Package VCF.Filters
Class PositionFilter
- java.lang.Object
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- VCF.Filters.PositionFilter
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- All Implemented Interfaces:
VCFFilter
- Direct Known Subclasses:
BiallelicFilter
,HasDepthFilter
,MAFFilter
,ParalogHWFilter
,PositionMissing
public abstract class PositionFilter extends java.lang.Object implements VCFFilter
Represents a position filter
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Constructor Summary
Constructors Constructor Description PositionFilter()
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Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description void
change(VCF vcf)
Apply this filter to a VCFabstract boolean
test(Position p)
Tests whether a position should be filtered out-
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface VCF.Filters.VCFFilter
getConfig, getSummary
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Method Detail
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test
public abstract boolean test(Position p) throws VCFDataException
Tests whether a position should be filtered out- Parameters:
p
- The position to test- Returns:
- Whether this position should be filtered out
- Throws:
VCFDataException
- If there is a problem with the data in the VCF
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change
public void change(VCF vcf) throws VCFDataException
Description copied from interface:VCFFilter
Apply this filter to a VCF- Specified by:
change
in interfaceVCFFilter
- Parameters:
vcf
- The VCF- Throws:
VCFDataException
- If there is a problem with the data in the VCF
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