public class VariantContextCompatibilityCheckerAutosomalRecessive extends AbstractVariantContextCompatibilityChecker
InheritanceVariantContextList
for compatibility with a Pedigree
and
autosomal recessive mode of inheritance.
VariantContextCompatibilityCheckerAutosomalRecessiveHomozygous
and
VariantContextCompatibilityCheckerAutosomalRecessiveCompoundHet
.Constructor and Description |
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VariantContextCompatibilityCheckerAutosomalRecessive(Pedigree pedigree,
InheritanceVariantContextList list)
Initialize compatibility checker for autosomal recessive and perform some sanity checks.
|
VariantContextCompatibilityCheckerAutosomalRecessive(Pedigree pedigree,
List<htsjdk.variant.variantcontext.VariantContext> list)
Initialize compatibility checker for Autosomal recessive 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 VariantContextCompatibilityCheckerAutosomalRecessive(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 VariantContextCompatibilityCheckerAutosomalRecessive(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 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.