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

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

    • 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.