Package htsjdk.variant.variantcontext.filter

Class HeterozygosityFilter

java.lang.Object

htsjdk.variant.variantcontext.filter.HeterozygosityFilter

All Implemented Interfaces:

VariantContextFilter, Predicate<VariantContext>

public class HeterozygosityFilter
extends Object
implements VariantContextFilter

A Predicate on VariantContexts that either returns true at heterozygous sites (invertible to false). if optional "sample" argument to constructor is given, the genotype of that sample will be examined, otherwise first genotype will be used. Missing sample, or no genotype will result in an exception being thrown.

Constructor Summary

Constructors

Constructor	Description
HeterozygosityFilter(boolean keepHets)	Constructor as above that doesn't take a sample, instead it will look at the first genotype of the variant context.
HeterozygosityFilter(boolean keepHets, String sample)	Constructor for a filter that will keep (or remove, if keepHets is false) VC for which the genotype of sample is heterozygous.

Method Summary

Modifier and Type	Method	Description
boolean	test(VariantContext variantContext)

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.function.Predicate

and, negate, or

Constructor Details

HeterozygosityFilter

public HeterozygosityFilter(boolean keepHets,
 String sample)

Constructor for a filter that will keep (or remove, if keepHets is false) VC for which the genotype of sample is heterozygous. If sample is null, the first genotype in the variant context will be used.

Parameters:

keepHets - determine whether to keep the het sites (true) or filter them out (false)

sample - the name of the sample in the variant context whose genotype should be examined.

HeterozygosityFilter

public HeterozygosityFilter(boolean keepHets)

Constructor as above that doesn't take a sample, instead it will look at the first genotype of the variant context.

Parameters:

keepHets - if true, the heterozygous variant contexts will pass the filter, otherwise they will fail.

Method Details

test

public boolean test(VariantContext variantContext)

Specified by:

test in interface Predicate<VariantContext>

Parameters:

variantContext - the record to examine for heterozygosity

Returns:

true if variantContext is to be kept, otherwise false Assumes that this.sample is a sample in the variantContext, if not null, otherwise looks for the first genotype (and assumes it exists).