org.broadinstitute.hellbender.engine

Class LocusWalkerByInterval

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.GATKTool

org.broadinstitute.hellbender.engine.WalkerBase

org.broadinstitute.hellbender.engine.LocusWalker

org.broadinstitute.hellbender.engine.LocusWalkerByInterval

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

Direct Known Subclasses:

DepthOfCoverage

public abstract class LocusWalkerByInterval
extends LocusWalker

An implementation of LocusWalker that supports arbitrary interval side inputs. The class works as follows: Before traversal getIntervalObjectsToQueryOver() will be called to generate a global list of Locatable that will be stored in memory for the duration of the traversal. For each site apply(AlignmentContext, ReferenceContext, FeatureContext, Set)} will be called with a set consisting of all the provided overlapping intervals. The first time any Locus overlaps with the traversal onIntervalStart(Locatable) will be called once. Once a the traversal locus no longer overlaps a Locatable, onIntervalEnd(Locatable) will be called once to perform any necessary post-processing. Otherwise See LocusWalker for general implementation details. NOTE: If there are Locatables provided by getIntervalObjectsToQueryOver() that are never covered by the traversal of the tool, onIntervalStart(Locatable) and onIntervalEnd(Locatable) will not be called on those intervals.

Field Summary

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

MAX_DEPTH_PER_SAMPLE_NAME, maxDepthPerSample

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
LocusWalkerByInterval()

Method Summary

Modifier and Type	Method and Description
void	apply(AlignmentContext alignmentContext, ReferenceContext referenceContext, FeatureContext featureContext) Process an individual AlignmentContext (with optional contextual information).
abstract void	apply(AlignmentContext alignmentContext, ReferenceContext referenceContext, FeatureContext featureContext, java.util.Set<htsjdk.samtools.util.Locatable> activeIntervals) Process an individual AlignmentContext (with optional contextual information).
abstract java.util.List<htsjdk.samtools.util.Locatable>	getIntervalObjectsToQueryOver() Tool-specified list of Locatable objects (which have been read into memory) that will have overlaps queried at each locus
abstract void	onIntervalEnd(htsjdk.samtools.util.Locatable activeInterval) Perform any closing operations needed once the provided getIntervalObjectsToQueryOver() interval has been passed by the tool NOTE: This will only ever be called on an interval that has been covered by onIntervalStart(Locatable)
abstract void	onIntervalStart(htsjdk.samtools.util.Locatable activeInterval) Perform any initialization needed the first time a provided interval is seen.
boolean	requiresIntervals() Does this tool require intervals? Traversals types and/or tools that do should override to return true.
void	traverse() Implementation of locus-based traversal.

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

defaultMaxDepthPerSample, emitEmptyLoci, getDefaultReadFilters, getDownsamplingInfo, getProgressMeterRecordLabel, includeDeletions, includeNs, keepUniqueReadListInLibs, onShutdown, onStartup, requiresReads

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, getBestAvailableSequenceDictionary, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getGenomicsDBOptions, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolName, getTransformedReadStream, getTraversalIntervals, hasFeatures, hasReads, hasReference, hasUserSuppliedIntervals, initializeProgressMeter, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeVariantAnnotations, onTraversalStart, onTraversalSuccess, requiresFeatures, 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 Detail

LocusWalkerByInterval

public LocusWalkerByInterval()

Method Detail

traverse

public void traverse()

Implementation of locus-based traversal. This implementation behaves similarly to LocusWalker.traverse() in that it iterates over all positions in the reference covered by filtered and transformed reads including deletions only if LocusWalker.includeDeletions() returns true. This method also keeps track of interval objects provided by getIntervalObjectsToQueryOver() and constructs a global overlaps detector for all of the intervals which is used by the apply(AlignmentContext, ReferenceContext, FeatureContext) method to track which locatable still have active hooks. This method also makes sure to close out the list of previous intervals when traversal has completed so that writers can be populated.

Overrides:

traverse in class LocusWalker

requiresIntervals

public final 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

getIntervalObjectsToQueryOver

public abstract java.util.List<htsjdk.samtools.util.Locatable> getIntervalObjectsToQueryOver()

Tool-specified list of Locatable objects (which have been read into memory) that will have overlaps queried at each locus

Returns:

A list of Locatable Objects that will be checked for overlap with each genomic location we traverse

apply

public final void apply(AlignmentContext alignmentContext,
                        ReferenceContext referenceContext,
                        FeatureContext featureContext)

Description copied from class: LocusWalker

Process an individual AlignmentContext (with optional contextual information). 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 LocusWalker

Parameters:

alignmentContext - current alignment context

referenceContext - Reference bases spanning the current locus. 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 locus by invoking ReferenceContext.setWindow(int, int) on this object before calling ReferenceContext.getBases()

featureContext - Features spanning the current locus. 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(AlignmentContext alignmentContext,
                           ReferenceContext referenceContext,
                           FeatureContext featureContext,
                           java.util.Set<htsjdk.samtools.util.Locatable> activeIntervals)

Process an individual AlignmentContext (with optional contextual information). Must be implemented by tool authors. Will provide a set of all intervals overlapping the given locus.

Parameters:

alignmentContext - current alignment context

referenceContext - Reference bases spanning the current locus. 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 locus by invoking ReferenceContext.setWindow(int, int) on this object before calling ReferenceContext.getBases()

featureContext - Features spanning the current locus. 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).

activeIntervals - Locatables from the set provided by getIntervalObjectsToQueryOver() spanning the current locus.

onIntervalStart

public abstract void onIntervalStart(htsjdk.samtools.util.Locatable activeInterval)

Perform any initialization needed the first time a provided interval is seen.

Parameters:

activeInterval - Locatable an interval from the set provided by getIntervalObjectsToQueryOver() to the walker to be initialized

onIntervalEnd

public abstract void onIntervalEnd(htsjdk.samtools.util.Locatable activeInterval)

Perform any closing operations needed once the provided getIntervalObjectsToQueryOver() interval has been passed by the tool NOTE: This will only ever be called on an interval that has been covered by onIntervalStart(Locatable)

Parameters:

activeInterval - Locatable provided to the walker to be closed