public abstract class WalkerBase extends GATKTool
ReadWalker and VariantWalker in the engine package that implement a standardized traversal should
extend this class rather than GATKTool. Actual concrete tool classes should extend one of the specific walker base
types (such as ReadWalker) or GATKTool directly rather than this class.
Classes that extend WalkerBase will be unable to directly access engine data sources unless they are in the
engine package. This is to allow walker base classes such as ReadWalker direct datasource access while disallowing
it for concrete walker tool implementations, which should get their data via their apply() method.addOutputSAMProgramRecord, addOutputVCFCommandLine, cloudIndexPrefetchBuffer, cloudPrefetchBuffer, createOutputBamIndex, createOutputBamMD5, createOutputVariantIndex, createOutputVariantMD5, disableBamIndexCaching, features, intervalArgumentCollection, lenientVCFProcessing, outputSitesOnlyVCFs, progressMeter, readArguments, referenceArguments, SECONDS_BETWEEN_PROGRESS_UPDATES_NAME, seqValidationArgumentsGATK_CONFIG_FILE, logger, NIO_MAX_REOPENS, NIO_PROJECT_FOR_REQUESTER_PAYS, QUIET, specialArgumentsCollection, tmpDir, useJdkDeflater, useJdkInflater, VERBOSITY| Constructor and Description |
|---|
WalkerBase() |
| Modifier and Type | Method and Description |
|---|---|
protected FeatureManager |
directlyAccessEngineFeatureManager()
Get the
FeatureManager for this GATKTool. |
protected ReadsDataSource |
directlyAccessEngineReadsDataSource()
Get the
ReadsDataSource for this GATKTool. |
protected ReferenceDataSource |
directlyAccessEngineReferenceDataSource()
Get the
ReferenceDataSource for this GATKTool. |
addFeatureInputsAfterInitialization, closeTool, createSAMWriter, createSAMWriter, createVCFWriter, createVCFWriter, doWork, getBestAvailableSequenceDictionary, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultReadFilters, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getGenomicsDBOptions, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getProgressMeterRecordLabel, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolName, getTransformedReadStream, getTraversalIntervals, hasFeatures, hasReads, hasReference, hasUserSuppliedIntervals, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeVariantAnnotations, onShutdown, onStartup, onTraversalStart, onTraversalSuccess, requiresFeatures, requiresIntervals, requiresReads, requiresReference, transformTraversalIntervals, traverse, useVariantAnnotationscustomCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getSupportInformation, getToolkitName, getToolkitShortName, getToolStatusWarning, getUsage, getVersion, instanceMain, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, parseArgs, printLibraryVersions, printSettings, printStartupMessage, runTool, setDefaultHeaders, warnOnToolStatusprotected final ReferenceDataSource directlyAccessEngineReferenceDataSource()
ReferenceDataSource for this GATKTool.
Will throw a GATKException if the reference is null.
Clients are expected to call the GATKTool.hasReference() method prior to calling this.
Should only be called by walker base classes in the engine (such as ReadWalker), or by "free-form" tools that
extend the GATKTool class directly rather than one of the built-in walker types.
Tools that extend a walker type should get their data via apply() rather than directly accessing
the engine datasources.
Walker tools outside of the engine package should not directly access the engine reference datasource.
They should get their reference data via apply() instead. Tools that need direct datasource access
(e.g., to implement custom traversal patterns) should extend GATKTool directly rather than a walker class,
or introduce a new walker base class for the new traversal.
We are overriding this method to prevent walker tool implementations outside of the engine package from
directly accessing the engine datasources, since walker tools should get their data via apply() instead.directlyAccessEngineReferenceDataSource in class GATKToolReferenceDataSource for this GATKTool. Never null.protected final ReadsDataSource directlyAccessEngineReadsDataSource()
ReadsDataSource for this GATKTool.
Will throw a GATKException if the reads are null.
Clients are expected to call the GATKTool.hasReads() method prior to calling this.
Should only be called by walker base classes in the engine (such as ReadWalker), or by "free-form" tools that
extend the GATKTool class directly rather than one of the built-in walker types.
Tools that extend a walker type should get their data via apply() rather than directly accessing
the engine datasources.
Walker tools outside of the engine package should not directly access the engine reads datasource.
They should get their reads data via apply() instead. Tools that need direct datasource access
(e.g., to implement custom traversal patterns) should extend GATKTool directly rather than a walker class,
or introduce a new walker base class for the new traversal.
We are overriding this method to prevent walker tool implementations outside of the engine package from
directly accessing the engine datasources, since walker tools should get their data via apply() instead.directlyAccessEngineReadsDataSource in class GATKToolReadsDataSource for this GATKTool. Never null.protected final FeatureManager directlyAccessEngineFeatureManager()
FeatureManager for this GATKTool.
Will throw a GATKException if the features are null.
Clients are expected to call the GATKTool.hasFeatures() method prior to calling this.
Should only be called by walker base classes in the engine (such as ReadWalker), or by "free-form" tools that
extend the GATKTool class directly rather than one of the built-in walker types.
Tools that extend a walker type should get their data via apply() rather than directly accessing
the engine datasources.
Walker tools outside of the engine package should not directly access the engine feature manager.
They should get their feature data via apply() instead. Tools that need direct datasource access
(e.g., to implement custom traversal patterns) should extend GATKTool directly rather than a walker class,
or introduce a new walker base class for the new traversal.
We are overriding this method to prevent walker tool implementations outside of the engine package from
directly accessing the engine datasources, since walker tools should get their data via apply() instead.directlyAccessEngineFeatureManager in class GATKToolFeatureManager for this GATKTool. Never null.