org.broadinstitute.hellbender.tools

Class CountReads

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.GATKTool

org.broadinstitute.hellbender.engine.WalkerBase

org.broadinstitute.hellbender.engine.ReadWalker

org.broadinstitute.hellbender.tools.CountReads

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@DocumentedFeature
public final class CountReads
extends ReadWalker

Calculate and print to the standard output the overall number of reads in a SAM/BAM/CRAM file

Input

• A single BAM file

Example

   gatk CountReads \
     -I input_reads.bam
 

Field Summary

Fields inherited from class org.broadinstitute.hellbender.engine.ReadWalker

FEATURE_CACHE_LOOKAHEAD

Fields inherited from class org.broadinstitute.hellbender.engine.GATKTool

addOutputSAMProgramRecord, addOutputVCFCommandLine, cloudIndexPrefetchBuffer, cloudPrefetchBuffer, createOutputBamIndex, createOutputBamMD5, createOutputVariantIndex, createOutputVariantMD5, disableBamIndexCaching, features, intervalArgumentCollection, lenientVCFProcessing, outputSitesOnlyVCFs, progressMeter, readArguments, referenceArguments, SECONDS_BETWEEN_PROGRESS_UPDATES_NAME, seqValidationArguments

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
CountReads()

Method Summary

Modifier and Type	Method and Description
void	apply(GATKRead read, ReferenceContext referenceContext, FeatureContext featureContext) Process an individual read (with optional contextual information).
java.lang.Object	onTraversalSuccess() Operations performed immediately after a successful traversal (ie when no uncaught exceptions were thrown during the traversal).

Methods inherited from class org.broadinstitute.hellbender.engine.ReadWalker

getDefaultReadFilters, getProgressMeterRecordLabel, onShutdown, onStartup, requiresReads, resetReadsDataSource, traverse

Methods inherited from class org.broadinstitute.hellbender.engine.WalkerBase

directlyAccessEngineFeatureManager, directlyAccessEngineReadsDataSource, directlyAccessEngineReferenceDataSource

Methods inherited from class org.broadinstitute.hellbender.engine.GATKTool

addFeatureInputsAfterInitialization, closeTool, createSAMWriter, createSAMWriter, createVCFWriter, createVCFWriter, doWork, getBestAvailableSequenceDictionary, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getGenomicsDBOptions, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolName, getTransformedReadStream, getTraversalIntervals, hasFeatures, hasReads, hasReference, hasUserSuppliedIntervals, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeVariantAnnotations, onTraversalStart, requiresFeatures, requiresIntervals, requiresReference, transformTraversalIntervals, useVariantAnnotations

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

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

CountReads

public CountReads()

Method Detail

apply

public void apply(GATKRead read,
                  ReferenceContext referenceContext,
                  FeatureContext featureContext)

Description copied from class: ReadWalker

Process an individual read (with optional contextual information). Must be implemented by tool authors. In general, tool authors should simply stream their output from apply(), and maintain as little internal state as possible. TODO: Determine whether and to what degree the GATK engine should provide a reduce operation TODO: to complement this operation. At a minimum, we should make apply() return a value to TODO: discourage statefulness in walkers, but how this value should be handled is TBD.

Specified by:

apply in class ReadWalker

Parameters:

read - current read

referenceContext - Reference bases spanning the current read. Will be an empty, but non-null, context object if there is no backing source of reference data (in which case all queries on it will return an empty array/iterator). Can request extra bases of context around the current read's interval by invoking ReferenceContext.setWindow(int, int) on this object before calling ReferenceContext.getBases()

featureContext - Features spanning the current read. Will be an empty, but non-null, context object if there is no backing source of Feature data (in which case all queries on it will return an empty List).

onTraversalSuccess

public java.lang.Object onTraversalSuccess()

Description copied from class: GATKTool

Operations performed immediately after a successful traversal (ie when no uncaught exceptions were thrown during the traversal). Should be overridden by tool authors who need to close local resources, etc., after traversal. Also allows tools to return a value representing the traversal result, which is printed by the engine. Default implementation does nothing and returns null.

Overrides:

onTraversalSuccess in class GATKTool

Returns:

Object representing the traversal result, or null if a tool does not return a value