@DocumentedFeature public final class LeftAlignIndels extends ReadWalker
This tool left-aligns any indels in the read data contained in a BAM or CRAM file. The same indel can often be placed at multiple positions and still represent the same haplotype. While it is a commonly used convention to place an indel at the left-most position, this doesn't always happen (either because upstream tools broke ties between equivalent representations randomly or used different aligning conventions), so this tool can be used to left-align them according to convention.
This tool will left-align reads with one and only one indel.
A BAM or CRAM file to left-align.
A left-aligned BAM or CRAM file.
gatk LeftAlignIndels \ -R reference.fasta \ -I input.bam \ -O output.bam
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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LeftAlignIndels() |
| Modifier and Type | Method and Description |
|---|---|
void |
apply(GATKRead read,
ReferenceContext ref,
FeatureContext featureContext)
Process an individual read (with optional contextual information).
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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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boolean |
requiresReference()
Does this tool require reference data? Traversals types and/or tools that do should override to return true.
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getDefaultReadFilters, getProgressMeterRecordLabel, onShutdown, onStartup, requiresReads, resetReadsDataSource, traversedirectlyAccessEngineFeatureManager, directlyAccessEngineReadsDataSource, directlyAccessEngineReferenceDataSourceaddFeatureInputsAfterInitialization, bamIndexCachingShouldBeEnabled, createSAMWriter, createVCFWriter, createVCFWriter, createVCFWriter, disableProgressMeter, 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, makeSamReaderFactory, makeVariantAnnotations, onTraversalSuccess, requiresFeatures, requiresIntervals, transformTraversalIntervals, useVariantAnnotationscustomCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getSupportInformation, getToolkitName, getToolkitShortName, getToolStatusWarning, getUsage, getVersion, instanceMain, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, parseArgs, printLibraryVersions, printSettings, printStartupMessage, runTool, setDefaultHeaders, warnOnToolStatuspublic boolean requiresReference()
GATKToolrequiresReference in class GATKToolpublic void onTraversalStart()
GATKToolonTraversalStart in class GATKToolpublic void apply(GATKRead read, ReferenceContext ref, FeatureContext featureContext)
ReadWalkerapply in class ReadWalkerread - current readref - 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.