mode.
protected void	changeTraversalModeToByVariant() Traverse by variant instead of by grouped by locus.
protected FeatureInput<htsjdk.variant.variantcontext.VariantContext>	getDrivingVariantsFeatureInput() Returns the feature input for the driving variants file.
htsjdk.variant.vcf.VCFHeader	getHeaderForVariants() Gets the header associated with our driving source of variants as a VCFHeader.
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.
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.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, createSAMWriter, createVCFWriter, createVCFWriter, doWork, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultReadFilters, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolName, getTransformedReadStream, getTraversalIntervals, hasFeatures, hasReads, hasReference, hasUserSuppliedIntervals, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeVariantAnnotations, onTraversalStart, onTraversalSuccess, 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

Field Detail

drivingVariantFile

@Argument(fullName="variant",
          shortName="V",
          doc="A VCF file containing variants",
          common=false,
          optional=false)
public java.lang.String drivingVariantFile

Constructor Detail

VariantLocusWalker

public VariantLocusWalker()

Method Detail

changeTraversalModeToByVariant

protected void changeTraversalModeToByVariant()

Traverse by variant instead of by grouped by locus. When true, the apply(htsjdk.samtools.util.Locatable, java.util.List<htsjdk.variant.variantcontext.VariantContext>, org.broadinstitute.hellbender.engine.ReadsContext, org.broadinstitute.hellbender.engine.ReferenceContext, org.broadinstitute.hellbender.engine.FeatureContext) method will be called for each individual variant in the driving variants input, instead of by locus, with all variants overlapping that locus. This mehtod must be called in OnTraversalStart();

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

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

getDrivingVariantsFeatureInput

protected final FeatureInput<htsjdk.variant.variantcontext.VariantContext> getDrivingVariantsFeatureInput()

Returns the feature input for the driving variants file.

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

requiresReference

public 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

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 variant-locus 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.samtools.util.Locatable loc,
                           java.util.List<htsjdk.variant.variantcontext.VariantContext> variants,
                           ReadsContext readsContext,
                           ReferenceContext referenceContext,
                           FeatureContext featureContext)

Process by locus, with all variants overlapping the current locus, or by individual variant when in by-variants traversal mode. 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:

loc - the current locus being traversed (in group by locus), or the span of the current variant (in by-variants traversal)

variants - The current variant(s) being processed. NOTE: When changeTraversalModeToByVariant() has been called, the apply(htsjdk.samtools.util.Locatable, java.util.List<htsjdk.variant.variantcontext.VariantContext>, org.broadinstitute.hellbender.engine.ReadsContext, org.broadinstitute.hellbender.engine.ReferenceContext, org.broadinstitute.hellbender.engine.FeatureContext) method will be called for each individual variant in the driving variants input. Otherwise, this method is called once for every locus that has overlapping variants, with all variants overlapping that locus.

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