Package de.charite.compbio.jannovar.htsjdk

Class VariantContextAnnotator

java.lang.Object

de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator

public final class VariantContextAnnotator
extends Object

Helper class for generating VariantAnnotations objects from VariantContexts.

Author:

Manuel Holtgrewe

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	VariantContextAnnotator.Options	Options class for VariantContextAnnotator.

Constructor Summary

Constructors

Constructor	Description
VariantContextAnnotator(de.charite.compbio.jannovar.data.ReferenceDictionary refDict, com.google.common.collect.ImmutableMap<Integer,de.charite.compbio.jannovar.data.Chromosome> chromosomeMap)	Construct annotator with default options.
VariantContextAnnotator(de.charite.compbio.jannovar.data.ReferenceDictionary refDict, com.google.common.collect.ImmutableMap<Integer,de.charite.compbio.jannovar.data.Chromosome> chromosomeMap, VariantContextAnnotator.Options options)	Construct Annotator.

Method Summary

Modifier and Type	Method	Description
htsjdk.variant.variantcontext.VariantContext	annotateVariantContext(htsjdk.variant.variantcontext.VariantContext vc)	Annotate variant vc and return annoated variant
htsjdk.variant.variantcontext.VariantContext	applyAnnotations(htsjdk.variant.variantcontext.VariantContext vc, List<de.charite.compbio.jannovar.annotation.VariantAnnotations> annos)	Write annotations from annos to vc l
htsjdk.variant.variantcontext.VariantContext	applySVAnnotations(htsjdk.variant.variantcontext.VariantContext vc, List<de.charite.compbio.jannovar.annotation.SVAnnotations> annos)
com.google.common.collect.ImmutableList<de.charite.compbio.jannovar.annotation.VariantAnnotations>	buildAnnotations(htsjdk.variant.variantcontext.VariantContext vc)	Given a VariantContext, generate one VariantAnnotations for each alternative allele.
de.charite.compbio.jannovar.annotation.VariantAnnotations	buildErrorAnnotations(de.charite.compbio.jannovar.reference.GenomeVariant change)
de.charite.compbio.jannovar.reference.GenomeVariant	buildGenomeVariant(htsjdk.variant.variantcontext.VariantContext vc, int alleleID)	Build a GenomeVariant from a VariantContext object.
com.google.common.collect.ImmutableList<de.charite.compbio.jannovar.annotation.SVAnnotations>	buildSVAnnotations(htsjdk.variant.variantcontext.VariantContext vc)
de.charite.compbio.jannovar.annotation.SVAnnotations	buildSVErrorAnnotations(de.charite.compbio.jannovar.reference.SVGenomeVariant change)
de.charite.compbio.jannovar.reference.SVGenomeVariant	buildSVGenomeVariant(htsjdk.variant.variantcontext.VariantContext vc)
htsjdk.variant.variantcontext.VariantContext	dispatchAnnotateVariantContext(htsjdk.variant.variantcontext.VariantContext vc)	Dispatch annotation of VariantContext depending on whether it describes a sequence or a structural variant.
de.charite.compbio.jannovar.annotation.VariantAnnotator	getAnnotator()
com.google.common.collect.ImmutableMap<Integer,de.charite.compbio.jannovar.data.Chromosome>	getChromosomeMap()
VariantContextAnnotator.Options	getOptions()
de.charite.compbio.jannovar.data.ReferenceDictionary	getRefDict()
void	putErrorAnnotation(htsjdk.variant.variantcontext.VariantContext vc, Set<de.charite.compbio.jannovar.annotation.AnnotationMessage> messages)	Put error annotation messages to a VariantContext into the ANN field in the INFO column.

Methods inherited from class java.lang.Object

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

Constructor Detail

VariantContextAnnotator

public VariantContextAnnotator(de.charite.compbio.jannovar.data.ReferenceDictionary refDict,
                               com.google.common.collect.ImmutableMap<Integer,de.charite.compbio.jannovar.data.Chromosome> chromosomeMap)

Construct annotator with default options.

Parameters:

refDict - Referencedictionary

chromosomeMap - the chomosomal map

VariantContextAnnotator

public VariantContextAnnotator(de.charite.compbio.jannovar.data.ReferenceDictionary refDict,
                               com.google.common.collect.ImmutableMap<Integer,de.charite.compbio.jannovar.data.Chromosome> chromosomeMap,
                               VariantContextAnnotator.Options options)

Construct Annotator.

Parameters:

refDict - ReferenceDictionary to use, probably from JannovarData

chromosomeMap - Chromosome map to use, probably from JannovarData

options - configuration of the Annotator, for applyAnnotations(htsjdk.variant.variantcontext.VariantContext, java.util.List<de.charite.compbio.jannovar.annotation.VariantAnnotations>)

Method Detail

getRefDict

public de.charite.compbio.jannovar.data.ReferenceDictionary getRefDict()

Returns:

The refDict

getChromosomeMap

public com.google.common.collect.ImmutableMap<Integer,de.charite.compbio.jannovar.data.Chromosome> getChromosomeMap()

Returns:

the chromosomal map

getOptions

public VariantContextAnnotator.Options getOptions()

Returns:

get the options of the VCAnnotator

getAnnotator

public de.charite.compbio.jannovar.annotation.VariantAnnotator getAnnotator()

Returns:

get the annotator

buildGenomeVariant

public de.charite.compbio.jannovar.reference.GenomeVariant buildGenomeVariant(htsjdk.variant.variantcontext.VariantContext vc,
                                                                              int alleleID)
                                                                       throws InvalidCoordinatesException

Build a GenomeVariant from a VariantContext object.

In the case of exceptions, you can use buildErrorAnnotations(de.charite.compbio.jannovar.reference.GenomeVariant) to build an VariantAnnotations with an error message.

Parameters:

vc - VariantContext describing the variant

alleleID - numeric identifier of the allele

Returns:

GenomeVariant corresponding to vc, guaranteed to be on Strand.FWD.

Throws:

InvalidCoordinatesException - in the case that the reference in vc is not known in refDict.

putErrorAnnotation

public void putErrorAnnotation(htsjdk.variant.variantcontext.VariantContext vc,
                               Set<de.charite.compbio.jannovar.annotation.AnnotationMessage> messages)

Put error annotation messages to a VariantContext into the ANN field in the INFO column.

Previous values are overwritten.

Parameters:

vc - VariantContext to add the error message to

messages - set of messages to write into the VariantContext

annotateVariantContext

public htsjdk.variant.variantcontext.VariantContext annotateVariantContext(htsjdk.variant.variantcontext.VariantContext vc)

Annotate variant vc and return annoated variant

Parameters:

vc - VariantContext to annotate

dispatchAnnotateVariantContext

public htsjdk.variant.variantcontext.VariantContext dispatchAnnotateVariantContext(htsjdk.variant.variantcontext.VariantContext vc)
                                                                            throws MixingSmallAndSVAlleles,
                                                                                   InvalidCoordinatesException,
                                                                                   MissingSVTypeInfoField,
                                                                                   MissingEndInfoField,
                                                                                   MultipleSVAlleles,
                                                                                   InvalidBreakendDescriptionException

Dispatch annotation of VariantContext depending on whether it describes a sequence or a structural variant.

This function looks at whether any of the alternate alleles is symbolic or the SVTYPE key of the INFO field is set.

Throws:

MixingSmallAndSVAlleles

InvalidCoordinatesException

MissingSVTypeInfoField

MissingEndInfoField

MultipleSVAlleles

InvalidBreakendDescriptionException

buildAnnotations

public com.google.common.collect.ImmutableList<de.charite.compbio.jannovar.annotation.VariantAnnotations> buildAnnotations(htsjdk.variant.variantcontext.VariantContext vc)
                                                                                                                    throws InvalidCoordinatesException

Given a VariantContext, generate one VariantAnnotations for each alternative allele.

Note that in the case of an exception being thrown, you have to add an error annotation yourself to the VariantContext yourself, e.g. by using putErrorAnnotation(htsjdk.variant.variantcontext.VariantContext, java.util.Set<de.charite.compbio.jannovar.annotation.AnnotationMessage>).

Parameters:

vc - the VCF record to annotate, remains unchanged

Returns:

ImmutableList of VariantAnnotationss, one for each alternative allele, in the order of the alternative alleles in vc

Throws:

InvalidCoordinatesException - in the case of problems with resolving coordinates internally, namely building the GenomeVariant object one one of the returned VariantAnnotationss.

applyAnnotations

public htsjdk.variant.variantcontext.VariantContext applyAnnotations(htsjdk.variant.variantcontext.VariantContext vc,
                                                                     List<de.charite.compbio.jannovar.annotation.VariantAnnotations> annos)

Write annotations from annos to vc l

Parameters:

vc - VariantContext to write the annotations to (to INFO column)

annos - annotations to apply (one for each alternative allele in vc)

Returns:

modified vc

buildErrorAnnotations

public de.charite.compbio.jannovar.annotation.VariantAnnotations buildErrorAnnotations(de.charite.compbio.jannovar.reference.GenomeVariant change)

Parameters:

change - GenomeVariant to build error annotation for

Returns:

VariantAnnotations having the message set to AnnotationMessage.ERROR_PROBLEM_DURING_ANNOTATION.

buildSVErrorAnnotations

public de.charite.compbio.jannovar.annotation.SVAnnotations buildSVErrorAnnotations(de.charite.compbio.jannovar.reference.SVGenomeVariant change)

Parameters:

change - SVGenomeVariant to build error annotation for

Returns:

VariantAnnotations having the message set to AnnotationMessage.ERROR_PROBLEM_DURING_ANNOTATION.

buildSVAnnotations

public com.google.common.collect.ImmutableList<de.charite.compbio.jannovar.annotation.SVAnnotations> buildSVAnnotations(htsjdk.variant.variantcontext.VariantContext vc)
                                                                                                                 throws MultipleSVAlleles,
                                                                                                                        MissingSVTypeInfoField,
                                                                                                                        MissingEndInfoField,
                                                                                                                        InvalidCoordinatesException,
                                                                                                                        InvalidBreakendDescriptionException

Throws:

MultipleSVAlleles

MissingSVTypeInfoField

MissingEndInfoField

InvalidCoordinatesException

InvalidBreakendDescriptionException

buildSVGenomeVariant

public de.charite.compbio.jannovar.reference.SVGenomeVariant buildSVGenomeVariant(htsjdk.variant.variantcontext.VariantContext vc)
                                                                           throws MissingSVTypeInfoField,
                                                                                  InvalidCoordinatesException,
                                                                                  MissingEndInfoField,
                                                                                  InvalidBreakendDescriptionException

Throws:

MissingSVTypeInfoField

InvalidCoordinatesException

MissingEndInfoField

InvalidBreakendDescriptionException

applySVAnnotations

public htsjdk.variant.variantcontext.VariantContext applySVAnnotations(htsjdk.variant.variantcontext.VariantContext vc,
                                                                       List<de.charite.compbio.jannovar.annotation.SVAnnotations> annos)