public class GenotypeQualityFilter extends java.lang.Object implements VariantContextFilter
Constructor and Description |
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GenotypeQualityFilter(int gqThreshold)
Constructor as above that doesn't take a sample, instead it will look at the first genotype of the variant context.
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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.
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Modifier and Type | Method and Description |
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boolean |
test(VariantContext variantContext)
Determines whether a VariantContext matches this filter
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public GenotypeQualityFilter(int gqThreshold, java.lang.String sample)
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.public GenotypeQualityFilter(int gqThreshold)
gqThreshold
- the smallest value of GQ that this filter will passpublic boolean test(VariantContext variantContext)
VariantContextFilter
test
in interface VariantContextFilter
variantContext
- the record to examine for GQ