org.broadinstitute.hellbender.tools.walkers.qc

Class CheckPileup

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.GATKTool

org.broadinstitute.hellbender.engine.WalkerBase

org.broadinstitute.hellbender.engine.LocusWalker

org.broadinstitute.hellbender.tools.walkers.qc.CheckPileup

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@DocumentedFeature
public final class CheckPileup
extends LocusWalker

Compare GATK's internal pileup to a reference Samtools pileup

This tool compares the mpileup data (reference base, aligned base from each overlapping read, and quality score) generated internally by GATK to a reference pileup data generated by Samtools, for each position in the requested interval. Note that this only considers the single-sample mpileup format. See the Pileup format documentation for more details on the format.

Inputs

• A BAM or CRAM file containing aligned read data.
• An mpileup file generated by Samtools covering the interval of interest. It should be accompanied by an index, e.g. that generated with IndexFeatureFile.

Output

A text file listing mismatches between the input mpileup and the GATK's internal pileup. If there are no mismatches, the output file is empty.

Usage example

   gatk CheckPileup \
     -R reference.fasta \
     -I input.bam \
     -O output.txt \
     --pileup samtools.pileup
 

Field Summary

Fields

Modifier and Type	Field and Description
boolean	continueAfterAnError By default the program will quit if it encounters an error (such as missing truth data for a given position).
boolean	ignoreOverlaps
FeatureInput<SAMPileupFeature>	mpileup This is the existing mpileup against which we'll compare GATK's internal pileup at each genome position in the desired interval.
java.io.File	outFile

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

MAX_DEPTH_PER_SAMPLE_NAME, maxDepthPerSample

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
CheckPileup()

Method Summary

Modifier and Type	Method and Description
void	apply(AlignmentContext context, ReferenceContext ref, FeatureContext featureContext) Process an individual AlignmentContext (with optional contextual information).
void	closeTool() This method is called by the GATK framework at the end of the GATKTool.doWork() template method.
java.util.List<ReadFilter>	getDefaultReadFilters() Returns the default list of CommandLineReadFilters that are used for this tool.
void	onTraversalStart() Operations performed just prior to the start of traversal.
java.lang.Object	onTraversalSuccess() Operations performed immediately after a successful traversal (ie when no uncaught exceptions were thrown during the traversal).
java.lang.String	pileupDiff(ReadPileup a, SAMPileupFeature b)
boolean	requiresReference() Does this tool require reference data? Traversals types and/or tools that do should override to return true.

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

defaultMaxDepthPerSample, emitEmptyLoci, getDownsamplingInfo, getProgressMeterRecordLabel, includeDeletions, includeNs, keepUniqueReadListInLibs, onShutdown, onStartup, requiresReads, traverse, validateEmitEmptyLociParameters

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

directlyAccessEngineFeatureManager, directlyAccessEngineReadsDataSource, directlyAccessEngineReferenceDataSource

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

addFeatureInputsAfterInitialization, 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, requiresFeatures, requiresIntervals, 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

Field Detail

mpileup

@Argument(fullName="pileup",
          doc="Pileup generated by Samtools")
public FeatureInput<SAMPileupFeature> mpileup

This is the existing mpileup against which we'll compare GATK's internal pileup at each genome position in the desired interval.

outFile

@Argument(fullName="output",
          shortName="O",
          doc="Output file (if not provided, defaults to STDOUT)",
          optional=true)
public java.io.File outFile

ignoreOverlaps

@Argument(fullName="ignore-overlaps",
          doc="Disable read-pair overlap detection",
          optional=true)
public boolean ignoreOverlaps

continueAfterAnError

@Argument(fullName="continue-after-error",
          doc="Continue after encountering an error",
          optional=true)
public boolean continueAfterAnError

By default the program will quit if it encounters an error (such as missing truth data for a given position). Use this flag to override the default behavior; the program will then simply print an error message and move on to the next position.

Constructor Detail

CheckPileup

public CheckPileup()

Method Detail

getDefaultReadFilters

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

Description copied from class: LocusWalker

Returns the default list of CommandLineReadFilters 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 and ReadFilterLibrary.MappedReadFilter 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 {link #getHeaderForReads}.

Overrides:

getDefaultReadFilters in class LocusWalker

Returns:

List of individual filters to be applied for this tool.

requiresReference

public boolean requiresReference()

Description copied from class: GATKTool

Does this tool require reference data? Traversals types and/or tools that do should override to return true.

Overrides:

requiresReference in class GATKTool

Returns:

true if this tool requires a reference, otherwise false

onTraversalStart

public void onTraversalStart()

Description copied from class: GATKTool

Operations performed just prior to the start of traversal. Should be overridden by tool authors who need to process arguments local to their tool or perform other kinds of local initialization. Default implementation does nothing.

Overrides:

onTraversalStart in class GATKTool

apply

public void apply(AlignmentContext context,
                  ReferenceContext ref,
                  FeatureContext featureContext)

Description copied from class: LocusWalker

Process an individual AlignmentContext (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.

Specified by:

apply in class LocusWalker

Parameters:

context - current alignment context

ref - Reference bases spanning the current locus. 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 locus by invoking ReferenceContext.setWindow(int, int) on this object before calling ReferenceContext.getBases()

featureContext - Features spanning the current locus. 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).

pileupDiff

public java.lang.String pileupDiff(ReadPileup a,
                                   SAMPileupFeature b)

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

closeTool

public void closeTool()

Description copied from class: GATKTool

This method is called by the GATK framework at the end of the GATKTool.doWork() template method. It is called regardless of whether the GATKTool.traverse() has succeeded or not. It is called after the GATKTool.onTraversalSuccess() has completed (successfully or not) but before the GATKTool.doWork() method returns. In other words, on successful runs both GATKTool.onTraversalSuccess() and GATKTool.closeTool() will be called (in this order) while on failed runs (when GATKTool.traverse() causes an exception), only GATKTool.closeTool() will be called. The default implementation does nothing. Subclasses should override this method to close any resources that must be closed regardless of the success of traversal.

Overrides:

closeTool in class GATKTool