org.broadinstitute.hellbender.tools.walkers.haplotypecaller

Class AssemblyBasedCallerGenotypingEngine

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine<AssemblyBasedCallerArgumentCollection>

org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerGenotypingEngine

Direct Known Subclasses:

HaplotypeCallerGenotypingEngine, SomaticGenotypingEngine

public abstract class AssemblyBasedCallerGenotypingEngine
extends GenotypingEngine<AssemblyBasedCallerArgumentCollection>

Created by davidben on 12/21/16.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AssemblyBasedCallerGenotypingEngine.CalledHaplotypes Carries the result of a call to #assignGenotypeLikelihoods

Field Summary

Fields

Modifier and Type	Field and Description
protected static int	ALLELE_EXTENSION
protected boolean	doPhysicalPhasing

Fields inherited from class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine

afCalculatorProvider, annotationEngine, configuration, logger, newAFCalculator, numberOfGenomes, samples

Constructor Summary

Constructors

Constructor and Description
AssemblyBasedCallerGenotypingEngine(AssemblyBasedCallerArgumentCollection configuration, SampleList samples, AFCalculatorProvider afCalculatorProvider, boolean doPhysicalPhasing)

Method Summary

Modifier and Type	Method and Description
protected static java.util.Map<htsjdk.variant.variantcontext.VariantContext,java.util.Set<Haplotype>>	constructHaplotypeMapping(java.util.List<htsjdk.variant.variantcontext.VariantContext> originalCalls, java.util.Set<Haplotype> calledHaplotypes) Construct the mapping from alternate allele to the set of haplotypes that contain that allele
protected static java.util.List<htsjdk.variant.variantcontext.VariantContext>	constructPhaseGroups(java.util.List<htsjdk.variant.variantcontext.VariantContext> originalCalls, java.util.Map<htsjdk.variant.variantcontext.VariantContext,org.apache.commons.lang3.tuple.Pair<java.lang.Integer,java.lang.String>> phaseSetMapping, int indexTo) Assemble the phase groups together and update the original calls accordingly
protected static int	constructPhaseSetMapping(java.util.List<htsjdk.variant.variantcontext.VariantContext> originalCalls, java.util.Map<htsjdk.variant.variantcontext.VariantContext,java.util.Set<Haplotype>> haplotypeMap, int totalAvailableHaplotypes, java.util.Map<htsjdk.variant.variantcontext.VariantContext,org.apache.commons.lang3.tuple.Pair<java.lang.Integer,java.lang.String>> phaseSetMapping) Construct the mapping from call (variant context) to phase set ID
protected static java.util.Map<htsjdk.variant.variantcontext.Allele,java.util.List<Haplotype>>	createAlleleMapper(java.util.List<htsjdk.variant.variantcontext.VariantContext> eventsAtThisLoc, htsjdk.variant.variantcontext.VariantContext mergedVC, int loc, java.util.List<Haplotype> haplotypes)
protected java.util.TreeSet<java.lang.Integer>	decomposeHaplotypesIntoVariantContexts(java.util.List<Haplotype> haplotypes, byte[] ref, SimpleInterval refLoc, java.util.List<htsjdk.variant.variantcontext.VariantContext> activeAllelesToGenotype, int maxMnpDistance) Go through the haplotypes we assembled, and decompose them into their constituent variant contexts
protected boolean	forceSiteEmission() Indicates whether we have to emit any site no matter what.
protected static java.util.List<htsjdk.variant.variantcontext.VariantContext>	getVCsAtThisLocation(java.util.List<Haplotype> haplotypes, int loc, java.util.List<htsjdk.variant.variantcontext.VariantContext> activeAllelesToGenotype)
protected static java.util.List<htsjdk.variant.variantcontext.VariantContext>	phaseCalls(java.util.List<htsjdk.variant.variantcontext.VariantContext> calls, java.util.Set<Haplotype> calledHaplotypes) Tries to phase the individual alleles based on pairwise comparisons to the other alleles based on all called haplotypes
protected ReadLikelihoods<htsjdk.variant.variantcontext.Allele>	prepareReadAlleleLikelihoodsForAnnotation(ReadLikelihoods<Haplotype> readHaplotypeLikelihoods, java.util.Map<java.lang.String,java.util.List<GATKRead>> perSampleFilteredReadList, boolean emitReferenceConfidence, java.util.Map<htsjdk.variant.variantcontext.Allele,java.util.List<Haplotype>> alleleMapper, ReadLikelihoods<htsjdk.variant.variantcontext.Allele> readAlleleLikelihoodsForGenotyping, htsjdk.variant.variantcontext.VariantContext call)

Methods inherited from class org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine

calculateGenotypes, calculateGenotypes, calculateSingleSampleRefVsAnyActiveStateProfileValue, callSourceString, composeAlleleFrequencyPriorProvider, composeCallAttributes, computeAlleleFrequencyPriors, confidentlyCalled, emptyCallContext, estimateLog10ReferenceConfidenceForOneSample, estimateReferenceConfidence, forceKeepAllele, getAlleleFrequencyPriors, getAppropriateVCFInfoHeaders, getConfiguration, hasTooManyAlternativeAlleles, passesCallThreshold, passesEmitThreshold, setAnnotationEngine, setLogger

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ALLELE_EXTENSION

protected static final int ALLELE_EXTENSION

See Also:

Constant Field Values

doPhysicalPhasing

protected final boolean doPhysicalPhasing

Constructor Detail

AssemblyBasedCallerGenotypingEngine

public AssemblyBasedCallerGenotypingEngine(AssemblyBasedCallerArgumentCollection configuration,
                                           SampleList samples,
                                           AFCalculatorProvider afCalculatorProvider,
                                           boolean doPhysicalPhasing)

Parameters:

configuration -

samples -

doPhysicalPhasing - whether to try physical phasing.

Method Detail

forceSiteEmission

protected boolean forceSiteEmission()

Description copied from class: GenotypingEngine

Indicates whether we have to emit any site no matter what.

Note: this has been added to allow differences between UG and HC GGA modes where the latter force emmitions of all given alleles sites even if there is no enough confidence.

Specified by:

forceSiteEmission in class GenotypingEngine<AssemblyBasedCallerArgumentCollection>

Returns:

true iff we force emissions.

decomposeHaplotypesIntoVariantContexts

protected java.util.TreeSet<java.lang.Integer> decomposeHaplotypesIntoVariantContexts(java.util.List<Haplotype> haplotypes,
                                                                                      byte[] ref,
                                                                                      SimpleInterval refLoc,
                                                                                      java.util.List<htsjdk.variant.variantcontext.VariantContext> activeAllelesToGenotype,
                                                                                      int maxMnpDistance)

Go through the haplotypes we assembled, and decompose them into their constituent variant contexts

Parameters:

haplotypes - the list of haplotypes we're working with

ref - the reference bases (over the same interval as the haplotypes)

refLoc - the span of the reference bases

activeAllelesToGenotype - alleles we want to ensure are scheduled for genotyping (GGA mode)

maxMnpDistance - Phased substitutions separated by this distance or less are merged into MNPs. More than two substitutions occurring in the same alignment block (ie the same M/X/EQ CIGAR element) are merged until a substitution is separated from the previous one by a greater distance. That is, if maxMnpDistance = 1, substitutions at positions 10,11,12,14,15,17 are partitioned into a MNP at 10-12, a MNP at 14-15, and a SNP at 17.

Returns:

never null but perhaps an empty list if there is no variants to report.

getVCsAtThisLocation

protected static java.util.List<htsjdk.variant.variantcontext.VariantContext> getVCsAtThisLocation(java.util.List<Haplotype> haplotypes,
                                                                                                   int loc,
                                                                                                   java.util.List<htsjdk.variant.variantcontext.VariantContext> activeAllelesToGenotype)

createAlleleMapper

protected static java.util.Map<htsjdk.variant.variantcontext.Allele,java.util.List<Haplotype>> createAlleleMapper(java.util.List<htsjdk.variant.variantcontext.VariantContext> eventsAtThisLoc,
                                                                                                                  htsjdk.variant.variantcontext.VariantContext mergedVC,
                                                                                                                  int loc,
                                                                                                                  java.util.List<Haplotype> haplotypes)

prepareReadAlleleLikelihoodsForAnnotation

protected ReadLikelihoods<htsjdk.variant.variantcontext.Allele> prepareReadAlleleLikelihoodsForAnnotation(ReadLikelihoods<Haplotype> readHaplotypeLikelihoods,
                                                                                                          java.util.Map<java.lang.String,java.util.List<GATKRead>> perSampleFilteredReadList,
                                                                                                          boolean emitReferenceConfidence,
                                                                                                          java.util.Map<htsjdk.variant.variantcontext.Allele,java.util.List<Haplotype>> alleleMapper,
                                                                                                          ReadLikelihoods<htsjdk.variant.variantcontext.Allele> readAlleleLikelihoodsForGenotyping,
                                                                                                          htsjdk.variant.variantcontext.VariantContext call)

phaseCalls

protected static java.util.List<htsjdk.variant.variantcontext.VariantContext> phaseCalls(java.util.List<htsjdk.variant.variantcontext.VariantContext> calls,
                                                                                         java.util.Set<Haplotype> calledHaplotypes)

Tries to phase the individual alleles based on pairwise comparisons to the other alleles based on all called haplotypes

Parameters:

calls - the list of called alleles

calledHaplotypes - the set of haplotypes used for calling

Returns:

a non-null list which represents the possibly phased version of the calls

constructHaplotypeMapping

protected static java.util.Map<htsjdk.variant.variantcontext.VariantContext,java.util.Set<Haplotype>> constructHaplotypeMapping(java.util.List<htsjdk.variant.variantcontext.VariantContext> originalCalls,
                                                                                                                                java.util.Set<Haplotype> calledHaplotypes)

Construct the mapping from alternate allele to the set of haplotypes that contain that allele

Parameters:

originalCalls - the original unphased calls

calledHaplotypes - the set of haplotypes used for calling

Returns:

non-null Map

constructPhaseSetMapping

protected static int constructPhaseSetMapping(java.util.List<htsjdk.variant.variantcontext.VariantContext> originalCalls,
                                              java.util.Map<htsjdk.variant.variantcontext.VariantContext,java.util.Set<Haplotype>> haplotypeMap,
                                              int totalAvailableHaplotypes,
                                              java.util.Map<htsjdk.variant.variantcontext.VariantContext,org.apache.commons.lang3.tuple.Pair<java.lang.Integer,java.lang.String>> phaseSetMapping)

Construct the mapping from call (variant context) to phase set ID

Parameters:

originalCalls - the original unphased calls

haplotypeMap - mapping from alternate allele to the set of haplotypes that contain that allele

totalAvailableHaplotypes - the total number of possible haplotypes used in calling

phaseSetMapping - the map to populate in this method; note that it is okay for this method NOT to populate the phaseSetMapping at all (e.g. in an impossible-to-phase situation)

Returns:

the next incremental unique index

constructPhaseGroups

protected static java.util.List<htsjdk.variant.variantcontext.VariantContext> constructPhaseGroups(java.util.List<htsjdk.variant.variantcontext.VariantContext> originalCalls,
                                                                                                   java.util.Map<htsjdk.variant.variantcontext.VariantContext,org.apache.commons.lang3.tuple.Pair<java.lang.Integer,java.lang.String>> phaseSetMapping,
                                                                                                   int indexTo)

Assemble the phase groups together and update the original calls accordingly

Parameters:

originalCalls - the original unphased calls

phaseSetMapping - mapping from call (variant context) to phase group ID

indexTo - last index (exclusive) of phase group IDs

Returns:

a non-null list which represents the possibly phased version of the calls