public class VariantContextCompatibilityCheckerAutosomalDominant extends AbstractVariantContextCompatibilityChecker
InheritanceVariantContextList
for compatibility with a Pedigree
and
autosomal dominant mode of inheritance.
Genotype
that is shared by all affected
individuals but no unaffected individuals in the pedigree.
We do not allow Genotype.HOMOZYGOUS_ALT
for any affected (and also for the one person in the case of
single-person pedigrees) since this is not the interesting case for users of this class.Constructor and Description |
---|
VariantContextCompatibilityCheckerAutosomalDominant(Pedigree pedigree,
InheritanceVariantContextList list)
Initialize compatibility checker for AutosomaöDominant and perform some sanity checks.
|
VariantContextCompatibilityCheckerAutosomalDominant(Pedigree pedigree,
List<htsjdk.variant.variantcontext.VariantContext> list)
Initialize compatibility checker for autosomal dominant and perform some sanity checks.
|
Modifier and Type | Method and Description |
---|---|
List<htsjdk.variant.variantcontext.VariantContext> |
run()
run.
|
void |
runMultiSampleCase()
All variants of the
InheritanceVariantContextList that are compatible with Pedigree and the mode
of inheritances will be set true for their compatibility. |
void |
runSingleSampleCase()
All variants of the
InheritanceVariantContextList that are compatible with index (first individual of the
VCF file) and the mode of inheritances will be set true for their compatibility |
getMatchedVariants
public VariantContextCompatibilityCheckerAutosomalDominant(Pedigree pedigree, List<htsjdk.variant.variantcontext.VariantContext> list) throws InheritanceCompatibilityCheckerException
pedigree
- the Pedigree
to use for the initializelist
- the InheritanceVariantContextList
to use for the initializationInheritanceCompatibilityCheckerException
- if the pedigree or variant list is invalidAbstractVariantContextCompatibilityChecker.AbstractVariantContextCompatibilityChecker(Pedigree, List)
public VariantContextCompatibilityCheckerAutosomalDominant(Pedigree pedigree, InheritanceVariantContextList list) throws InheritanceCompatibilityCheckerException
pedigree
- a Pedigree
object.list
- a InheritanceVariantContextList
object.InheritanceCompatibilityCheckerException
- if the pedigree or variant list is invalidAbstractVariantContextCompatibilityChecker.AbstractVariantContextCompatibilityChecker(Pedigree,
InheritanceVariantContextList)
public List<htsjdk.variant.variantcontext.VariantContext> run() throws InheritanceCompatibilityCheckerException
InterfaceVariantContextCompatibilityChecker
run.
run
in interface InterfaceVariantContextCompatibilityChecker
run
in class AbstractVariantContextCompatibilityChecker
InheritanceVariantContextList
that are
compatible with Pedigree
and the mode of inheritances.InheritanceCompatibilityCheckerException
- if the VCF VariantContext
does not match to the
Pedigree
public void runSingleSampleCase()
InterfaceVariantContextCompatibilityChecker
InheritanceVariantContextList
that are compatible with index (first individual of the
VCF file) and the mode of inheritances will be set true
for their compatibilitypublic void runMultiSampleCase()
InterfaceVariantContextCompatibilityChecker
InheritanceVariantContextList
that are compatible with Pedigree
and the mode
of inheritances will be set true
for their compatibility.Copyright © 2016. All rights reserved.