public abstract class TwoPassVariantWalker extends MultiplePassVariantWalker
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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TwoPassVariantWalker() |
| Modifier and Type | Method and Description |
|---|---|
protected abstract void |
afterFirstPass()
Process the data collected during the first pass.
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protected void |
afterNthPass(int n)
Process the data collected during the first pass.
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protected abstract void |
firstPassApply(htsjdk.variant.variantcontext.VariantContext variant,
ReadsContext readsContext,
ReferenceContext referenceContext,
FeatureContext featureContext) |
protected 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 int |
numberOfPasses() |
protected abstract void |
secondPassApply(htsjdk.variant.variantcontext.VariantContext variant,
ReadsContext readsContext,
ReferenceContext referenceContext,
FeatureContext featureContext) |
apply, traversegetDrivingVariantsFeatureInput, 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 final int numberOfPasses()
numberOfPasses in class MultiplePassVariantWalkerprotected final void nthPassApply(htsjdk.variant.variantcontext.VariantContext variant,
ReadsContext readsContext,
ReferenceContext referenceContext,
FeatureContext featureContext,
int n)
MultiplePassVariantWalkerMultiplePassVariantWalker.afterNthPass(int) before making a second passnthPassApply in class MultiplePassVariantWalkervariant - 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 final void afterNthPass(int n)
MultiplePassVariantWalkerafterNthPass in class MultiplePassVariantWalkerprotected abstract void firstPassApply(htsjdk.variant.variantcontext.VariantContext variant,
ReadsContext readsContext,
ReferenceContext referenceContext,
FeatureContext featureContext)
protected abstract void afterFirstPass()
protected abstract void secondPassApply(htsjdk.variant.variantcontext.VariantContext variant,
ReadsContext readsContext,
ReferenceContext referenceContext,
FeatureContext featureContext)