org.broadinstitute.hellbender.engine

Class VariantWalkerBase

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.GATKTool

org.broadinstitute.hellbender.engine.WalkerBase

org.broadinstitute.hellbender.engine.VariantWalkerBase

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

Direct Known Subclasses:

MultiVariantWalker, VariantLocusWalker, VariantWalker

public abstract class VariantWalkerBase
extends WalkerBase

Base class for variant walkers, which process variants from one or more sources of variants, with optional contextual information from a reference, sets of reads, and/or supplementary sources of Features. Subclasses must implement the GATKTool.traverse() method to process variants, initializeDrivingVariants(), getHeaderForVariants(), getSequenceDictionaryForDrivingVariants(), getSpliteratorForDrivingVariants(), and may optionally implement GATKTool.onTraversalStart(), GATKTool.onTraversalSuccess() and/or GATKTool.closeTool().

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_DRIVING_VARIANTS_LOOKAHEAD_BASES Default value to control the size of the cache for our driving variants input(s) (specifically, the number of additional bases worth of overlapping records to cache for queries on the driving variants).
protected GenomicsDBOptions	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
VariantWalkerBase()

Method Summary

Modifier and Type	Method and Description
htsjdk.samtools.SAMSequenceDictionary	getBestAvailableSequenceDictionary() Overriding the superclass method to preferentially choose the sequence dictionary from the driving source of variants.
protected int	getDrivingVariantCacheLookAheadBases() When performing a query on the driving variants input(s), the number of additional bases beyond the end of the query for which overlapping variants should be pre-fetched and cached.
protected GenomicsDBOptions	getGenomicsDBOptions() Get the GenomicsDB read settings for the current tool
abstract htsjdk.variant.vcf.VCFHeader	getHeaderForVariants() Return the VCFHeader to be used for the driving variants for this tool.
java.lang.String	getProgressMeterRecordLabel()
protected abstract htsjdk.samtools.SAMSequenceDictionary	getSequenceDictionaryForDrivingVariants() Return the primary sequence dictionary to be used for the driving variants for this tool.
protected abstract java.util.Spliterator<htsjdk.variant.variantcontext.VariantContext>	getSpliteratorForDrivingVariants() Return a spliterator to be used to iterate over the elements of the driving variants.
protected java.util.stream.Stream<htsjdk.variant.variantcontext.VariantContext>	getTransformedVariantStream(CountingVariantFilter filter) Returns a stream over the variants, which are: 1.
protected java.util.stream.Stream<htsjdk.variant.variantcontext.VariantContext>	getTransformedVariantStream(java.util.Spliterator<htsjdk.variant.variantcontext.VariantContext> source, VariantTransformer preTransformer, CountingVariantFilter filter, VariantTransformer postTransformer) Returns a stream over the variants returned by source, which are: 1.
protected abstract 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.
VariantTransformer	makePostVariantFilterTransformer() Returns the post-filter variant transformer (simple or composite) that will be applied to the variants after filtering.
VariantTransformer	makePreVariantFilterTransformer() Returns the pre-filter variant transformer (simple or composite) that will be applied to the variants before filtering.
protected CountingVariantFilter	makeVariantFilter() Returns the variant filter (simple or composite) that will be applied to the variants before calling #apply.
boolean	requiresFeatures() Does this tool require features? Traversals types and/or tools that do should override to return true.

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, onShutdown, onStartup, onTraversalStart, onTraversalSuccess, requiresIntervals, requiresReads, requiresReference, transformTraversalIntervals, traverse, 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

DEFAULT_DRIVING_VARIANTS_LOOKAHEAD_BASES

public static final int DEFAULT_DRIVING_VARIANTS_LOOKAHEAD_BASES

Default value to control the size of the cache for our driving variants input(s) (specifically, the number of additional bases worth of overlapping records to cache for queries on the driving variants).

See Also:

Constant Field Values

genomicsDBOptions

protected GenomicsDBOptions genomicsDBOptions

Constructor Detail

VariantWalkerBase

public VariantWalkerBase()

Method Detail

requiresFeatures

public boolean requiresFeatures()

Description copied from class: GATKTool

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

Overrides:

requiresFeatures in class GATKTool

Returns:

true if this tool requires reads, 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")

getGenomicsDBOptions

protected GenomicsDBOptions getGenomicsDBOptions()

Description copied from class: GATKTool

Get the GenomicsDB read settings for the current tool

Overrides:

getGenomicsDBOptions in class GATKTool

Returns:

By default, just return the vanilla options

getBestAvailableSequenceDictionary

public htsjdk.samtools.SAMSequenceDictionary getBestAvailableSequenceDictionary()

Overriding the superclass method to preferentially choose the sequence dictionary from the driving source of variants.

Overrides:

getBestAvailableSequenceDictionary in class GATKTool

Returns:

best available sequence dictionary given our inputs or null if no one dictionary is the best one.

initializeDrivingVariants

protected abstract 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. Called by the framework during feature initialization.

getHeaderForVariants

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

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

Returns:

VCFHeader to be used for the driving variants.

getSequenceDictionaryForDrivingVariants

protected abstract htsjdk.samtools.SAMSequenceDictionary getSequenceDictionaryForDrivingVariants()

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

getSpliteratorForDrivingVariants

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

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

getDrivingVariantCacheLookAheadBases

protected int getDrivingVariantCacheLookAheadBases()

When performing a query on the driving variants input(s), the number of additional bases beyond the end of the query for which overlapping variants should be pre-fetched and cached. Defaults to DEFAULT_DRIVING_VARIANTS_LOOKAHEAD_BASES Subclasses can customize this value by overriding this method.

Returns:

the number of additional bases to prefetch and cache beyond a query on the driving variants

makePreVariantFilterTransformer

public VariantTransformer makePreVariantFilterTransformer()

Returns the pre-filter variant transformer (simple or composite) that will be applied to the variants before filtering. The default implementation uses the VariantTransformer.identity(). Default implementation of GATKTool.traverse() calls this method once before iterating over the variants and reuses the transformer object to avoid object allocation. Subclasses can extend to provide own transformers (i.e. override and call super). Multiple transformers can be composed by using VariantTransformer composition methods.

makePostVariantFilterTransformer

public VariantTransformer makePostVariantFilterTransformer()

Returns the post-filter variant transformer (simple or composite) that will be applied to the variants after filtering. The default implementation uses the VariantTransformer.identity(). Default implementation of GATKTool.traverse() calls this method once before iterating over the variants and reuses the transformer object to avoid object allocation. Subclasses can extend to provide own transformers (i.e. override and call super). Multiple transformers can be composed by using VariantTransformer composition methods.

getTransformedVariantStream

protected java.util.stream.Stream<htsjdk.variant.variantcontext.VariantContext> getTransformedVariantStream(CountingVariantFilter filter)

Returns a stream over the variants, which are: 1. Transformed with makePreVariantFilterTransformer(). 2. Filtered with filter. 3. Transformed with makePostVariantFilterTransformer().

getTransformedVariantStream

protected java.util.stream.Stream<htsjdk.variant.variantcontext.VariantContext> getTransformedVariantStream(java.util.Spliterator<htsjdk.variant.variantcontext.VariantContext> source,
                                                                                                            VariantTransformer preTransformer,
                                                                                                            CountingVariantFilter filter,
                                                                                                            VariantTransformer postTransformer)

Returns a stream over the variants returned by source, which are: 1. Transformed with preTransformer. 2. Filtered with filter. 3. Transformed with postTransformer.

makeVariantFilter

protected CountingVariantFilter makeVariantFilter()

Returns the variant filter (simple or composite) that will be applied to the variants before calling #apply. The default implementation filters nothing. Default implementation of GATKTool.traverse() calls this method once before iterating over the reads and reuses the filter object to avoid object allocation. Nevertheless, keeping state in filter objects is strongly discouraged. Subclasses can extend to provide own filters (ie override and call super). Multiple filters can be composed by using VariantFilter composition methods.