GenotypeQualityFilter (htsjdk 2.18.2 API)

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

All Methods Instance Methods Concrete Methods
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 Detail
  - 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 Detail
  - 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).