picard.vcf.filter

Class QdFilter

java.lang.Object

picard.vcf.filter.QdFilter

All Implemented Interfaces:

VariantFilter

public class QdFilter
extends java.lang.Object
implements VariantFilter

Filters out sites that have a QD annotation applied to them and where the QD value is lower than a lower limit.

Author:

Tim Fennell

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	FILTER_NAME

Constructor Summary

Constructors

Constructor and Description
QdFilter(double minimumQd)

Method Summary

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

Field Detail

FILTER_NAME

public static final java.lang.String FILTER_NAME

See Also:

Constant Field Values

Constructor Detail

QdFilter

public QdFilter(double minimumQd)

Method Detail

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

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