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.
    • Method Summary

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

      • filter

        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

        List<htsjdk.variant.vcf.VCFFilterHeaderLine> headerLines()
        Return VCF header lines that define filters that may be applied by the VariantFilter.