picard.vcf.filter

Class FisherStrandFilter

java.lang.Object

picard.vcf.filter.FisherStrandFilter

All Implemented Interfaces:

VariantFilter

public class FisherStrandFilter
extends java.lang.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 and Description
FisherStrandFilter(double maxPhredScalePValue)

Method Summary

Methods

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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

FisherStrandFilter

public FisherStrandFilter(double maxPhredScalePValue)

Method Detail

headerLines

public java.util.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 java.lang.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