Package org.broadinstitute.hellbender.tools.spark.pipelines

Class BwaAndMarkDuplicatesPipelineSpark

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram

org.broadinstitute.hellbender.engine.spark.GATKSparkTool

org.broadinstitute.hellbender.tools.spark.pipelines.BwaAndMarkDuplicatesPipelineSpark

All Implemented Interfaces:

Serializable, org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@DocumentedFeature
@BetaFeature
public final class BwaAndMarkDuplicatesPipelineSpark
extends GATKSparkTool

Runs BWA and MarkDuplicates on Spark. It's an example of how to compose those two tools.

See Also:

• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.broadinstitute.hellbender.engine.spark.GATKSparkTool

GATKSparkTool.ReadInputMergingPolicy

Nested classes/interfaces inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram

CommandLineProgram.AutoCloseableNoCheckedExceptions

Field Summary

Fields

Modifier and Type	Field	Description
final BwaArgumentCollection	bwaArgs
protected MarkDuplicatesSparkArgumentCollection	markDuplicatesSparkArgumentCollection
protected String	output

Fields inherited from class org.broadinstitute.hellbender.engine.spark.GATKSparkTool

addOutputVCFCommandLine, BAM_PARTITION_SIZE_LONG_NAME, bamPartitionSplitSize, CREATE_OUTPUT_BAM_SPLITTING_INDEX_LONG_NAME, createOutputBamIndex, createOutputBamSplittingIndex, createOutputVariantIndex, features, intervalArgumentCollection, NUM_REDUCERS_LONG_NAME, numReducers, OUTPUT_SHARD_DIR_LONG_NAME, readArguments, referenceArguments, sequenceDictionaryValidationArguments, SHARDED_OUTPUT_LONG_NAME, shardedOutput, shardedPartsDir, SPLITTING_INDEX_GRANULARITY, splittingIndexGranularity, USE_NIO, useNio

Fields inherited from class org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram

programName, SPARK_PROGRAM_NAME_LONG_NAME, sparkArgs

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	Description
BwaAndMarkDuplicatesPipelineSpark()

Method Summary

Modifier and Type	Method	Description
protected SequenceDictionaryValidationArgumentCollection	getSequenceDictionaryValidationArgumentCollection()	subclasses can override this to provide different default behavior for sequence dictionary validation
boolean	requiresReads()	Does this tool require reads? Tools that do should override to return true.
boolean	requiresReference()	Does this tool require reference data? Tools that do should override to return true.
protected void	runTool(org.apache.spark.api.java.JavaSparkContext ctx)	Runs the tool itself after initializing and validating inputs.

Methods inherited from class org.broadinstitute.hellbender.engine.spark.GATKSparkTool

addReferenceFilesForSpark, addVCFsForSpark, editIntervals, getBestAvailableSequenceDictionary, getDefaultReadFilters, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getGatkReadJavaRDD, getHeaderForReads, getHeaderForReadsInput, getIntervals, getPluginDescriptors, getReadInputMergingPolicy, getReads, getReadSourceName, getRecommendedNumReducers, getReference, getReferenceSequenceDictionary, getReferenceWindowFunction, getTargetPartitionSize, getUnfilteredReads, hasReads, hasReference, hasUserSuppliedIntervals, makeReadFilter, makeReadFilter, makeVariantAnnotations, requiresIntervals, runPipeline, useVariantAnnotations, validateSequenceDictionaries, writeReads, writeReads

Methods inherited from class org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram

afterPipeline, doWork, getProgramName

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

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getSupportInformation, getToolkitName, getToolkitShortName, getToolStatusWarning, getUsage, getVersion, instanceMain, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, onShutdown, onStartup, 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 Details

bwaArgs

@ArgumentCollection
public final BwaArgumentCollection bwaArgs

output

@Argument(doc="the output bam",
          shortName="O",
          fullName="output")
protected String output

markDuplicatesSparkArgumentCollection

@ArgumentCollection
protected MarkDuplicatesSparkArgumentCollection markDuplicatesSparkArgumentCollection

Constructor Details

BwaAndMarkDuplicatesPipelineSpark

public BwaAndMarkDuplicatesPipelineSpark()

Method Details

requiresReads

public boolean requiresReads()

Description copied from class: GATKSparkTool

Does this tool require reads? Tools that do should override to return true.

Overrides:

requiresReads in class GATKSparkTool

Returns:

true if this tool requires reads, otherwise false

requiresReference

public boolean requiresReference()

Description copied from class: GATKSparkTool

Does this tool require reference data? Tools that do should override to return true.

Overrides:

requiresReference in class GATKSparkTool

Returns:

true if this tool requires a reference, otherwise false

getSequenceDictionaryValidationArgumentCollection

protected SequenceDictionaryValidationArgumentCollection getSequenceDictionaryValidationArgumentCollection()

Description copied from class: GATKSparkTool

subclasses can override this to provide different default behavior for sequence dictionary validation

Overrides:

getSequenceDictionaryValidationArgumentCollection in class GATKSparkTool

Returns:

a SequenceDictionaryValidationArgumentCollection

runTool

protected void runTool(org.apache.spark.api.java.JavaSparkContext ctx)

Description copied from class: GATKSparkTool

Runs the tool itself after initializing and validating inputs. Must be implemented by subclasses.

Specified by:

runTool in class GATKSparkTool

Parameters:

ctx - our Spark context