public class VariantContextMendelianAnnotator extends Object
VariantContext
or a Collection
thereof for compatibility with
Mendelian inheritanceConstructor and Description |
---|
VariantContextMendelianAnnotator(Pedigree pedigree) |
Modifier and Type | Method and 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<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 |
public VariantContextMendelianAnnotator(Pedigree pedigree)
public htsjdk.variant.variantcontext.VariantContext annotateRecord(htsjdk.variant.variantcontext.VariantContext vc) throws CannotAnnotateMendelianInheritance
VariantContext
with compatibility for Mendelian inheritancevc
- VariantContext
to check for compatibility and to annotatevc
with mendelian inheritance compatibility annotationCannotAnnotateMendelianInheritance
- on problems with annotating the VariantContext
public com.google.common.collect.ImmutableList<htsjdk.variant.variantcontext.VariantContext> annotateRecords(List<htsjdk.variant.variantcontext.VariantContext> vcs) throws CannotAnnotateMendelianInheritance
List
of VariantContext
objectsvcs
- VariantContext
objects to annotateImmutableList
of VariantContext
copies of vcs
CannotAnnotateMendelianInheritance
- on problems with annotating the VariantContext
spublic com.google.common.collect.ImmutableMap<ModeOfInheritance,com.google.common.collect.ImmutableList<htsjdk.variant.variantcontext.VariantContext>> computeCompatibleInheritanceModes(List<htsjdk.variant.variantcontext.VariantContext> vcs) throws CannotAnnotateMendelianInheritance
VariantContext
objectsvcs
- VariantContext
objects to check for compatibilityMap
from ModeOfInheritance
to the list of VariantContext
in vcs
that is compatible with each modeCannotAnnotateMendelianInheritance
- on problems with annotating mendelian inheritanceCopyright © 2016. All rights reserved.