de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar

Class VariantContextCompatibilityCheckerAutosomalRecessiveHomozygous

java.lang.Object

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

de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar.VariantContextCompatibilityCheckerAutosomalRecessiveHomozygous

All Implemented Interfaces:

InterfaceVariantContextCompatibilityChecker

public class VariantContextCompatibilityCheckerAutosomalRecessiveHomozygous
extends AbstractVariantContextCompatibilityChecker

Helper class for checking a InheritanceVariantContextList for compatibility with a Pedigree and autosomal recessive homozygous mode of inheritance.

Compatibility Check

In the case of a single individual, we require Genotype.HOMOZYGOUS_ALT. In the case of multiple individuals, we require that the affects are compatible, that the unaffected parents of affected individuals are not Genotype.HOMOZYGOUS_REF or Genotype.HOMOZYGOUS_ALT and that the unaffected individuals are not Genotype.HOMOZYGOUS_ALT. The affected individuals are compatible if no affected individual is Genotype.HOMOZYGOUS_REF or Genotype.HETEROZYGOUS and there is at least one affected individual that is Genotype.HOMOZYGOUS_ALT.

Version:

0.15-SNAPSHOT

Author:

Manuel Holtgrewe, Max Schubach, Peter N Robinson

Constructor Summary

Constructors

Constructor and Description
VariantContextCompatibilityCheckerAutosomalRecessiveHomozygous(Pedigree pedigree, InheritanceVariantContextList list) Initialize compatibility checker for autosomal recessive homozygout and perform some sanity checks.

Method Summary

Modifier and Type	Method and Description
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, run

Methods inherited from class java.lang.Object

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

Constructor Detail

VariantContextCompatibilityCheckerAutosomalRecessiveHomozygous

public VariantContextCompatibilityCheckerAutosomalRecessiveHomozygous(Pedigree pedigree,
                                                                      InheritanceVariantContextList list)
                                                               throws InheritanceCompatibilityCheckerException

Initialize compatibility checker for autosomal recessive homozygout 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

runSingleSampleCase

public void runSingleSampleCase()

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

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.