de.charite.compbio.jannovar.pedigree.compatibilitychecker

Class InheritanceCompatibilityChecker

java.lang.Object

de.charite.compbio.jannovar.pedigree.compatibilitychecker.InheritanceCompatibilityChecker

public class InheritanceCompatibilityChecker
extends Object

Decorator for Pedigree that allows checking whether a Genotype call of a VariantContext is compatible with a selected mode of inheritance.

Version:

0.15-SNAPSHOT

Author:

Max Schubach

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	InheritanceCompatibilityChecker.Builder Builder for a compatibility checker.

Method Summary

Modifier and Type	Method and Description
Map<htsjdk.variant.variantcontext.VariantContext,Set<ModeOfInheritance>>	check(List<htsjdk.variant.variantcontext.VariantContext> vcList) Method for checking whether a List of VariantContext is compatible with a given ModeOfInheritance and Pedigree.
Set<ModeOfInheritance>	getAllCompatibleModes(List<htsjdk.variant.variantcontext.VariantContext> vcList) Method for checking whether a List of VariantContext is compatible with ALL possible modes of inheritance (UNINITIALIZED is excluded) and the given Pedigree.
List<htsjdk.variant.variantcontext.VariantContext>	getCompatibleWith(List<htsjdk.variant.variantcontext.VariantContext> vcList) Method for filtering whether a List of VariantContext is compatible with a given ModeOfInheritance and Pedigree.
com.google.common.collect.ImmutableSet<ModeOfInheritance>	getInheritanceModes() Getter for the field inheritanceModes.
Pedigree	getPedigree() Getter for the field pedigree.

Methods inherited from class java.lang.Object

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

Method Detail

getPedigree

public Pedigree getPedigree()

Getter for the field pedigree.

Returns:

The pedigree used in this InheritanceCompatibilityChecker

getInheritanceModes

public com.google.common.collect.ImmutableSet<ModeOfInheritance> getInheritanceModes()

Getter for the field inheritanceModes.

Returns:

mode of inheritances to check in this InheritanceCompatibilityChecker

getCompatibleWith

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

Method for filtering whether a List of VariantContext is compatible with a given ModeOfInheritance and Pedigree.

Parameters:

vcList - List of VariantContext to check for compatibility

Returns:

A list with all VariantContext that matches the mode of inheritances.

Throws:

InheritanceCompatibilityCheckerException - if there are problems with list or pedigree.

getAllCompatibleModes

public Set<ModeOfInheritance> getAllCompatibleModes(List<htsjdk.variant.variantcontext.VariantContext> vcList)
                                             throws InheritanceCompatibilityCheckerException

Method for checking whether a List of VariantContext is compatible with ALL possible modes of inheritance (UNINITIALIZED is excluded) and the given Pedigree.

Parameters:

vcList - List of VariantContext to check for compatibility

Returns:

A set with all possible modes of inheritance in the given list.

Throws:

InheritanceCompatibilityCheckerException - if there are problems with list or pedigree.

check

public Map<htsjdk.variant.variantcontext.VariantContext,Set<ModeOfInheritance>> check(List<htsjdk.variant.variantcontext.VariantContext> vcList)
                                                                               throws InheritanceCompatibilityCheckerException

Method for checking whether a List of VariantContext is compatible with a given ModeOfInheritance and Pedigree.

Parameters:

vcList - List of VariantContext to check for compatibility

Returns:

A Map with all VariantContext and a set to which inheritance mode they belong.

Throws:

InheritanceCompatibilityCheckerException - if there are problems with list or pedigree.