GATKTool (gatk 4.1.7.0 API)

java.lang.Object
- org.broadinstitute.hellbender.cmdline.CommandLineProgram
- - org.broadinstitute.hellbender.engine.GATKTool

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

Direct Known Subclasses:

AnalyzeSaturationMutagenesis, AnnotateIntervals, CombineSegmentBreakpoints, GenomicsDBImport, GetSampleName, MergeAnnotatedRegions, MergeAnnotatedRegionsByAnnotation, PostprocessGermlineCNVCalls, PreprocessIntervals, PrintReadsHeader, SplitIntervals, TagGermlineEvents, WalkerBase
```
public abstract class GATKTool
extends CommandLineProgram
```
Base class for all GATK tools. Tool authors that wish to write a "GATK" tool but not use one of the pre-packaged Walker traversals should feel free to extend this class directly. All other GATK tools should extend one of the Walker classes instead.

Field Summary

Fields
Modifier and Type	Field and Description
`boolean`	`addOutputSAMProgramRecord`
`boolean`	`addOutputVCFCommandLine`
`int`	`cloudIndexPrefetchBuffer`
`int`	`cloudPrefetchBuffer`
`boolean`	`createOutputBamIndex`
`boolean`	`createOutputBamMD5`
`boolean`	`createOutputVariantIndex`
`boolean`	`createOutputVariantMD5`
`boolean`	`disableBamIndexCaching`
`FeatureManager`	`features` Our source of Feature data (null if no source of Features was provided)
`protected IntervalArgumentCollection`	`intervalArgumentCollection`
`protected boolean`	`lenientVCFProcessing`
`boolean`	`outputSitesOnlyVCFs`
`protected ProgressMeter`	`progressMeter` Progress meter to print out traversal statistics.
`protected ReadInputArgumentCollection`	`readArguments`
`protected ReferenceInputArgumentCollection`	`referenceArguments`
`static java.lang.String`	`SECONDS_BETWEEN_PROGRESS_UPDATES_NAME`
`protected SequenceDictionaryValidationArgumentCollection`	`seqValidationArguments`

Fields inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram
GATK_CONFIG_FILE, logger, NIO_MAX_REOPENS, NIO_PROJECT_FOR_REQUESTER_PAYS, QUIET, specialArgumentsCollection, tmpDir, useJdkDeflater, useJdkInflater, VERBOSITY

Constructor Summary

Constructors
Constructor and Description

GATKTool()

Constructors
Constructor and Description
`GATKTool()`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`FeatureInput<? extends htsjdk.tribble.Feature>`	`addFeatureInputsAfterInitialization(java.lang.String filePath, java.lang.String name, java.lang.Class<? extends htsjdk.tribble.Feature> featureType, int featureQueryLookahead)` A method to allow a user to inject `FeatureInput`s after initialization that were not specified as command-line arguments.
`void`	`closeTool()` This method is called by the GATK framework at the end of the `doWork()` template method.
`SAMFileGATKReadWriter`	`createSAMWriter(java.io.File outputFile, boolean preSorted)`
`SAMFileGATKReadWriter`	`createSAMWriter(java.nio.file.Path outputPath, boolean preSorted)`
`htsjdk.variant.variantcontext.writer.VariantContextWriter`	`createVCFWriter(java.io.File outFile)` Creates a VariantContextWriter whose outputFile type is determined by the vcfOutput's extension, using the best available sequence dictionary for this tool, and default index, leniency and md5 generation settings.
`htsjdk.variant.variantcontext.writer.VariantContextWriter`	`createVCFWriter(java.nio.file.Path outPath)` Creates a VariantContextWriter whose outputFile type is determined by vcfOutput's extension, using the best available sequence dictionary for this tool, and default index, leniency and md5 generation settings.
`protected FeatureManager`	`directlyAccessEngineFeatureManager()` Get the `FeatureManager` for this `GATKTool`.
`protected ReadsDataSource`	`directlyAccessEngineReadsDataSource()` Get the `ReadsDataSource` for this `GATKTool`.
`protected ReferenceDataSource`	`directlyAccessEngineReferenceDataSource()` Get the `ReferenceDataSource` for this `GATKTool`.
`protected java.lang.Object`	`doWork()` Do the work after command line has been parsed.
`htsjdk.samtools.SAMSequenceDictionary`	`getBestAvailableSequenceDictionary()` Returns the "best available" sequence dictionary or `null` if there is no single best dictionary.
`int`	`getDefaultCloudIndexPrefetchBufferSize()`
`int`	`getDefaultCloudPrefetchBufferSize()`
`java.util.List<ReadFilter>`	`getDefaultReadFilters()` Returns the default list of ReadFilters that are used for this tool.
`protected java.util.Set<htsjdk.variant.vcf.VCFHeaderLine>`	`getDefaultToolVCFHeaderLines()`
`java.util.List<java.lang.Class<? extends Annotation>>`	`getDefaultVariantAnnotationGroups()` Returns the default list of annotation groups that are used for this tool.
`java.util.List<Annotation>`	`getDefaultVariantAnnotations()` Returns the default list of `Annotation`s that are used for this tool.
`protected GenomicsDBOptions`	`getGenomicsDBOptions()` Get the GenomicsDB read settings for the current tool
`<T extends htsjdk.tribble.Feature> java.lang.Object`	`getHeaderForFeatures(FeatureInput<T> featureDescriptor)` Returns the header for the specified source of Features
`htsjdk.samtools.SAMFileHeader`	`getHeaderForReads()` Returns the SAM header for the reads data source.
`protected htsjdk.samtools.SAMFileHeader`	`getHeaderForSAMWriter()` Returns the SAM header suitable for writing SAM/BAM/CRAM files produced by this tool.
`htsjdk.samtools.SAMSequenceDictionary`	`getMasterSequenceDictionary()` Returns the master sequence dictionary if it has been set, otherwise null.
`java.util.List<? extends org.broadinstitute.barclay.argparser.CommandLinePluginDescriptor<?>>`	`getPluginDescriptors()` Return the list of GATKCommandLinePluginDescriptors to be used for this tool.
`java.lang.String`	`getProgressMeterRecordLabel()`
`htsjdk.samtools.SAMSequenceDictionary`	`getReferenceDictionary()` Returns the reference sequence dictionary if there is a reference (hasReference() == true), otherwise null.
`protected SequenceDictionaryValidationArgumentCollection`	`getSequenceDictionaryValidationArgumentCollection()` Get the `SequenceDictionaryValidationArgumentCollection` for the tool.
`java.lang.String`	`getToolName()` Returns the name of this tool.
`protected java.util.stream.Stream<GATKRead>`	`getTransformedReadStream(ReadFilter filter)` Returns a stream over the reads, which are: 1.
`java.util.List<SimpleInterval>`	`getTraversalIntervals()` Returns the list of intervals to iterate, either limited to the user-supplied intervals or the entire reference genome if none were specified.
`boolean`	`hasFeatures()` Are sources of Features available?
`boolean`	`hasReads()` Are sources of reads available?
`boolean`	`hasReference()` Is a source of reference data available?
`boolean`	`hasUserSuppliedIntervals()` Are sources of intervals available?
`ReadTransformer`	`makePostReadFilterTransformer()` Returns the post-filter read transformer (simple or composite) that will be applied to the reads after filtering.
`ReadTransformer`	`makePreReadFilterTransformer()` Returns the pre-filter read transformer (simple or composite) that will be applied to the reads before filtering.
`CountingReadFilter`	`makeReadFilter()` Returns a read filter (simple or composite) that can be applied to reads.
`java.util.Collection<Annotation>`	`makeVariantAnnotations()` Returns a list of annotations that can be applied to VariantContexts.
`protected void`	`onShutdown()` Close all data sources on shutdown.
`protected void`	`onStartup()` Initialize our data sources, make sure that all tool requirements for input data have been satisfied and start the progress meter.
`void`	`onTraversalStart()` Operations performed just prior to the start of traversal.
`java.lang.Object`	`onTraversalSuccess()` Operations performed immediately after a successful traversal (ie when no uncaught exceptions were thrown during the traversal).
`boolean`	`requiresFeatures()` Does this tool require features? Traversals types and/or tools that do should override to return true.
`boolean`	`requiresIntervals()` Does this tool require intervals? Traversals types and/or tools that do should override to return true.
`boolean`	`requiresReads()` Does this tool require reads? Traversals types and/or tools that do should override to return true.
`boolean`	`requiresReference()` Does this tool require reference data? Traversals types and/or tools that do should override to return true.
`protected java.util.List<SimpleInterval>`	`transformTraversalIntervals(java.util.List<SimpleInterval> getIntervals, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary)`
`abstract void`	`traverse()` A complete traversal from start to finish.
`boolean`	`useVariantAnnotations()` Must be overridden in order to add annotation arguments to the engine.

Methods inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getSupportInformation, getToolkitName, getToolkitShortName, getToolStatusWarning, getUsage, getVersion, instanceMain, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, parseArgs, printLibraryVersions, printSettings, printStartupMessage, runTool, setDefaultHeaders, warnOnToolStatus

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - intervalArgumentCollection
```
@ArgumentCollection
protected IntervalArgumentCollection intervalArgumentCollection
```
  - readArguments
```
@ArgumentCollection
protected final ReadInputArgumentCollection readArguments
```
  - referenceArguments
```
@ArgumentCollection
protected final ReferenceInputArgumentCollection referenceArguments
```
  - SECONDS_BETWEEN_PROGRESS_UPDATES_NAME
```
public static final java.lang.String SECONDS_BETWEEN_PROGRESS_UPDATES_NAME
```
    See Also:
    
    Constant Field Values
  - seqValidationArguments
```
@ArgumentCollection
protected SequenceDictionaryValidationArgumentCollection seqValidationArguments
```
  - createOutputBamIndex
```
@Argument(fullName="create-output-bam-index",
          shortName="OBI",
          doc="If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.",
          optional=true,
          common=true)
public boolean createOutputBamIndex
```
  - createOutputBamMD5
```
@Argument(fullName="create-output-bam-md5",
          shortName="OBM",
          doc="If true, create a MD5 digest for any BAM/SAM/CRAM file created",
          optional=true,
          common=true)
public boolean createOutputBamMD5
```
  - createOutputVariantIndex
```
@Argument(fullName="create-output-variant-index",
          shortName="OVI",
          doc="If true, create a VCF index when writing a coordinate-sorted VCF file.",
          optional=true,
          common=true)
public boolean createOutputVariantIndex
```
  - createOutputVariantMD5
```
@Argument(fullName="create-output-variant-md5",
          shortName="OVM",
          doc="If true, create a a MD5 digest any VCF file created.",
          optional=true,
          common=true)
public boolean createOutputVariantMD5
```
  - lenientVCFProcessing
```
@Argument(fullName="lenient",
          shortName="LE",
          doc="Lenient processing of VCF files",
          common=true,
          optional=true)
protected boolean lenientVCFProcessing
```
  - addOutputSAMProgramRecord
```
@Argument(fullName="add-output-sam-program-record",
          shortName="add-output-sam-program-record",
          doc="If true, adds a PG tag to created SAM/BAM/CRAM files.",
          optional=true,
          common=true)
public boolean addOutputSAMProgramRecord
```
  - addOutputVCFCommandLine
```
@Argument(fullName="add-output-vcf-command-line",
          shortName="add-output-vcf-command-line",
          doc="If true, adds a command line header line to created VCF files.",
          optional=true,
          common=true)
public boolean addOutputVCFCommandLine
```
  - cloudPrefetchBuffer
```
@Argument(fullName="cloud-prefetch-buffer",
          shortName="CPB",
          doc="Size of the cloud-only prefetch buffer (in MB; 0 to disable).",
          optional=true)
public int cloudPrefetchBuffer
```
  - cloudIndexPrefetchBuffer
```
@Argument(fullName="cloud-index-prefetch-buffer",
          shortName="CIPB",
          doc="Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.",
          optional=true)
public int cloudIndexPrefetchBuffer
```
  - disableBamIndexCaching
```
@Argument(fullName="disable-bam-index-caching",
          shortName="DBIC",
          doc="If true, don\'t cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified.  Caching is automatically disabled if there are no intervals specified.",
          optional=true)
public boolean disableBamIndexCaching
```
  - outputSitesOnlyVCFs
```
@Argument(fullName="sites-only-vcf-output",
          doc="If true, don\'t emit genotype fields when writing vcf file output.",
          optional=true)
public boolean outputSitesOnlyVCFs
```
  - features
```
public FeatureManager features
```
    Our source of Feature data (null if no source of Features was provided)
  - progressMeter
```
protected ProgressMeter progressMeter
```
    Progress meter to print out traversal statistics. Subclasses must invoke ProgressMeter.update(Locatable) after each record processed from the primary input in their traverse() method.
- Constructor Detail
  - GATKTool
```
public GATKTool()
```
- Method Detail
  - directlyAccessEngineReferenceDataSource
```
protected ReferenceDataSource directlyAccessEngineReferenceDataSource()
```
    Get the ReferenceDataSource for this GATKTool. Will throw a GATKException if the reference is null. Clients are expected to call the hasReference() method prior to calling this. Should only be called by walker base classes in the engine (such as ReadWalker), or by "free-form" tools that extend the GATKTool class directly rather than one of the built-in walker types. Tools that extend a walker type should get their data via apply() rather than directly accessing the engine datasources.
    
    Returns:
    
    the ReferenceDataSource for this GATKTool. Never null.
  - directlyAccessEngineReadsDataSource
```
protected ReadsDataSource directlyAccessEngineReadsDataSource()
```
    Get the ReadsDataSource for this GATKTool. Will throw a GATKException if the reads are null. Clients are expected to call the hasReads() method prior to calling this. Should only be called by walker base classes in the engine (such as ReadWalker), or by "free-form" tools that extend the GATKTool class directly rather than one of the built-in walker types. Tools that extend a walker type should get their data via apply() rather than directly accessing the engine datasources.
    
    Returns:
    
    the ReadsDataSource for this GATKTool. Never null.
  - directlyAccessEngineFeatureManager
```
protected FeatureManager directlyAccessEngineFeatureManager()
```
    Get the FeatureManager for this GATKTool. Will throw a GATKException if the features are null. Clients are expected to call the hasFeatures() method prior to calling this. Should only be called by walker base classes in the engine (such as ReadWalker), or by "free-form" tools that extend the GATKTool class directly rather than one of the built-in walker types. Tools that extend a walker type should get their data via apply() rather than directly accessing the engine datasources.
    
    Returns:
    
    the FeatureManager for this GATKTool. Never null.
  - getPluginDescriptors
```
public java.util.List<? extends org.broadinstitute.barclay.argparser.CommandLinePluginDescriptor<?>> getPluginDescriptors()
```
    Return the list of GATKCommandLinePluginDescriptors to be used for this tool. Uses the read filter plugin.
    
    Specified by:
    
    getPluginDescriptors in interface org.broadinstitute.barclay.argparser.CommandLinePluginProvider
    
    Overrides:
    
    getPluginDescriptors in class CommandLineProgram
  - getDefaultReadFilters
```
public java.util.List<ReadFilter> getDefaultReadFilters()
```
    Returns the default list of ReadFilters that are used for this tool. The filters returned by this method are subject to selective enabling/disabling by the user via the command line. The default implementation returns an empty list. Subclasses can override to provide alternative filters. Note: this method is called before command line parsing begins, and thus before a SAMFileHeader is available through getHeaderForReads(). The actual SAMFileHeader is propagated to the read filters by makeReadFilter() after the filters have been merged with command line arguments.
    
    Returns:
    
    List of individual filters to be applied for this tool.
  - makeReadFilter
```
public CountingReadFilter makeReadFilter()
```
    Returns a read filter (simple or composite) that can be applied to reads. This implementation combines the default read filters for this tool (returned by getDefaultReadFilters() along with any read filter command line directives specified by the user (such as enabling other filters or disabling default filters); wraps each filter in the resulting list with a CountingReadFilter; and returns a single composite filter resulting from the list by and'ing them together. NOTE: Most tools will not need to override the method, and should only do so in order to provide custom behavior or processing of the final merged read filter. To change the default read filters used by the tool, override getDefaultReadFilters() instead. Implementations of traverse() should call this method once before iterating over the reads, in order to unnecessary avoid object allocation. Nevertheless, keeping state in filter objects is strongly discouraged. Multiple filters can be composed by using ReadFilter composition methods.
  - useVariantAnnotations
```
public boolean useVariantAnnotations()
```
    Must be overridden in order to add annotation arguments to the engine. If this is set to true the engine will dynamically discover all Annotations in the package defined by org.broadinstitute.hellbender.cmdline.GATKPlugin.GATKAnnotationPluginDescriptor#pluginPackageName and automatically generate and add command line arguments allowing the user to specify which annotations or groups of annotations to use. To specify default annotations for a tool simply specify them using getDefaultVariantAnnotationGroups() or getDefaultVariantAnnotations() To access instantiated annotation objects simply use makeVariantAnnotations().
  - getDefaultVariantAnnotations
```
public java.util.List<Annotation> getDefaultVariantAnnotations()
```
    Returns the default list of Annotations that are used for this tool. The annotations returned by this method are subject to selective enabling/disabling by the user via the command line. The default implementation returns an empty list. Subclasses can override to provide alternative annotations.
    
    Returns:
    
    List of individual annotations to be applied for this tool.
  - getDefaultVariantAnnotationGroups
```
public java.util.List<java.lang.Class<? extends Annotation>> getDefaultVariantAnnotationGroups()
```
    Returns the default list of annotation groups that are used for this tool. The annotations returned by this method will have default arguments, which can be overridden with specific arguments using getDefaultVariantAnnotations(). Returned annotation groups are subject to selective enabling/disabling by the user via the command line. The default implementation returns an empty list.
    
    Returns:
    
    List of annotation groups to be applied for this tool.
  - makeVariantAnnotations
```
public java.util.Collection<Annotation> makeVariantAnnotations()
```
    Returns a list of annotations that can be applied to VariantContexts. This implementation combines the default annotations for this tool (returned by getDefaultVariantAnnotations() and getDefaultVariantAnnotationGroups()) along with any annotations command line directives specified by the user (such as enabling other annotations/groups or disabling default annotations) and returns a collection of all the annotation arguments instantiated. NOTE: Most tools will not need to override the method, and should only do so in order to provide custom behavior or processing of the final annotations based on other command line input. To change the default annotations used by the tool, override getDefaultVariantAnnotations() instead. To apply returned annotations to a VariantContext, simply use a VariantAnnotatorEngine constructed with the discovered annotations.
  - makePreReadFilterTransformer
```
public ReadTransformer makePreReadFilterTransformer()
```
    Returns the pre-filter read transformer (simple or composite) that will be applied to the reads before filtering. The default implementation uses the ReadTransformer.identity(). Default implementation of traverse() calls this method once before iterating over the reads and reuses the transformer object to avoid object allocation. Subclasses can extend to provide own transformers (ie override and call super). Multiple transformers can be composed by using ReadTransformer composition methods.
  - makePostReadFilterTransformer
```
public ReadTransformer makePostReadFilterTransformer()
```
    Returns the post-filter read transformer (simple or composite) that will be applied to the reads after filtering. The default implementation uses the ReadTransformer.identity(). Default implementation of traverse() calls this method once before iterating over the reads and reuses the transformer object to avoid object allocation. Subclasses can extend to provide own transformers (ie override and call super). Multiple transformers can be composed by using ReadTransformer composition methods.
  - getTransformedReadStream
```
protected java.util.stream.Stream<GATKRead> getTransformedReadStream(ReadFilter filter)
```
    Returns a stream over the reads, which are: 1. Transformed with makePreReadFilterTransformer(). 2. Filtered with filter. 3. Transformed with makePostReadFilterTransformer(). Note: the filter is passed to keep the state of CountingReadFilter, obtained with makeReadFilter().
  - getDefaultCloudPrefetchBufferSize
```
public int getDefaultCloudPrefetchBufferSize()
```
    Returns:
    
    Default size in MB of the cloud prefetch buffer. May be overridden by individual tools. The default implementation returns a value (40 MB) that is suitable for tools with a small number of large cloud inputs. Tools with large numbers of cloud inputs will likely want to override to specify a smaller size. This value is maintained in the GATKConfig file.
  - getDefaultCloudIndexPrefetchBufferSize
```
public int getDefaultCloudIndexPrefetchBufferSize()
```
    Returns:
    
    Default size in MB of the cloud index prefetch buffer. May be overridden by individual tools. A return value of -1 means to use the same value as returned by getDefaultCloudPrefetchBufferSize(). The default implementation returns -1. This value is maintained in the GATKConfig file.
  - getProgressMeterRecordLabel
```
public java.lang.String getProgressMeterRecordLabel()
```
    Returns:
    
    String label to use for records in progress meter output. Defaults to ProgressMeter.DEFAULT_RECORD_LABEL, but tools may override to provide a more appropriate label (like "reads" or "regions")
  - transformTraversalIntervals
```
protected java.util.List<SimpleInterval> transformTraversalIntervals(java.util.List<SimpleInterval> getIntervals,
                                                                     htsjdk.samtools.SAMSequenceDictionary sequenceDictionary)
```
  - getGenomicsDBOptions
```
protected GenomicsDBOptions getGenomicsDBOptions()
```
    Get the GenomicsDB read settings for the current tool
    
    Returns:
    
    By default, just return the vanilla options
  - hasReference
```
public final boolean hasReference()
```
    Is a source of reference data available?
    
    Returns:
    
    true if a reference is available, otherwise false
  - hasReads
```
public final boolean hasReads()
```
    Are sources of reads available?
    
    Returns:
    
    true if reads are available, otherwise false
  - hasFeatures
```
public final boolean hasFeatures()
```
    Are sources of Features available?
    
    Returns:
    
    true if sources of Features are available, otherwise false
  - hasUserSuppliedIntervals
```
public final boolean hasUserSuppliedIntervals()
```
    Are sources of intervals available?
    
    Returns:
    
    true if user-supplied intervals are available, otherwise false
  - requiresReference
```
public boolean requiresReference()
```
    Does this tool require reference data? Traversals types and/or tools that do should override to return true.
    
    Returns:
    
    true if this tool requires a reference, otherwise false
  - requiresFeatures
```
public boolean requiresFeatures()
```
    Does this tool require features? Traversals types and/or tools that do should override to return true.
    
    Returns:
    
    true if this tool requires reads, otherwise false
  - requiresReads
```
public boolean requiresReads()
```
    Does this tool require reads? Traversals types and/or tools that do should override to return true.
    
    Returns:
    
    true if this tool requires reads, otherwise false
  - requiresIntervals
```
public boolean requiresIntervals()
```
    Does this tool require intervals? Traversals types and/or tools that do should override to return true.
    
    Returns:
    
    true if this tool requires intervals, otherwise false
  - getSequenceDictionaryValidationArgumentCollection
```
protected SequenceDictionaryValidationArgumentCollection getSequenceDictionaryValidationArgumentCollection()
```
    Get the SequenceDictionaryValidationArgumentCollection for the tool. Subclasses may override this method in order to customize validation options.
    
    Returns:
    
    a SequenceDictionaryValidationArgumentCollection
  - getReferenceDictionary
```
public final htsjdk.samtools.SAMSequenceDictionary getReferenceDictionary()
```
    Returns the reference sequence dictionary if there is a reference (hasReference() == true), otherwise null.
    
    Returns:
    
    reference sequence dictionary if any, or null
  - getMasterSequenceDictionary
```
public final htsjdk.samtools.SAMSequenceDictionary getMasterSequenceDictionary()
```
    Returns the master sequence dictionary if it has been set, otherwise null. In practice, this should only be called after engine initialization in onStartup()
    
    Returns:
    
    Master sequence dictionary if specified, or null.
  - getBestAvailableSequenceDictionary
```
public htsjdk.samtools.SAMSequenceDictionary getBestAvailableSequenceDictionary()
```
    Returns the "best available" sequence dictionary or null if there is no single best dictionary. The algorithm for selecting the best dictionary is as follows: 1) If a master sequence dictionary was specified, use that dictionary 2) if there is a reference, then the best dictionary is the reference sequence dictionary 3) Otherwise, if there are reads, then the best dictionary is the sequence dictionary constructed from the reads. 4) Otherwise, if there are features and the feature data source has only one dictionary, then that one is the best dictionary. 5) Otherwise, the result is null. TODO: check interval file(s) as well for a sequence dictionary Subclasses may override if they prefer a different algorithm.
    
    Returns:
    
    best available sequence dictionary given our inputs or null if no one dictionary is the best one.
  - getHeaderForReads
```
public final htsjdk.samtools.SAMFileHeader getHeaderForReads()
```
    Returns the SAM header for the reads data source. Will be a merged header if there are multiple inputs for the reads. If there is only a single input, returns its header directly. Null if there are no reads.
    
    Returns:
    
    SAM header for our source of reads (null if there are no reads)
  - getHeaderForFeatures
```
public final <T extends htsjdk.tribble.Feature> java.lang.Object getHeaderForFeatures(FeatureInput<T> featureDescriptor)
```
    Returns the header for the specified source of Features
    
    Type Parameters:
    
    T - type of Feature in our FeatureInput
    
    Parameters:
    
    featureDescriptor - FeatureInput whose header to retrieve
    
    Returns:
    
    header for the provided FeatureInput (null if we have no sources of Features)
  - onStartup
```
protected void onStartup()
```
    Initialize our data sources, make sure that all tool requirements for input data have been satisfied and start the progress meter. The data sources are initialized in the following order: initializeReference initializeReads (must be initialized after reference for CRAM files) initializeFeatures initializeIntervals (must be initialized after all other sources, because they require a sequence dictionary) Then, data sources are checked by calls to: validateSequenceDictionaries (unless disabled by disableSequenceDictionaryValidation) checkToolRequirements Subclasses may extend (ie, they should call super and add functionality).
    
    Overrides:
    
    onStartup in class CommandLineProgram
  - createSAMWriter
```
public final SAMFileGATKReadWriter createSAMWriter(java.io.File outputFile,
                                                   boolean preSorted)
```
  - createSAMWriter
```
public final SAMFileGATKReadWriter createSAMWriter(java.nio.file.Path outputPath,
                                                   boolean preSorted)
```
  - createVCFWriter
```
public htsjdk.variant.variantcontext.writer.VariantContextWriter createVCFWriter(java.io.File outFile)
```
    Creates a VariantContextWriter whose outputFile type is determined by the vcfOutput's extension, using the best available sequence dictionary for this tool, and default index, leniency and md5 generation settings. Deprecated, use createVCFWriter(Path) instead.
    
    Parameters:
    
    outFile - output File for this writer. May not be null.
  - createVCFWriter
```
public htsjdk.variant.variantcontext.writer.VariantContextWriter createVCFWriter(java.nio.file.Path outPath)
```
    Creates a VariantContextWriter whose outputFile type is determined by vcfOutput's extension, using the best available sequence dictionary for this tool, and default index, leniency and md5 generation settings.
    
    Parameters:
    
    outPath - output Path for this writer. May not be null.
  - getHeaderForSAMWriter
```
protected htsjdk.samtools.SAMFileHeader getHeaderForSAMWriter()
```
    Returns the SAM header suitable for writing SAM/BAM/CRAM files produced by this tool. The default implementation calls getHeaderForReads() (and makes an empty header if that call returns null) and optionally adds program tag to the header with a program version CommandLineProgram.getVersion(), program name getToolName() and command line CommandLineProgram.getCommandLine(). Subclasses may override.
    
    Returns:
    
    SAM header for the SAM writer with (optionally, if addOutputSAMProgramRecord is true) program record appropriately.
  - getDefaultToolVCFHeaderLines
```
protected java.util.Set<htsjdk.variant.vcf.VCFHeaderLine> getDefaultToolVCFHeaderLines()
```
    Returns:
    
    If addOutputVCFCommandLine is true, a set of VCF header lines containing the tool name, version, date and command line, otherwise an empty set.
  - addFeatureInputsAfterInitialization
```
public FeatureInput<? extends htsjdk.tribble.Feature> addFeatureInputsAfterInitialization(java.lang.String filePath,
                                                                                          java.lang.String name,
                                                                                          java.lang.Class<? extends htsjdk.tribble.Feature> featureType,
                                                                                          int featureQueryLookahead)
```
    A method to allow a user to inject FeatureInputs after initialization that were not specified as command-line arguments.
    
    Parameters:
    
    filePath - path to the Feature file to register
    
    name - what to call the Feature input
    
    featureType - class of features
    
    featureQueryLookahead - look ahead this many bases during queries that produce cache misses
    
    Returns:
    
    The FeatureInput used as the key for this data source.
  - getToolName
```
public java.lang.String getToolName()
```
    Returns the name of this tool. The default implementation returns the result of calling CommandLineProgram.getToolkitShortName() followed by the simple name of the class. Subclasses may override.
  - getTraversalIntervals
```
public java.util.List<SimpleInterval> getTraversalIntervals()
```
    Returns the list of intervals to iterate, either limited to the user-supplied intervals or the entire reference genome if none were specified. If no reference was supplied, null is returned
  - onShutdown
```
protected void onShutdown()
```
    Close all data sources on shutdown. Subclasses may extend (ie they must call super).
    
    Overrides:
    
    onShutdown in class CommandLineProgram
  - onTraversalStart
```
public void onTraversalStart()
```
    Operations performed just prior to the start of traversal. Should be overridden by tool authors who need to process arguments local to their tool or perform other kinds of local initialization. Default implementation does nothing.
  - traverse
```
public abstract void traverse()
```
    A complete traversal from start to finish. Tool authors who wish to "roll their own" traversal from scratch can extend this class directly and implement this method. Walker authors should instead extend a Walker class and implement the Walker-appropriate apply() method, since the Walker base classes implement the various kinds of traversals for you.
  - onTraversalSuccess
```
public java.lang.Object onTraversalSuccess()
```
    Operations performed immediately after a successful traversal (ie when no uncaught exceptions were thrown during the traversal). Should be overridden by tool authors who need to close local resources, etc., after traversal. Also allows tools to return a value representing the traversal result, which is printed by the engine. Default implementation does nothing and returns null.
    
    Returns:
    
    Object representing the traversal result, or null if a tool does not return a value
  - doWork
```
protected final java.lang.Object doWork()
```
    Description copied from class: CommandLineProgram
    
    Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.
    
    Specified by:
    
    doWork in class CommandLineProgram
    
    Returns:
    
    the return value or null is there is none.
  - closeTool
```
public void closeTool()
```
    This method is called by the GATK framework at the end of the doWork() template method. It is called regardless of whether the traverse() has succeeded or not. It is called after the onTraversalSuccess() has completed (successfully or not) but before the doWork() method returns. In other words, on successful runs both onTraversalSuccess() and closeTool() will be called (in this order) while on failed runs (when traverse() causes an exception), only 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.

Class GATKTool

Field Summary

Fields inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram

Constructor Summary

Method Summary

Methods inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram

Methods inherited from class java.lang.Object

Field Detail

intervalArgumentCollection

readArguments

referenceArguments

SECONDS_BETWEEN_PROGRESS_UPDATES_NAME

seqValidationArguments

createOutputBamIndex

createOutputBamMD5

createOutputVariantIndex

createOutputVariantMD5

lenientVCFProcessing

addOutputSAMProgramRecord

addOutputVCFCommandLine

cloudPrefetchBuffer

cloudIndexPrefetchBuffer

disableBamIndexCaching

outputSitesOnlyVCFs

features

progressMeter

Constructor Detail

GATKTool

Method Detail

directlyAccessEngineReferenceDataSource

directlyAccessEngineReadsDataSource

directlyAccessEngineFeatureManager

getPluginDescriptors

getDefaultReadFilters

makeReadFilter

useVariantAnnotations

getDefaultVariantAnnotations

getDefaultVariantAnnotationGroups

makeVariantAnnotations

makePreReadFilterTransformer

makePostReadFilterTransformer

getTransformedReadStream

getDefaultCloudPrefetchBufferSize

getDefaultCloudIndexPrefetchBufferSize

getProgressMeterRecordLabel

transformTraversalIntervals

getGenomicsDBOptions

hasReference

hasReads

hasFeatures

hasUserSuppliedIntervals

requiresReference

requiresFeatures

requiresReads

requiresIntervals

getSequenceDictionaryValidationArgumentCollection

getReferenceDictionary

getMasterSequenceDictionary

getBestAvailableSequenceDictionary

getHeaderForReads

getHeaderForFeatures

onStartup

createSAMWriter

createSAMWriter

createVCFWriter

createVCFWriter

getHeaderForSAMWriter

getDefaultToolVCFHeaderLines

addFeatureInputsAfterInitialization

getToolName

getTraversalIntervals

onShutdown

onTraversalStart

traverse

onTraversalSuccess

doWork

closeTool