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

Class CollectQualityYieldMetricsSpark

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.metrics.MetricsCollectorSparkTool<QualityYieldMetricsArgumentCollection>

org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSpark

All Implemented Interfaces:

Serializable, org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@DocumentedFeature
@BetaFeature
public final class CollectQualityYieldMetricsSpark
extends MetricsCollectorSparkTool<QualityYieldMetricsArgumentCollection>

Collects quality yield metrics in SAM/BAM/CRAM file(s). The tool leverages the Spark framework for faster operation.

Usage example

 gatk CollectQualityYieldMetricsSpark \
   -R reference.fasta \
   -I input.bam \
   -O quality_yield_metrics.txt
 

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 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
CollectQualityYieldMetricsSpark()

Method Summary

Modifier and Type	Method	Description
protected void	collectMetrics(org.apache.spark.api.java.JavaRDD<GATKRead> filteredReads, htsjdk.samtools.SAMFileHeader samHeader)
List<ReadFilter>	getDefaultReadFilters()	The following MetricsCollectorSpark methods must be implemented by subclasses and should be forwarded to the embedded collector.
protected htsjdk.samtools.SAMFileHeader.SortOrder	getExpectedSortOrder()
protected QualityYieldMetricsArgumentCollection	getInputArguments()	To be implemented by subclasses; return the fully initialized and populated argument collection that will be passed to the collector
protected void	initialize(QualityYieldMetricsArgumentCollection inputArgs, htsjdk.samtools.SAMFileHeader samHeader, List<htsjdk.samtools.metrics.Header> defaultHeaders)
protected void	saveMetrics(String inputName)

Methods inherited from class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.MetricsCollectorSparkTool

requiresReads, runTool

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

addReferenceFilesForSpark, addVCFsForSpark, editIntervals, getBestAvailableSequenceDictionary, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getGatkReadJavaRDD, getHeaderForReads, getHeaderForReadsInput, getIntervals, getPluginDescriptors, getReadInputMergingPolicy, getReads, 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

Constructor Details

CollectQualityYieldMetricsSpark

public CollectQualityYieldMetricsSpark()

Method Details

getExpectedSortOrder

protected htsjdk.samtools.SAMFileHeader.SortOrder getExpectedSortOrder()

Specified by:

getExpectedSortOrder in class MetricsCollectorSparkTool<QualityYieldMetricsArgumentCollection>

getInputArguments

protected QualityYieldMetricsArgumentCollection getInputArguments()

Description copied from class: MetricsCollectorSparkTool

To be implemented by subclasses; return the fully initialized and populated argument collection that will be passed to the collector

Specified by:

getInputArguments in class MetricsCollectorSparkTool<QualityYieldMetricsArgumentCollection>

getDefaultReadFilters

public List<ReadFilter> getDefaultReadFilters()

Description copied from class: MetricsCollectorSparkTool

The following MetricsCollectorSpark methods must be implemented by subclasses and should be forwarded to the embedded collector.

Specified by:

getDefaultReadFilters in class MetricsCollectorSparkTool<QualityYieldMetricsArgumentCollection>

Returns:

List of individual filters to be applied for this tool.

initialize

protected void initialize(QualityYieldMetricsArgumentCollection inputArgs,
 htsjdk.samtools.SAMFileHeader samHeader,
 List<htsjdk.samtools.metrics.Header> defaultHeaders)

Specified by:

initialize in class MetricsCollectorSparkTool<QualityYieldMetricsArgumentCollection>

collectMetrics

protected void collectMetrics(org.apache.spark.api.java.JavaRDD<GATKRead> filteredReads,
 htsjdk.samtools.SAMFileHeader samHeader)

Specified by:

collectMetrics in class MetricsCollectorSparkTool<QualityYieldMetricsArgumentCollection>

saveMetrics

protected void saveMetrics(String inputName)

Specified by:

saveMetrics in class MetricsCollectorSparkTool<QualityYieldMetricsArgumentCollection>