public abstract class AbstractVariantContextCompatibilityChecker extends Object implements InterfaceVariantContextCompatibilityChecker
List
of VariantContext
for compatibility with a Pedigree
.
This class summarizes the builder compatibility checks.Constructor and Description |
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AbstractVariantContextCompatibilityChecker(Pedigree pedigree,
InheritanceVariantContextList vcList)
Initialize compatibility checker and perform some sanity checks.
|
AbstractVariantContextCompatibilityChecker(Pedigree pedigree,
List<htsjdk.variant.variantcontext.VariantContext> list)
Initialize compatibility checker and perform some sanity checks.
|
Modifier and Type | Method and Description |
---|---|
List<htsjdk.variant.variantcontext.VariantContext> |
getMatchedVariants()
Getter for all
VariantContext that matched the ModeOfInheritance . |
List<htsjdk.variant.variantcontext.VariantContext> |
run()
run.
|
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
runMultiSampleCase, runSingleSampleCase
public AbstractVariantContextCompatibilityChecker(Pedigree pedigree, List<htsjdk.variant.variantcontext.VariantContext> list) throws InheritanceCompatibilityCheckerException
List
of VariantContext
is transformed to a InheritanceVariantContextList
, passed to
the constructor and is expected to represent all of the variants found in a certain gene (possibly after
filtering for rarity or predicted pathogenicity).pedigree
- the Pedigree
to use for the compatibilitylist
- the List
of VariantContext
to use for the initializationInheritanceCompatibilityCheckerException
- if the pedigree or variant list is invalidpublic AbstractVariantContextCompatibilityChecker(Pedigree pedigree, InheritanceVariantContextList vcList) throws InheritanceCompatibilityCheckerException
InheritanceVariantContextList
object passed to the constructor is expected to represent all of the
variants found in a certain gene (possibly after filtering for rarity or predicted pathogenicity).pedigree
- the Pedigree
to use for the compatibilityvcList
- the InheritanceVariantContextList
to use for the initializationInheritanceCompatibilityCheckerException
- if the pedigree or variant list is invalidpublic List<htsjdk.variant.variantcontext.VariantContext> run() throws InheritanceCompatibilityCheckerException
InterfaceVariantContextCompatibilityChecker
run.
run
in interface InterfaceVariantContextCompatibilityChecker
InheritanceVariantContextList
that are
compatible with Pedigree
and the mode of inheritances.InheritanceCompatibilityCheckerException
- if the VCF VariantContext
does not match to the
Pedigree
public List<htsjdk.variant.variantcontext.VariantContext> getMatchedVariants()
VariantContext
that matched the ModeOfInheritance
.VariantContext
that are true
for
InheritanceVariantContext.isMatchInheritance()
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