public class VariantContextCompatibilityCheckerAutosomalRecessiveCompoundHet extends AbstractVariantContextCompatibilityChecker
InheritanceVariantContextList
for compatibility with a Pedigree
and
autosomal recessive compound het mode of inheritance.
Genotype.HETEROZYGOUS
genotype calls.Constructor and Description |
---|
VariantContextCompatibilityCheckerAutosomalRecessiveCompoundHet(Pedigree pedigree,
InheritanceVariantContextList list)
Initialize compatibility checker for autosomal recessive compund het and perform some sanity checks.
|
Modifier and Type | Method and Description |
---|---|
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, run
public VariantContextCompatibilityCheckerAutosomalRecessiveCompoundHet(Pedigree pedigree, InheritanceVariantContextList 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,
InheritanceVariantContextList)
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.