Class GenotypeQualityFilter
- java.lang.Object
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- htsjdk.variant.variantcontext.filter.GenotypeQualityFilter
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- 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).
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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.
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Constructor Detail
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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 passsample
- the name of the sample in the variant context whose genotype should be examined.
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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
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Method Detail
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test
public boolean test(VariantContext variantContext)
- Specified by:
test
in interfacePredicate<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).
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