Package htsjdk.variant.variantcontext.filter

Class GenotypeQualityFilter

java.lang.Object

htsjdk.variant.variantcontext.filter.GenotypeQualityFilter

All Implemented Interfaces:

VariantContextFilter, Predicate<VariantContext>

public class GenotypeQualityFilter
extends Object
implements VariantContextFilter

A Predicate on VariantContexts that returns true at sites that are either unfiltered, or passing (as variants).

Constructor Summary

Constructors

Constructor	Description
GenotypeQualityFilter(int gqThreshold)	Constructor as above that doesn't take a sample, instead it will look at the first genotype of the variant context.
GenotypeQualityFilter(int gqThreshold, String sample)	Constructor for a filter that will keep VC for which the genotype quality (GQ) of sample passes a threshold.

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

GenotypeQualityFilter

public GenotypeQualityFilter(int gqThreshold,
 String sample)

Constructor for a filter that will keep VC for which the genotype quality (GQ) of sample passes a threshold. If sample is null, the first genotype in the variant context will be used.

Parameters:

gqThreshold - the smallest value of GQ that this filter will pass

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

GenotypeQualityFilter

public GenotypeQualityFilter(int gqThreshold)

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

Parameters:

gqThreshold - the smallest value of GQ that this filter will pass

Method Details

test

public boolean test(VariantContext variantContext)

Specified by:

test in interface Predicate<VariantContext>

Parameters:

variantContext - the record to examine for GQ

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).