Package VCF.Filters
Class MAFFilter
- java.lang.Object
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- VCF.Filters.PositionFilter
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- VCF.Filters.MAFFilter
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- All Implemented Interfaces:
VCFFilter
public class MAFFilter extends PositionFilter
Filters positions based on minor allele frequency
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Constructor Summary
Constructors Constructor Description MAFFilter(double maf, int minDepth, int maxDepth, Caller caller)
ConstructorMAFFilter(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
Constructor from a config (read in from a XML file)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description org.apache.commons.configuration2.tree.ImmutableNode
getConfig()
Get the config for this filterjava.lang.String
getSummary()
Gets a string summary of this filterboolean
test(Position p)
Tests whether a position should be filtered out-
Methods inherited from class VCF.Filters.PositionFilter
change
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Constructor Detail
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MAFFilter
public MAFFilter(double maf, int minDepth, int maxDepth, Caller caller)
Constructor- Parameters:
maf
- Minor allele frequencyminDepth
- A genotype must have at least this number of reads to be used in the MAF calculationmaxDepth
- A genotype must have less than (or equal) this number of reads to be used in the MAF calculationcaller
- The caller to be used when calling genotypes
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MAFFilter
public MAFFilter(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
Constructor from a config (read in from a XML file)- Parameters:
params
- The config
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Method Detail
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test
public boolean test(Position p) throws VCFDataException
Description copied from class:PositionFilter
Tests whether a position should be filtered out- Specified by:
test
in classPositionFilter
- 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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getConfig
public org.apache.commons.configuration2.tree.ImmutableNode getConfig()
Description copied from interface:VCFFilter
Get the config for this filter- Returns:
- The config
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getSummary
public java.lang.String getSummary()
Description copied from interface:VCFFilter
Gets a string summary of this filter- Returns:
- The string
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