Package Callers
Class BiasedBinomialCaller
- java.lang.Object
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- Callers.Caller
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- Callers.BiasedBinomialCaller
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- Direct Known Subclasses:
BinomialCaller
public class BiasedBinomialCaller extends Caller
A biased binomial caller, that is one where each read is not equally likely in the case of a hetrozygote
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Constructor Summary
Constructors Constructor Description BiasedBinomialCaller(double error, double bias)
Creates a biased caller with the given error and biasBiasedBinomialCaller(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
Creates the caller from the given configuration
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double[]
callSingle(int[] d)
Calls a genotype based on readsorg.apache.commons.configuration2.tree.ImmutableNode
getConfig()
Get the config for the callerdouble
getError()
Get the eror rate used in the caller
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Constructor Detail
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BiasedBinomialCaller
public BiasedBinomialCaller(double error, double bias)
Creates a biased caller with the given error and bias- Parameters:
error
- The error ratebias
- The bias - given as the probability of the allele coded 0
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BiasedBinomialCaller
public BiasedBinomialCaller(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
Creates the caller from the given configuration- Parameters:
params
- The configuration
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Method Detail
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callSingle
public double[] callSingle(int[] d)
Calls a genotype based on reads- Specified by:
callSingle
in classCaller
- Parameters:
d
- The reads- Returns:
- The called genotype
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getConfig
public org.apache.commons.configuration2.tree.ImmutableNode getConfig()
Description copied from class:Caller
Get the config for the caller
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getError
public double getError()
Get the eror rate used in the caller- Returns:
- The error rate
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