org.broadinstitute.hellbender.tools.copynumber

Class CollectAllelicCountsSpark

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.LocusWalkerSpark

org.broadinstitute.hellbender.tools.copynumber.CollectAllelicCountsSpark

All Implemented Interfaces:

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

public class CollectAllelicCountsSpark
extends LocusWalkerSpark

See CollectAllelicCounts. This behaves the same, except that it supports spark.

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.LocusWalkerSpark

maxDepthPerSample, readShardSize, shuffle

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
CollectAllelicCountsSpark()

Method Summary

Modifier and Type	Method and Description
boolean	emitEmptyLoci() Does this tool emit information for uncovered loci? Tools that do should override to return true.
java.util.List<ReadFilter>	getDefaultReadFilters() Returns the default list of ReadFilters that are used for this tool.
protected void	processAlignments(org.apache.spark.api.java.JavaRDD<LocusWalkerContext> rdd, org.apache.spark.api.java.JavaSparkContext ctx) Process the alignments and write output.
boolean	requiresIntervals() Does this tool require intervals? Tools that do should override to return true.
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.LocusWalkerSpark

defaultMaxDepthPerSample, getAlignments, getDownsamplingInfo, requiresReads, runTool

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

addReferenceFilesForSpark, addVCFsForSpark, editIntervals, getBestAvailableSequenceDictionary, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getGatkReadJavaRDD, getHeaderForReads, getIntervals, getPluginDescriptors, getReadInputMergingPolicy, getReads, getReadSourceHeaderMap, getReadSourceName, getRecommendedNumReducers, getReference, getReferenceSequenceDictionary, getReferenceWindowFunction, getSequenceDictionaryValidationArgumentCollection, getTargetPartitionSize, getUnfilteredReads, hasReads, hasReference, hasUserSuppliedIntervals, makeReadFilter, makeReadFilter, makeVariantAnnotations, 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

CollectAllelicCountsSpark

public CollectAllelicCountsSpark()

Method Detail

emitEmptyLoci

public boolean emitEmptyLoci()

Description copied from class: LocusWalkerSpark

Does this tool emit information for uncovered loci? Tools that do should override to return true. NOTE: Typically, this should only be used when intervals are specified. NOTE: If MappedReadFilter is removed, then emitting empty loci will fail. NOTE: If there is no available sequence dictionary and this is set to true, there should be a failure. Please consider requiring reads and/or references for all tools that wish to set this to true.

Overrides:

emitEmptyLoci in class LocusWalkerSpark

Returns:

true if this tool requires uncovered loci information to be emitted, false otherwise

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

requiresIntervals

public boolean requiresIntervals()

Description copied from class: GATKSparkTool

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

Overrides:

requiresIntervals in class GATKSparkTool

Returns:

true if this tool requires intervals, otherwise false

getDefaultReadFilters

public java.util.List<ReadFilter> getDefaultReadFilters()

Description copied from class: GATKSparkTool

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 uses the WellformedReadFilter filter with all default options. 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 GATKSparkTool.getHeaderForReads(). The actual SAMFileHeader is propagated to the read filters by GATKSparkTool.makeReadFilter() after the filters have been merged with command line arguments.

Overrides:

getDefaultReadFilters in class GATKSparkTool

Returns:

List of individual filters to be applied for this tool.

processAlignments

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

Description copied from class: LocusWalkerSpark

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

Specified by:

processAlignments in class LocusWalkerSpark

Parameters:

rdd - a distributed collection of LocusWalkerContext

ctx - our Spark context