picard.vcf.filter

Interface VariantFilter

All Known Implementing Classes:

AlleleBalanceFilter, FisherStrandFilter, QdFilter

public interface VariantFilter

Interface for classes that can generate filters for VariantContexts. The contract is that a VariantContext is provided, and if the variant should be filtered out then the filter string should be returned, otherwise null.

Author:

tfennell

Method Summary

Modifier and Type	Method and Description
java.lang.String	filter(htsjdk.variant.variantcontext.VariantContext ctx) Check to see if the VariantContext should have a filter applied to it.
java.util.List<htsjdk.variant.vcf.VCFFilterHeaderLine>	headerLines() Return VCF header lines that define filters that may be applied by the VariantFilter.

Method Detail

filter

java.lang.String filter(htsjdk.variant.variantcontext.VariantContext ctx)

Check to see if the VariantContext should have a filter applied to it. If so return the filter string, otherwise return null.

headerLines

java.util.List<htsjdk.variant.vcf.VCFFilterHeaderLine> headerLines()

Return VCF header lines that define filters that may be applied by the VariantFilter.