org.broadinstitute.hellbender.engine

Class AbstractConcordanceWalker

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.engine.GATKTool

org.broadinstitute.hellbender.engine.WalkerBase

org.broadinstitute.hellbender.engine.AbstractConcordanceWalker

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

Direct Known Subclasses:

Concordance, EvaluateInfoFieldConcordance, MergeMutect2CallsWithMC3, ReferenceBlockConcordance

public abstract class AbstractConcordanceWalker
extends WalkerBase

Base class for concordance walkers, which process one variant at a time from one or more sources of variants, with optional contextual information from a reference, sets of reads, and/or supplementary sources of Features. Subclasses must implement the apply(org.broadinstitute.hellbender.engine.AbstractConcordanceWalker.TruthVersusEval, org.broadinstitute.hellbender.engine.ReadsContext, org.broadinstitute.hellbender.engine.ReferenceContext) and areVariantsAtSameLocusConcordant(htsjdk.variant.variantcontext.VariantContext, htsjdk.variant.variantcontext.VariantContext) methods to process each variant and may optionally implement GATKTool.onTraversalStart() and/or GATKTool.onTraversalSuccess(). Created by Takuto Sato 1/30/17, abstractified by David Benjamin on 2/22/17. GATKTool.onTraversalStart(), GATKTool.onTraversalSuccess() and/or GATKTool.closeTool().

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	AbstractConcordanceWalker.TruthVersusEval store a truth vc in case of a false negative, an eval vc in case of a false positive, or a concordance pair of truth and eval in case of a true positive.

Field Summary

Fields

Modifier and Type	Field and Description
static int	CACHE_LOOKAHEAD
static java.lang.String	CONFIDENCE_REGION_LONG_NAME
static java.lang.String	CONFIDENCE_REGION_SHORT_NAME
protected htsjdk.samtools.SAMSequenceDictionary	dict
static java.lang.String	EVAL_VARIANTS_LONG_NAME
static java.lang.String	EVAL_VARIANTS_SHORT_NAME
java.lang.String	evalVariantsFile
protected java.io.File	highConfidenceRegion
static java.lang.String	TRUTH_VARIANTS_LONG_NAME
java.lang.String	truthVariantsFile

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
AbstractConcordanceWalker()

Method Summary

Modifier and Type	Method and Description
protected abstract void	apply(AbstractConcordanceWalker.TruthVersusEval truthVersusEval, ReadsContext readsContext, ReferenceContext refContext)
protected abstract boolean	areVariantsAtSameLocusConcordant(htsjdk.variant.variantcontext.VariantContext truth, htsjdk.variant.variantcontext.VariantContext eval)
htsjdk.samtools.SAMSequenceDictionary	getBestAvailableSequenceDictionary() Returns the "best available" sequence dictionary or null if there is no single best dictionary.
htsjdk.variant.vcf.VCFHeader	getEvalHeader()
htsjdk.variant.vcf.VCFHeader	getTruthHeader()
protected org.apache.commons.collections4.Predicate<htsjdk.variant.variantcontext.VariantContext>	makeEvalVariantFilter()
protected org.apache.commons.collections4.Predicate<htsjdk.variant.variantcontext.VariantContext>	makeTruthVariantFilter()
protected void	onShutdown() Close all data sources on shutdown.
protected void	onStartup() Initialize our data sources, make sure that all tool requirements for input data have been satisfied and start the progress meter.
void	traverse() A complete traversal from start to finish.

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

directlyAccessEngineFeatureManager, directlyAccessEngineReadsDataSource, directlyAccessEngineReferenceDataSource

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

addFeatureInputsAfterInitialization, bamIndexCachingShouldBeEnabled, closeTool, createSAMWriter, createVCFWriter, createVCFWriter, createVCFWriter, disableProgressMeter, doWork, getDefaultCloudIndexPrefetchBufferSize, getDefaultCloudPrefetchBufferSize, getDefaultReadFilters, getDefaultToolVCFHeaderLines, getDefaultVariantAnnotationGroups, getDefaultVariantAnnotations, getGenomicsDBOptions, getHeaderForFeatures, getHeaderForReads, getHeaderForSAMWriter, getMasterSequenceDictionary, getPluginDescriptors, getProgressMeterRecordLabel, getReferenceDictionary, getSequenceDictionaryValidationArgumentCollection, getToolName, getTransformedReadStream, getTraversalIntervals, hasFeatures, hasReads, hasReference, hasUserSuppliedIntervals, initializeProgressMeter, makePostReadFilterTransformer, makePreReadFilterTransformer, makeReadFilter, makeSamReaderFactory, makeVariantAnnotations, onTraversalStart, onTraversalSuccess, requiresFeatures, requiresIntervals, requiresReads, 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

Field Detail

TRUTH_VARIANTS_LONG_NAME

public static final java.lang.String TRUTH_VARIANTS_LONG_NAME

See Also:

Constant Field Values

EVAL_VARIANTS_SHORT_NAME

public static final java.lang.String EVAL_VARIANTS_SHORT_NAME

See Also:

Constant Field Values

EVAL_VARIANTS_LONG_NAME

public static final java.lang.String EVAL_VARIANTS_LONG_NAME

See Also:

Constant Field Values

CONFIDENCE_REGION_LONG_NAME

public static final java.lang.String CONFIDENCE_REGION_LONG_NAME

See Also:

Constant Field Values

CONFIDENCE_REGION_SHORT_NAME

public static final java.lang.String CONFIDENCE_REGION_SHORT_NAME

See Also:

Constant Field Values

CACHE_LOOKAHEAD

public static final int CACHE_LOOKAHEAD

See Also:

Constant Field Values

truthVariantsFile

@Argument(shortName="truth",
          fullName="truth",
          doc="A VCF containing truth variants",
          optional=false)
public java.lang.String truthVariantsFile

evalVariantsFile

@Argument(shortName="eval",
          fullName="evaluation",
          doc="A VCF containing variants to be compared to the truth",
          optional=false)
public java.lang.String evalVariantsFile

highConfidenceRegion

@Argument(doc="TO BE IMPLEMENTED",
          fullName="confidence",
          shortName="C",
          optional=true)
protected java.io.File highConfidenceRegion

dict

protected htsjdk.samtools.SAMSequenceDictionary dict

Constructor Detail

AbstractConcordanceWalker

public AbstractConcordanceWalker()

Method Detail

getBestAvailableSequenceDictionary

public final htsjdk.samtools.SAMSequenceDictionary getBestAvailableSequenceDictionary()

Description copied from class: GATKTool

Returns the "best available" sequence dictionary or null if there is no single best dictionary. The algorithm for selecting the best dictionary is as follows: 1) If a master sequence dictionary was specified, use that dictionary 2) if there is a reference, then the best dictionary is the reference sequence dictionary 3) Otherwise, if there are reads, then the best dictionary is the sequence dictionary constructed from the reads. 4) Otherwise, if there are features and the feature data source has only one dictionary, then that one is the best dictionary. 5) Otherwise, the result is null. TODO: check interval file(s) as well for a sequence dictionary Subclasses may override if they prefer a different algorithm.

Overrides:

getBestAvailableSequenceDictionary in class GATKTool

Returns:

best available sequence dictionary given our inputs or null if no one dictionary is the best one.

makeTruthVariantFilter

protected org.apache.commons.collections4.Predicate<htsjdk.variant.variantcontext.VariantContext> makeTruthVariantFilter()

makeEvalVariantFilter

protected org.apache.commons.collections4.Predicate<htsjdk.variant.variantcontext.VariantContext> makeEvalVariantFilter()

onStartup

protected final void onStartup()

Description copied from class: GATKTool

Initialize our data sources, make sure that all tool requirements for input data have been satisfied and start the progress meter. The data sources are initialized in the following order: initializeReference initializeReads (must be initialized after reference for CRAM files) initializeFeatures initializeIntervals (must be initialized after all other sources, because they require a sequence dictionary) Then, data sources are checked by calls to: validateSequenceDictionaries (unless disabled by disableSequenceDictionaryValidation) checkToolRequirements Subclasses may extend (ie, they should call super and add functionality).

Overrides:

onStartup in class GATKTool

apply

protected abstract void apply(AbstractConcordanceWalker.TruthVersusEval truthVersusEval,
                              ReadsContext readsContext,
                              ReferenceContext refContext)

traverse

public void traverse()

A complete traversal from start to finish. Tool authors who wish to "roll their own" traversal from scratch can extend this class directly and implement this method. Walker authors should instead extend a Walker class and implement the Walker-appropriate apply() method, since the Walker base classes implement the various kinds of traversals for you. Implementation of concordance traversal. NOTE: You should only override traverse() if you are writing a new walker base class in the engine package that extends this class. It is not meant to be overridden by tools outside of the engine package.

Specified by:

traverse in class GATKTool

onShutdown

protected final void onShutdown()

Description copied from class: GATKTool

Close all data sources on shutdown. Subclasses may extend (ie they must call super).

Overrides:

onShutdown in class GATKTool

getTruthHeader

public final htsjdk.variant.vcf.VCFHeader getTruthHeader()

getEvalHeader

public final htsjdk.variant.vcf.VCFHeader getEvalHeader()

areVariantsAtSameLocusConcordant

protected abstract boolean areVariantsAtSameLocusConcordant(htsjdk.variant.variantcontext.VariantContext truth,
                                                            htsjdk.variant.variantcontext.VariantContext eval)