org.broadinstitute.hellbender.engine

Class MultiVariantWalkerGroupedOnStart

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

org.broadinstitute.hellbender.engine.MultiVariantWalkerGroupedOnStart

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

Direct Known Subclasses:

CombineGVCFs, FilterAlignmentArtifacts, JointGermlineCNVSegmentation, VariantEval

public abstract class MultiVariantWalkerGroupedOnStart
extends MultiVariantWalker

A MultiVariantWalker that walks over multiple variant context sources in reference order and emits to client tools groups of all input variant contexts by their start position. This is intended to mimic GATK3 traversal behavior for some tools. As such, the argument '-ignore-variants-starting-outside-interval' has been provided to mimic GATK3's behavior only presenting variants that start inside the requested interval regardless of whether there is a spanning variant. Client tools must implement apply(List variantContexts, ReferenceContext referenceContext)

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	COMBINE_VARIANTS_DISTANCE
protected int	distanceToCombineVariants
static java.lang.String	IGNORE_VARIANTS_THAT_START_OUTSIDE_INTERVAL
protected boolean	ignoreIntervalsOutsideStart this option has no effect unless intervals are specified.
static java.lang.String	MAX_COMBINED_DISTANCE
protected int	maxCombinedDistance
static java.lang.String	REFERENCE_WINDOW_PADDING
protected int	referenceWindowPadding

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

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
MultiVariantWalkerGroupedOnStart()

Method Summary

Modifier and Type	Method and Description
void	apply(java.util.List<htsjdk.variant.variantcontext.VariantContext> variantContexts, java.util.List<ReadsContext> readsContexts)
abstract void	apply(java.util.List<htsjdk.variant.variantcontext.VariantContext> variantContexts, ReferenceContext referenceContext, java.util.List<ReadsContext> readsContexts) This method must be implemented by tool authors.
void	apply(htsjdk.variant.variantcontext.VariantContext variant, ReadsContext readsContext, ReferenceContext referenceContext, FeatureContext featureContext) This method keeps track of all the variants it is passed and will feed all the variants that start at the same site to the reduce method.
protected int	defaultDistanceToGroupVariants()
protected int	defaultMaxGroupedSpan()
protected int	defaultReferenceWindowPadding()
protected boolean	isWithinInterval(htsjdk.samtools.util.Locatable loc)
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.MultiVariantWalker

doDictionaryCrossValidation, getDrivingVariantsFeatureInputs, getHeaderForVariants, getMultiVariantInputArgumentCollection, getSamplesForVariants, 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, hasFeatures, hasReads, hasReference, hasUserSuppliedIntervals, initializeProgressMeter, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeSamReaderFactory, 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

IGNORE_VARIANTS_THAT_START_OUTSIDE_INTERVAL

public static final java.lang.String IGNORE_VARIANTS_THAT_START_OUTSIDE_INTERVAL

See Also:

Constant Field Values

COMBINE_VARIANTS_DISTANCE

public static final java.lang.String COMBINE_VARIANTS_DISTANCE

See Also:

Constant Field Values

MAX_COMBINED_DISTANCE

public static final java.lang.String MAX_COMBINED_DISTANCE

See Also:

Constant Field Values

REFERENCE_WINDOW_PADDING

public static final java.lang.String REFERENCE_WINDOW_PADDING

See Also:

Constant Field Values

ignoreIntervalsOutsideStart

@Advanced
 @Argument(fullName="ignore-variants-starting-outside-interval",
          doc="Restrict variant output to sites that start within provided intervals (only applies when an interval is specified)",
          optional=true)
protected boolean ignoreIntervalsOutsideStart

this option has no effect unless intervals are specified.

This exists to mimic GATK3 interval traversal patterns

distanceToCombineVariants

@Advanced
 @Argument(fullName="combine-variants-distance",
          doc="Maximum distance for variants to be grouped together",
          optional=true)
protected int distanceToCombineVariants

maxCombinedDistance

@Advanced
 @Argument(fullName="max-distance",
          doc="Maximum distance for variants to be grouped together",
          optional=true)
protected int maxCombinedDistance

referenceWindowPadding

@Advanced
 @Argument(fullName="ref-padding",
          doc="Number of bases on either side to expand spanning reference window",
          optional=true)
protected int referenceWindowPadding

Constructor Detail

MultiVariantWalkerGroupedOnStart

public MultiVariantWalkerGroupedOnStart()

Method Detail

defaultDistanceToGroupVariants

protected int defaultDistanceToGroupVariants()

defaultReferenceWindowPadding

protected int defaultReferenceWindowPadding()

defaultMaxGroupedSpan

protected int defaultMaxGroupedSpan()

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

apply

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

This method keeps track of all the variants it is passed and will feed all the variants that start at the same site to the reduce method. 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.

Specified by:

apply in class MultiVariantWalker

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).

apply

public abstract void apply(java.util.List<htsjdk.variant.variantcontext.VariantContext> variantContexts,
                           ReferenceContext referenceContext,
                           java.util.List<ReadsContext> readsContexts)

This method must be implemented by tool authors. This is the primary traversal for any MultiVariantWalkerGroupedOnStart walkers. Will traverse over input variant contexts and call #apply() exactly once for each unique reference start position. All variants starting at each locus across source files will be grouped and passed as a list of VariantContext objects.

Parameters:

variantContexts - VariantContexts from driving variants with matching start position NOTE: This will never be empty

referenceContext - ReferenceContext object covering the reference of the longest spanning VariantContext

readsContexts -

apply

public void apply(java.util.List<htsjdk.variant.variantcontext.VariantContext> variantContexts,
                  java.util.List<ReadsContext> readsContexts)

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 MultiVariantWalker.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 multi-variant grouped on start 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.

Overrides:

traverse in class MultiVariantWalker

isWithinInterval

protected final boolean isWithinInterval(htsjdk.samtools.util.Locatable loc)

Parameters:

loc - locatable to query

Returns:

true if the query loc is entirely contained by the interval, true if no interval