@DocumentedFeature public final class CountVariants extends VariantWalker
gatk CountVariants \
-V input_variants.vcf
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 |
|---|
CountVariants() |
| Modifier and Type | Method and Description |
|---|---|
void |
apply(htsjdk.variant.variantcontext.VariantContext variant,
ReadsContext readsContext,
ReferenceContext referenceContext,
FeatureContext featureContext)
Process an individual variant.
|
java.lang.Object |
onTraversalSuccess()
Operations performed immediately after a successful traversal (ie when no uncaught exceptions were thrown during the traversal).
|
getDrivingVariantsFeatureInput, getHeaderForVariants, getSequenceDictionaryForDrivingVariants, getSpliteratorForDrivingVariants, initializeDrivingVariants, onShutdown, onStartup, traversegetBestAvailableSequenceDictionary, getDrivingVariantCacheLookAheadBases, getGenomicsDBOptions, getProgressMeterRecordLabel, getTransformedVariantStream, getTransformedVariantStream, makePostVariantFilterTransformer, makePreVariantFilterTransformer, makeVariantFilter, requiresFeaturesdirectlyAccessEngineFeatureManager, directlyAccessEngineReadsDataSource, directlyAccessEngineReferenceDataSourceaddFeatureInputsAfterInitialization, closeTool, createSAMWriter, createSAMWriter, createVCFWriter, createVCFWriter, doWork, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultReadFilters, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolName, getTransformedReadStream, getTraversalIntervals, hasFeatures, hasReads, hasReference, hasUserSuppliedIntervals, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeVariantAnnotations, onTraversalStart, 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, warnOnToolStatuspublic void apply(htsjdk.variant.variantcontext.VariantContext variant,
ReadsContext readsContext,
ReferenceContext referenceContext,
FeatureContext featureContext)
VariantWalkerapply 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).public java.lang.Object onTraversalSuccess()
GATKToolonTraversalSuccess in class GATKTool