de.charite.compbio.jannovar.pedigree.compatibilitychecker.xd

Class VariantContextCompatibilityCheckerXDominant

java.lang.Object

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

de.charite.compbio.jannovar.pedigree.compatibilitychecker.xd.VariantContextCompatibilityCheckerXDominant

All Implemented Interfaces:

InterfaceVariantContextCompatibilityChecker

public class VariantContextCompatibilityCheckerXDominant
extends AbstractVariantContextCompatibilityChecker

Helper class for checking a InheritanceVariantContextList for compatibility with a Pedigree and X dominant mode of inheritance.

Compatibility Check

For X-chromosomal dominant inheritance, there must be at least one Genotype that is shared by all affected individuals but no unaffected individuals in the pedigree.

Version:

0.15-SNAPSHOT

Author:

Manuel Holtgrewe, Max Schubach, Peter N Robinson

Constructor Summary

Constructors

Constructor and Description
VariantContextCompatibilityCheckerXDominant(Pedigree pedigree, InheritanceVariantContextList list) Initialize compatibility checker for X dominant t and perform some sanity checks.
VariantContextCompatibilityCheckerXDominant(Pedigree pedigree, List<htsjdk.variant.variantcontext.VariantContext> list) Initialize compatibility checker for X dominant and perform some sanity checks.

Method Summary

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

Methods inherited from class de.charite.compbio.jannovar.pedigree.compatibilitychecker.AbstractVariantContextCompatibilityChecker

getMatchedVariants

Methods inherited from class java.lang.Object

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

Constructor Detail

VariantContextCompatibilityCheckerXDominant

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

Initialize compatibility checker for X dominant and perform some sanity checks.

Parameters:

pedigree - the Pedigree to use for the initialize

list - the InheritanceVariantContextList to use for the initialization

Throws:

InheritanceCompatibilityCheckerException - if the pedigree or variant list is invalid

See Also:

AbstractVariantContextCompatibilityChecker.AbstractVariantContextCompatibilityChecker(Pedigree, List)

VariantContextCompatibilityCheckerXDominant

public VariantContextCompatibilityCheckerXDominant(Pedigree pedigree,
                                                   InheritanceVariantContextList list)
                                            throws InheritanceCompatibilityCheckerException

Initialize compatibility checker for X dominant t and perform some sanity checks.

Parameters:

pedigree - the Pedigree to use for the initialize

list - the InheritanceVariantContextList to use for the initialization

Throws:

InheritanceCompatibilityCheckerException - if the pedigree or variant list is invalid

See Also:

AbstractVariantContextCompatibilityChecker.AbstractVariantContextCompatibilityChecker(Pedigree, InheritanceVariantContextList)

Method Detail

run

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

Description copied from interface: InterfaceVariantContextCompatibilityChecker

run.

Specified by:

run in interface InterfaceVariantContextCompatibilityChecker

Overrides:

run in class AbstractVariantContextCompatibilityChecker

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

runSingleSampleCase

public void runSingleSampleCase()
                         throws InheritanceCompatibilityCheckerException

Description copied from interface: InterfaceVariantContextCompatibilityChecker

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

Throws:

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

runMultiSampleCase

public void runMultiSampleCase()

Description copied from interface: InterfaceVariantContextCompatibilityChecker

All variants of the InheritanceVariantContextList that are compatible with Pedigree and the mode of inheritances will be set true for their compatibility.