Package VCF.Filters
Class SampleMissing
- java.lang.Object
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- VCF.Filters.SampleFilter
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- VCF.Filters.SampleMissing
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- All Implemented Interfaces:
VCFFilter
public class SampleMissing extends SampleFilter
Filters a sample based on a maximum allowed amount of missing genotypes
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Constructor Summary
Constructors Constructor Description SampleMissing(double threshold, int minDepth)
ConstructorSampleMissing(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(Sample s)
Tests whether a sample should be filtered out-
Methods inherited from class VCF.Filters.SampleFilter
change
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Constructor Detail
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SampleMissing
public SampleMissing(double threshold, int minDepth)
Constructor- Parameters:
threshold
- The missing thresholdminDepth
- The minimum number of reads required for a genotype to be considered present
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SampleMissing
public SampleMissing(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(Sample s) throws VCFDataException
Description copied from class:SampleFilter
Tests whether a sample should be filtered out- Specified by:
test
in classSampleFilter
- Parameters:
s
- The sample to test- Returns:
- Whether this sample 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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