Package de.charite.compbio.jannovar.mendel.bridge

Class VariantContextMendelianAnnotator

java.lang.Object

de.charite.compbio.jannovar.mendel.bridge.VariantContextMendelianAnnotator

public class VariantContextMendelianAnnotator
extends Object

Helper class for annotating one VariantContext or a Collection thereof for compatibility with Mendelian inheritance

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor	Description
VariantContextMendelianAnnotator(de.charite.compbio.jannovar.pedigree.Pedigree pedigree, boolean interpretGenotypeFilters, boolean interpretVariantFilters)

Method Summary

Modifier and Type	Method	Description
htsjdk.variant.variantcontext.VariantContext	annotateRecord(htsjdk.variant.variantcontext.VariantContext vc)	Annotate VariantContext with compatibility for Mendelian inheritance
com.google.common.collect.ImmutableList<htsjdk.variant.variantcontext.VariantContext>	annotateRecords(List<htsjdk.variant.variantcontext.VariantContext> vcs)	Annotate List of VariantContext objects
com.google.common.collect.ImmutableMap<de.charite.compbio.jannovar.mendel.ModeOfInheritance,com.google.common.collect.ImmutableList<htsjdk.variant.variantcontext.VariantContext>>	computeCompatibleInheritanceModes(List<htsjdk.variant.variantcontext.VariantContext> vcs)	Compute compatible modes of inheritance for a list of VariantContext objects
com.google.common.collect.ImmutableMap<de.charite.compbio.jannovar.mendel.SubModeOfInheritance,com.google.common.collect.ImmutableList<htsjdk.variant.variantcontext.VariantContext>>	computeCompatibleInheritanceSubModes(List<htsjdk.variant.variantcontext.VariantContext> vcs)	Compute compatible modes of inheritance for a list of VariantContext objects

Methods inherited from class java.lang.Object

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

Constructor Detail

VariantContextMendelianAnnotator

public VariantContextMendelianAnnotator(de.charite.compbio.jannovar.pedigree.Pedigree pedigree,
                                        boolean interpretGenotypeFilters,
                                        boolean interpretVariantFilters)

Method Detail

annotateRecord

public htsjdk.variant.variantcontext.VariantContext annotateRecord(htsjdk.variant.variantcontext.VariantContext vc)
                                                            throws CannotAnnotateMendelianInheritance

Annotate VariantContext with compatibility for Mendelian inheritance

Parameters:

vc - VariantContext to check for compatibility and to annotate

Returns:

Copy of vc with mendelian inheritance compatibility annotation

Throws:

CannotAnnotateMendelianInheritance - on problems with annotating the VariantContext

annotateRecords

public com.google.common.collect.ImmutableList<htsjdk.variant.variantcontext.VariantContext> annotateRecords(List<htsjdk.variant.variantcontext.VariantContext> vcs)
                                                                                                      throws CannotAnnotateMendelianInheritance

Annotate List of VariantContext objects

If self.interpretVariantFilters then the variant contexts to be considered for compound heterozygous will be prefiltered to those with appropriately high frequency and not being annotated as synonymous variant.

Parameters:

vcs - VariantContext objects to annotate

Returns:

An ImmutableList of VariantContext copies of vcs

Throws:

CannotAnnotateMendelianInheritance - on problems with annotating the VariantContexts

computeCompatibleInheritanceModes

public com.google.common.collect.ImmutableMap<de.charite.compbio.jannovar.mendel.ModeOfInheritance,com.google.common.collect.ImmutableList<htsjdk.variant.variantcontext.VariantContext>> computeCompatibleInheritanceModes(List<htsjdk.variant.variantcontext.VariantContext> vcs)
                                                                                                                                                                                                                           throws CannotAnnotateMendelianInheritance

Compute compatible modes of inheritance for a list of VariantContext objects

Parameters:

vcs - VariantContext objects to check for compatibility

Returns:

A Map from ModeOfInheritance to the list of VariantContext in vcs that is compatible with each mode

Throws:

CannotAnnotateMendelianInheritance - on problems with annotating mendelian inheritance

computeCompatibleInheritanceSubModes

public com.google.common.collect.ImmutableMap<de.charite.compbio.jannovar.mendel.SubModeOfInheritance,com.google.common.collect.ImmutableList<htsjdk.variant.variantcontext.VariantContext>> computeCompatibleInheritanceSubModes(List<htsjdk.variant.variantcontext.VariantContext> vcs)
                                                                                                                                                                                                                                 throws CannotAnnotateMendelianInheritance

Compute compatible modes of inheritance for a list of VariantContext objects

Parameters:

vcs - VariantContext objects to check for compatibility

Returns:

A Map from ModeOfInheritance to the list of VariantContext in vcs that is compatible with each mode

Throws:

CannotAnnotateMendelianInheritance - on problems with annotating mendelian inheritance