Class VariantContextMendelianAnnotator
- java.lang.Object
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- de.charite.compbio.jannovar.mendel.bridge.VariantContextMendelianAnnotator
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public class VariantContextMendelianAnnotator extends Object
Helper class for annotating oneVariantContext
or aCollection
thereof for compatibility with Mendelian inheritance- Author:
- Manuel Holtgrewe
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Constructor Summary
Constructors Constructor Description VariantContextMendelianAnnotator(de.charite.compbio.jannovar.pedigree.Pedigree pedigree, boolean interpretGenotypeFilters, boolean interpretVariantFilters)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description htsjdk.variant.variantcontext.VariantContext
annotateRecord(htsjdk.variant.variantcontext.VariantContext vc)
AnnotateVariantContext
with compatibility for Mendelian inheritancecom.google.common.collect.ImmutableList<htsjdk.variant.variantcontext.VariantContext>
annotateRecords(List<htsjdk.variant.variantcontext.VariantContext> vcs)
AnnotateList
ofVariantContext
objectscom.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 ofVariantContext
objectscom.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 ofVariantContext
objects
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Method Detail
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annotateRecord
public htsjdk.variant.variantcontext.VariantContext annotateRecord(htsjdk.variant.variantcontext.VariantContext vc) throws CannotAnnotateMendelianInheritance
AnnotateVariantContext
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 theVariantContext
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annotateRecords
public com.google.common.collect.ImmutableList<htsjdk.variant.variantcontext.VariantContext> annotateRecords(List<htsjdk.variant.variantcontext.VariantContext> vcs) throws CannotAnnotateMendelianInheritance
AnnotateList
ofVariantContext
objectsIf
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
ofVariantContext
copies ofvcs
- Throws:
CannotAnnotateMendelianInheritance
- on problems with annotating theVariantContext
s
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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 ofVariantContext
objects- Parameters:
vcs
-VariantContext
objects to check for compatibility- Returns:
- A
Map
fromModeOfInheritance
to the list ofVariantContext
invcs
that is compatible with each mode - Throws:
CannotAnnotateMendelianInheritance
- on problems with annotating mendelian inheritance
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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 ofVariantContext
objects- Parameters:
vcs
-VariantContext
objects to check for compatibility- Returns:
- A
Map
fromModeOfInheritance
to the list ofVariantContext
invcs
that is compatible with each mode - Throws:
CannotAnnotateMendelianInheritance
- on problems with annotating mendelian inheritance
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