public abstract class MultiplePassVariantWalker extends VariantWalker
drivingVariantFileDEFAULT_DRIVING_VARIANTS_LOOKAHEAD_BASES, genomicsDBOptionsaddOutputSAMProgramRecord, 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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MultiplePassVariantWalker() |
| Modifier and Type | Method and Description |
|---|---|
protected abstract void |
afterNthPass(int n)
Process the data collected during the first pass.
|
void |
apply(htsjdk.variant.variantcontext.VariantContext variant,
ReadsContext readsContext,
ReferenceContext referenceContext,
FeatureContext featureContext)
Make final to hide it from subclasses
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protected abstract void |
nthPassApply(htsjdk.variant.variantcontext.VariantContext variant,
ReadsContext readsContext,
ReferenceContext referenceContext,
FeatureContext featureContext,
int n)
nth pass through the variants.
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protected abstract int |
numberOfPasses() |
void |
traverse()
Implementation of variant-based traversal.
|
getDrivingVariantsFeatureInput, getHeaderForVariants, getSequenceDictionaryForDrivingVariants, getSpliteratorForDrivingVariants, initializeDrivingVariants, onShutdown, onStartupgetBestAvailableSequenceDictionary, getDrivingVariantCacheLookAheadBases, getGenomicsDBOptions, getProgressMeterRecordLabel, getTransformedVariantStream, getTransformedVariantStream, makePostVariantFilterTransformer, makePreVariantFilterTransformer, makeVariantFilter, requiresFeaturesdirectlyAccessEngineFeatureManager, directlyAccessEngineReadsDataSource, directlyAccessEngineReferenceDataSourceaddFeatureInputsAfterInitialization, 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, onTraversalStart, onTraversalSuccess, requiresIntervals, requiresReads, requiresReference, transformTraversalIntervals, useVariantAnnotationscustomCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getSupportInformation, getToolkitName, getToolkitShortName, getToolStatusWarning, getUsage, getVersion, instanceMain, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, parseArgs, printLibraryVersions, printSettings, printStartupMessage, runTool, setDefaultHeaders, warnOnToolStatusprotected abstract int numberOfPasses()
public void traverse()
VariantWalker.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.
Implementation of multiple-pass variant traversal.
Overrides the default, single-pass traversal framework of VariantWalkerBase allowing for multiple
passes.
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.traverse in class VariantWalkerprotected abstract void nthPassApply(htsjdk.variant.variantcontext.VariantContext variant,
ReadsContext readsContext,
ReferenceContext referenceContext,
FeatureContext featureContext,
int n)
afterNthPass(int) before making a second passvariant - A variant record in a vcfreadsContext - Reads overlapping the current variant. Will be empty if a read source (e.g. bam) isn't providedreferenceContext - Reference bases spanning the current variantfeatureContext - A record overlapping the current variant from an auxiliary data source (e.g. gnomad)n - Which pass it is (zero-indexed)protected abstract void afterNthPass(int n)
public final void apply(htsjdk.variant.variantcontext.VariantContext variant,
ReadsContext readsContext,
ReferenceContext referenceContext,
FeatureContext featureContext)
apply in class VariantWalkervariant - 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).