org.broadinstitute.hellbender.engine.spark

Class ReadWalkerSpark

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram

org.broadinstitute.hellbender.engine.spark.GATKSparkTool

org.broadinstitute.hellbender.engine.spark.ReadWalkerSpark

All Implemented Interfaces:

java.io.Serializable, org.broadinstitute.barclay.argparser.CommandLinePluginProvider

Direct Known Subclasses:

ExampleReadWalkerWithReferenceSpark, ExampleReadWalkerWithVariantsSpark

public abstract class ReadWalkerSpark
extends GATKSparkTool

A Spark version of ReadWalker. Subclasses should implement processReads(JavaRDD, JavaSparkContext) and operate on the passed in RDD.

See Also:

ExampleReadWalkerWithReferenceSpark, ExampleReadWalkerWithVariantsSpark, Serialized Form

Nested Class Summary

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

GATKSparkTool.ReadInputMergingPolicy

Field Summary

Fields

Modifier and Type	Field and Description
static int	FEATURE_CACHE_LOOKAHEAD This number controls the size of the cache for our FeatureInputs (specifically, the number of additional bases worth of overlapping records to cache when querying feature sources).

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, 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 and Description
ReadWalkerSpark()

Method Summary

Modifier and Type	Method and Description
org.apache.spark.api.java.JavaRDD<ReadWalkerContext>	getReads(org.apache.spark.api.java.JavaSparkContext ctx) Loads reads and the corresponding reference and features into a JavaRDD for the intervals specified.
protected abstract void	processReads(org.apache.spark.api.java.JavaRDD<ReadWalkerContext> rdd, org.apache.spark.api.java.JavaSparkContext ctx) Process the reads and write output.
boolean	requiresReads() Does this tool require reads? 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, getIntervals, getPluginDescriptors, getReadInputMergingPolicy, getReads, getReadSourceHeaderMap, getReadSourceName, getRecommendedNumReducers, getReference, getReferenceSequenceDictionary, getReferenceWindowFunction, getSequenceDictionaryValidationArgumentCollection, getTargetPartitionSize, getUnfilteredReads, hasReads, hasReference, hasUserSuppliedIntervals, makeReadFilter, makeReadFilter, makeVariantAnnotations, requiresIntervals, requiresReference, 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 Detail

FEATURE_CACHE_LOOKAHEAD

public static final int FEATURE_CACHE_LOOKAHEAD

This number controls the size of the cache for our FeatureInputs (specifically, the number of additional bases worth of overlapping records to cache when querying feature sources).

See Also:

Constant Field Values

Constructor Detail

ReadWalkerSpark

public ReadWalkerSpark()

Method Detail

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

getReads

public org.apache.spark.api.java.JavaRDD<ReadWalkerContext> getReads(org.apache.spark.api.java.JavaSparkContext ctx)

Loads reads and the corresponding reference and features into a JavaRDD for the intervals specified. If no intervals were specified, returns all the reads.

Returns:

all reads as a JavaRDD, bounded by intervals if specified.

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

processReads

protected abstract void processReads(org.apache.spark.api.java.JavaRDD<ReadWalkerContext> rdd,
                                     org.apache.spark.api.java.JavaSparkContext ctx)

Process the reads and write output. Must be implemented by subclasses.

Parameters:

rdd - a distributed collection of ReadWalkerContext

ctx - our Spark context