org.broadinstitute.hellbender.tools.examples

Class ExampleReadWalkerWithReferenceSpark

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

org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReferenceSpark

All Implemented Interfaces:

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

public final class ExampleReadWalkerWithReferenceSpark
extends ReadWalkerSpark

Example/toy program that prints reads from the provided file or files with corresponding reference bases (if a reference is provided). Intended to show how to implement the ReadWalker interface.

See Also:

Serialized Form

Nested Class Summary

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

GATKSparkTool.ReadInputMergingPolicy

Field Summary

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

FEATURE_CACHE_LOOKAHEAD

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 and Description
ExampleReadWalkerWithReferenceSpark()

Method Summary

Modifier and Type	Method and Description
protected void	processReads(org.apache.spark.api.java.JavaRDD<ReadWalkerContext> rdd, org.apache.spark.api.java.JavaSparkContext ctx) Process the reads and write output.
boolean	requiresReference() Does this tool require reference data? Tools that do should override to return true.

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

getReads, requiresReads, runTool

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, 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

Constructor Detail

ExampleReadWalkerWithReferenceSpark

public ExampleReadWalkerWithReferenceSpark()

Method Detail

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

processReads

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

Description copied from class: ReadWalkerSpark

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

Specified by:

processReads in class ReadWalkerSpark

Parameters:

rdd - a distributed collection of ReadWalkerContext

ctx - our Spark context