htsjdk.variant.variantcontext.filter

Class GenotypeQualityFilter

java.lang.Object

htsjdk.variant.variantcontext.filter.GenotypeQualityFilter

All Implemented Interfaces:

VariantContextFilter

public class GenotypeQualityFilter
extends java.lang.Object
implements VariantContextFilter

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

Constructor Summary

Constructors

Constructor and 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, java.lang.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 and Description
boolean	test(VariantContext variantContext) Determines whether a VariantContext matches this filter

Methods inherited from class java.lang.Object

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

Constructor Detail

GenotypeQualityFilter

public GenotypeQualityFilter(int gqThreshold,
                             java.lang.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 Detail

test

public boolean test(VariantContext variantContext)

Description copied from interface: VariantContextFilter

Determines whether a VariantContext matches this filter

Specified by:

test in interface VariantContextFilter

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).