public final class InheritanceVariantContextList extends Object
List
of VariantContext
. It
transforms every VariantContext
into an
InheritanceVariantContext
. At also has teh ability to find out if the
variants are XChromosomal or autosomal (or both).Constructor and Description |
---|
InheritanceVariantContextList(List<htsjdk.variant.variantcontext.VariantContext> vcList)
Default constructor.
|
Modifier and Type | Method and Description |
---|---|
Map<htsjdk.variant.variantcontext.VariantContext,Set<ModeOfInheritance>> |
getAnnotatedMap()
Getter for all
ModeOfInheritance for every variant context |
Set<ModeOfInheritance> |
getMatchedModeOfInheritances()
Getter for all possible associated
ModeOfInheritance . |
List<htsjdk.variant.variantcontext.VariantContext> |
getMatchedVariants()
Getter for all
VariantContext that matched the
ModeOfInheritance . |
com.google.common.collect.ImmutableList<String> |
getNames()
the list of individual names
|
List<InheritanceVariantContext> |
getVcList()
Getter for the field
vcList . |
boolean |
isAutosomal()
whether or not the variants are on the Autosome
|
boolean |
isXChromosomal()
whether or not the variants are on the X chromsome
|
boolean |
namesEqual(Pedigree pedigree)
Check whether the
names of this GenotypeCalls are the same as the names of the members of
pedigree . |
String |
toString() |
public com.google.common.collect.ImmutableList<String> getNames()
ImmutableList
object.public boolean isXChromosomal()
public boolean isAutosomal()
public List<InheritanceVariantContext> getVcList()
Getter for the field vcList
.
List
object.public boolean namesEqual(Pedigree pedigree)
names
of this GenotypeCalls are the same as the names of the members of
pedigree
.
For this, the order of the names has to be the same as the number of the names. This check is important for the
PedigreeDiseaseCompatibilityDecorator
, where the names in the pedigree must be the same as the names
in the genotype list.public List<htsjdk.variant.variantcontext.VariantContext> getMatchedVariants()
VariantContext
that matched the
ModeOfInheritance
.VariantContext
that are true
for
InheritanceVariantContext.isMatchInheritance()
.public Set<ModeOfInheritance> getMatchedModeOfInheritances()
ModeOfInheritance
.ModeOfInheritance
that are associated with the list.public Map<htsjdk.variant.variantcontext.VariantContext,Set<ModeOfInheritance>> getAnnotatedMap()
ModeOfInheritance
for every variant contextVariantContext
and a set to which inheritance mode
they belong.Copyright © 2016. All rights reserved.