Package picard.vcf.filter
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
All Methods Instance Methods Concrete 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
-
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 interfaceVariantFilter
-
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 interfaceVariantFilter
-
-