Class FisherStrandFilter

java.lang.Object
picard.vcf.filter.FisherStrandFilter
All Implemented Interfaces:
VariantFilter

public class FisherStrandFilter extends Object implements VariantFilter
Filters records based on the phred scaled p-value from the Fisher Strand test stored in the FS attribute.
  • Constructor Summary

    Constructors
    Constructor
    Description
    FisherStrandFilter(double maxPhredScalePValue)
     
  • 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.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  • Constructor Details

    • FisherStrandFilter

      public FisherStrandFilter(double maxPhredScalePValue)
  • Method Details

    • headerLines

      public List<htsjdk.variant.vcf.VCFFilterHeaderLine> headerLines()
      Description copied from interface: VariantFilter
      Return VCF header lines that define filters that may be applied by the VariantFilter.
      Specified by:
      headerLines in interface VariantFilter
    • filter

      public String filter(htsjdk.variant.variantcontext.VariantContext ctx)
      Description copied from interface: VariantFilter
      Check to see if the VariantContext should have a filter applied to it. If so return the filter string, otherwise return null.
      Specified by:
      filter in interface VariantFilter