de.charite.compbio.jannovar.mendel.impl

Class MendelianCheckerARCompoundHet

java.lang.Object

de.charite.compbio.jannovar.mendel.impl.AbstractMendelianChecker

de.charite.compbio.jannovar.mendel.impl.MendelianCheckerARCompoundHet

public class MendelianCheckerARCompoundHet
extends AbstractMendelianChecker

Helper class for checking a Collection of GenotypeCalls for compatibility with a Pedigree and autosomal recessive compound het mode of inheritance.

Compatibility Check

In the case of a single individual, we require at least two heterozygous genotype calls.

Author:

Manuel Holtgrewe, Max Schubach, Peter N Robinson

Constructor Summary

Constructors

Constructor and Description
MendelianCheckerARCompoundHet(MendelianInheritanceChecker parent)

Method Summary

Modifier and Type	Method and Description
com.google.common.collect.ImmutableList<GenotypeCalls>	filterCompatibleRecords(Collection<GenotypeCalls> calls) Filter list of GenotypeCalls for fitting to mode

Methods inherited from class java.lang.Object

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

Constructor Detail

MendelianCheckerARCompoundHet

public MendelianCheckerARCompoundHet(MendelianInheritanceChecker parent)

Method Detail

filterCompatibleRecords

public com.google.common.collect.ImmutableList<GenotypeCalls> filterCompatibleRecords(Collection<GenotypeCalls> calls)
                                                                               throws IncompatiblePedigreeException

Description copied from class: AbstractMendelianChecker

Filter list of GenotypeCalls for fitting to mode

Specified by:

filterCompatibleRecords in class AbstractMendelianChecker

Parameters:

calls - The list of calls to check for compatibility

Returns:

Filtered ImmutableList of GenotypeCalls objects, subset of calls

Throws:

IncompatiblePedigreeException - if calls is incompatible with the pedigree