de.charite.compbio.jannovar.pedigree.compatibilitychecker

Class AbstractVariantContextCompatibilityChecker

java.lang.Object

de.charite.compbio.jannovar.pedigree.compatibilitychecker.AbstractVariantContextCompatibilityChecker

All Implemented Interfaces:

InterfaceVariantContextCompatibilityChecker

Direct Known Subclasses:

VariantContextCompatibilityCheckerAutosomalDominant, VariantContextCompatibilityCheckerAutosomalRecessive, VariantContextCompatibilityCheckerAutosomalRecessiveCompoundHet, VariantContextCompatibilityCheckerAutosomalRecessiveHomozygous, VariantContextCompatibilityCheckerXDominant, VariantContextCompatibilityCheckerXRecessive

public abstract class AbstractVariantContextCompatibilityChecker
extends Object
implements InterfaceVariantContextCompatibilityChecker

Abstract helper class for checking a List of VariantContext for compatibility with a Pedigree . This class summarizes the builder compatibility checks.

Version:

0.15-SNAPSHOT

Author:

Max Schubach

Constructor Summary

Constructors

Constructor and Description
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.

Method Summary

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.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface de.charite.compbio.jannovar.pedigree.compatibilitychecker.InterfaceVariantContextCompatibilityChecker

runMultiSampleCase, runSingleSampleCase

Constructor Detail

AbstractVariantContextCompatibilityChecker

public AbstractVariantContextCompatibilityChecker(Pedigree pedigree,
                                                  List<htsjdk.variant.variantcontext.VariantContext> list)
                                           throws InheritanceCompatibilityCheckerException

Initialize compatibility checker and perform some sanity checks. The 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).

Parameters:

pedigree - the Pedigree to use for the compatibility

list - the List of VariantContext to use for the initialization

Throws:

InheritanceCompatibilityCheckerException - if the pedigree or variant list is invalid

AbstractVariantContextCompatibilityChecker

public AbstractVariantContextCompatibilityChecker(Pedigree pedigree,
                                                  InheritanceVariantContextList vcList)
                                           throws InheritanceCompatibilityCheckerException

Initialize compatibility checker and perform some sanity checks. The 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).

Parameters:

pedigree - the Pedigree to use for the compatibility

vcList - the InheritanceVariantContextList to use for the initialization

Throws:

InheritanceCompatibilityCheckerException - if the pedigree or variant list is invalid

Method Detail

run

public List<htsjdk.variant.variantcontext.VariantContext> run()
                                                       throws InheritanceCompatibilityCheckerException

Description copied from interface: InterfaceVariantContextCompatibilityChecker

run.

Specified by:

run in interface InterfaceVariantContextCompatibilityChecker

Returns:

All variants of the InheritanceVariantContextList that are compatible with Pedigree and the mode of inheritances.

Throws:

InheritanceCompatibilityCheckerException - if the VCF VariantContext does not match to the Pedigree

getMatchedVariants

public List<htsjdk.variant.variantcontext.VariantContext> getMatchedVariants()

Getter for all VariantContext that matched the ModeOfInheritance.

Returns:

A List of VariantContext that are true for InheritanceVariantContext.isMatchInheritance().