org.broadinstitute.hellbender.engine

Class AssemblyRegionWalker

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.GATKTool

org.broadinstitute.hellbender.engine.WalkerBase

org.broadinstitute.hellbender.engine.AssemblyRegionWalker

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

Direct Known Subclasses:

ExampleAssemblyRegionWalker, HaplotypeCaller, Mutect2

public abstract class AssemblyRegionWalker
extends WalkerBase

An AssemblyRegionWalker is a tool that processes an entire region of reads at a time, each marked as either "active" (containing possible variation) or "inactive" (not likely to contain actual variation). Tool authors must implement assemblyRegionEvaluator() to provide a means of determining whether a site is active or not, as well as apply(org.broadinstitute.hellbender.engine.AssemblyRegion, org.broadinstitute.hellbender.engine.ReferenceContext, org.broadinstitute.hellbender.engine.FeatureContext) to process each region. Authors must also implement methods providing default values for the various traversal parameters. Each region passed to apply(org.broadinstitute.hellbender.engine.AssemblyRegion, org.broadinstitute.hellbender.engine.ReferenceContext, org.broadinstitute.hellbender.engine.FeatureContext) will come pre-marked as either "active" or "inactive" using the results of the configured assemblyRegionEvaluator(). The assemblyRegionEvaluator() is used to evaluate the probability that each individual locus is active, and these probabilities are used to determine the bounds of each active and inactive region. apply(org.broadinstitute.hellbender.engine.AssemblyRegion, org.broadinstitute.hellbender.engine.ReferenceContext, org.broadinstitute.hellbender.engine.FeatureContext) will be called once for each active AND inactive region, and it is up to the implementation how to handle/process active vs. inactive regions. Internally, the reads are loaded in chunks called read shards, which are then subdivided into active/inactive regions for processing by the tool implementation. One read shard is created per contig.

Field Summary

Fields

Modifier and Type	Field and Description
AssemblyRegionArgumentCollection	assemblyRegionArgs
protected java.lang.String	assemblyRegionOut If provided, this walker will write out its assembly regions to this file in the IGV formatted TAB-delimited output: http://www.broadinstitute.org/software/igv/IGV Intended to make debugging the active region calculations easier

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
AssemblyRegionWalker()

Method Summary

Modifier and Type	Method and Description
abstract void	apply(AssemblyRegion region, ReferenceContext referenceContext, FeatureContext featureContext) Process an individual AssemblyRegion.
abstract AssemblyRegionEvaluator	assemblyRegionEvaluator()
protected ReadsDownsampler	createDownsampler()
java.util.List<ReadFilter>	getDefaultReadFilters() Returns the default list of CommandLineReadFilters that are used for this tool.
java.lang.String	getProgressMeterRecordLabel()
protected void	onShutdown() Shutdown data sources.
protected void	onStartup() Initialize data sources for traversal.
boolean	requiresReads() Does this tool require reads? Traversals types and/or tools that do should override to return true.
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.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, requiresIntervals, 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

assemblyRegionArgs

@ArgumentCollection
public final AssemblyRegionArgumentCollection assemblyRegionArgs

assemblyRegionOut

@Argument(fullName="assembly-region-out",
          doc="Output the assembly region to this IGV formatted file",
          optional=true)
protected java.lang.String assemblyRegionOut

If provided, this walker will write out its assembly regions to this file in the IGV formatted TAB-delimited output: http://www.broadinstitute.org/software/igv/IGV Intended to make debugging the active region calculations easier

Constructor Detail

AssemblyRegionWalker

public AssemblyRegionWalker()

Method Detail

requiresReads

public final boolean requiresReads()

Description copied from class: GATKTool

Does this tool require reads? Traversals types and/or tools that do should override to return true.

Overrides:

requiresReads in class GATKTool

Returns:

true if this tool requires reads, otherwise false

requiresReference

public final 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

getProgressMeterRecordLabel

public java.lang.String getProgressMeterRecordLabel()

Overrides:

getProgressMeterRecordLabel in class GATKTool

Returns:

String label to use for records in progress meter output. Defaults to ProgressMeter.DEFAULT_RECORD_LABEL, but tools may override to provide a more appropriate label (like "reads" or "regions")

onStartup

protected final void onStartup()

Initialize data sources for traversal. Marked final so that tool authors don't override it. Tool authors should override onTraversalStart() instead.

Overrides:

onStartup in class GATKTool

getDefaultReadFilters

public java.util.List<ReadFilter> getDefaultReadFilters()

Returns the default list of CommandLineReadFilters that are used for this tool. The filters returned by this method are subject to selective enabling/disabling and customization by the user via the command line. The default implementation uses the WellformedReadFilter filter with all default options, as well as the ReadFilterLibrary.MappedReadFilter. Subclasses can override to provide alternative filters. Note: this method is called before command line parsing begins, and thus before a SAMFileHeader is available through {link #getHeaderForReads}.

Overrides:

getDefaultReadFilters in class GATKTool

Returns:

List of default filter instances to be applied for this tool.

createDownsampler

protected ReadsDownsampler createDownsampler()

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 assembly region 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

onShutdown

protected final void onShutdown()

Shutdown data sources. Marked final so that tool authors don't override it. Tool authors should override onTraversalDone() instead.

Overrides:

onShutdown in class GATKTool

assemblyRegionEvaluator

public abstract AssemblyRegionEvaluator assemblyRegionEvaluator()

Returns:

The evaluator to be used to determine whether each locus is active or not. Must be implemented by tool authors. The results of this per-locus evaluator are used to determine the bounds of each active and inactive region.

apply

public abstract void apply(AssemblyRegion region,
                           ReferenceContext referenceContext,
                           FeatureContext featureContext)

Process an individual AssemblyRegion. Must be implemented by tool authors. Each region will come pre-marked as either "active" or "inactive" using the results of the configured assemblyRegionEvaluator(). This method will be called once for each active AND inactive region, and it is up to the implementation how to handle/process active vs. inactive regions.

Parameters:

region - region to process (pre-marked as either active or inactive)

referenceContext - reference data overlapping the padded span of the assembly region

featureContext - features overlapping the padded span of the assembly region