public final class ExampleReadWalkerWithVariants extends ReadWalker
FEATURE_CACHE_LOOKAHEADaddOutputSAMProgramRecord, 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 |
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ExampleReadWalkerWithVariants() |
| Modifier and Type | Method and Description |
|---|---|
void |
apply(GATKRead read,
ReferenceContext referenceContext,
FeatureContext featureContext)
Process an individual read (with optional contextual information).
|
void |
closeTool()
This method is called by the GATK framework at the end of the
GATKTool.doWork() template method. |
void |
onTraversalStart()
Operations performed just prior to the start of traversal.
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getDefaultReadFilters, getProgressMeterRecordLabel, onShutdown, onStartup, requiresReads, resetReadsDataSource, traversedirectlyAccessEngineFeatureManager, directlyAccessEngineReadsDataSource, directlyAccessEngineReferenceDataSourceaddFeatureInputsAfterInitialization, 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, onTraversalSuccess, requiresFeatures, requiresIntervals, requiresReference, transformTraversalIntervals, useVariantAnnotationscustomCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getSupportInformation, getToolkitName, getToolkitShortName, getToolStatusWarning, getUsage, getVersion, instanceMain, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, parseArgs, printLibraryVersions, printSettings, printStartupMessage, runTool, setDefaultHeaders, warnOnToolStatuspublic void onTraversalStart()
GATKToolonTraversalStart in class GATKToolpublic void apply(GATKRead read, ReferenceContext referenceContext, FeatureContext featureContext)
ReadWalkerapply in class ReadWalkerread - current readreferenceContext - Reference bases spanning the current read. 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 read's interval
by invoking ReferenceContext.setWindow(int, int) on this object before calling ReferenceContext.getBases()featureContext - Features spanning the current read. 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).public void closeTool()
GATKToolGATKTool.doWork() template method.
It is called regardless of whether the GATKTool.traverse() has succeeded or not.
It is called after the GATKTool.onTraversalSuccess() has completed (successfully or not)
but before the GATKTool.doWork() method returns.
In other words, on successful runs both GATKTool.onTraversalSuccess() and GATKTool.closeTool() will be called (in this order) while
on failed runs (when GATKTool.traverse() causes an exception), only GATKTool.closeTool() will be called.
The default implementation does nothing.
Subclasses should override this method to close any resources that must be closed regardless of the success of traversal.