public final class ExampleVariantWalker extends VariantWalker
drivingVariantFileFEATURE_CACHE_LOOKAHEADaddOutputSAMProgramRecord, addOutputVCFCommandLine, cloudIndexPrefetchBuffer, cloudPrefetchBuffer, createOutputBamIndex, createOutputBamMD5, createOutputVariantIndex, createOutputVariantMD5, disableBamIndexCaching, intervalArgumentCollection, lenientVCFProcessing, outputSitesOnlyVCFs, progressMeter, readArguments, referenceArguments, SECONDS_BETWEEN_PROGRESS_UPDATES_NAMEGATK_CONFIG_FILE, logger, NIO_MAX_REOPENS, QUIET, specialArgumentsCollection, TMP_DIR, useJdkDeflater, useJdkInflater, VERBOSITY| Constructor and Description |
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ExampleVariantWalker() |
| Modifier and Type | Method and Description |
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void |
apply(htsjdk.variant.variantcontext.VariantContext variant,
ReadsContext readsContext,
ReferenceContext referenceContext,
FeatureContext featureContext)
Process an individual variant.
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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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getDrivingVariantsFeatureInput, getHeaderForVariants, getSequenceDictionaryForDrivingVariants, getSpliteratorForDrivingVariants, initializeDrivingVariants, onShutdown, onStartupgetBestAvailableSequenceDictionary, getProgressMeterRecordLabel, makeVariantFilter, requiresFeatures, traverseaddFeatureInputsAfterInitialization, createSAMWriter, createSAMWriter, createVCFWriter, doWork, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultReadFilters, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolkitShortName, getToolName, getTransformedReadStream, hasFeatures, hasIntervals, hasReads, hasReference, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeVariantAnnotations, onTraversalSuccess, requiresIntervals, requiresReads, requiresReference, useVariantAnnotationscustomCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getSupportInformation, getToolkitName, getToolStatusWarning, getUsage, getVersion, instanceMain, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, parseArgs, printLibraryVersions, printSettings, printStartupMessage, runTool, setDefaultHeaders, warnOnToolStatuspublic void onTraversalStart()
GATKToolonTraversalStart in class GATKToolpublic void apply(htsjdk.variant.variantcontext.VariantContext variant,
ReadsContext readsContext,
ReferenceContext referenceContext,
FeatureContext featureContext)
VariantWalkerBaseapply in class VariantWalkerBasevariant - Current variant being processed.readsContext - Reads overlapping the current variant. Will be an empty, but non-null, context object
if there is no backing source of reads data (in which case all queries on it will return
an empty array/iterator)referenceContext - Reference bases spanning the current variant. 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 variant's interval
by invoking ReferenceContext.setWindow(int, int)
on this object before calling ReferenceContext.getBases()featureContext - Features spanning the current variant. 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.