Package Callers
Class Caller
- java.lang.Object
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- Callers.Caller
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- Direct Known Subclasses:
BiasedBinomialCaller
,LogBiasedBinomialCaller
public abstract class Caller extends java.lang.Object
Represents a genotype caller
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Constructor Summary
Constructors Constructor Description Caller()
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Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description double[][][]
call(int[][][] reads)
Calls genotypes for every genotypejava.util.List<SingleGenotypeProbability>
call(java.util.List<SingleGenotypeReads> list)
Call the selected genotypesabstract double[]
callSingle(int[] reads)
Call a single genotypeabstract org.apache.commons.configuration2.tree.ImmutableNode
getConfig()
Get the config for the caller
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Method Detail
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callSingle
public abstract double[] callSingle(int[] reads)
Call a single genotype- Parameters:
reads
- Array of size two with the reads for the two alleles- Returns:
- The probability of each genotype (size 3 - genotype 0, 1, 2)
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call
public double[][][] call(int[][][] reads)
Calls genotypes for every genotype- Parameters:
reads
- Array of reads, dimensions are number of positions, number of snps, 2 (i.e. counts for each allele)- Returns:
- The probability of each genotypes
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call
public java.util.List<SingleGenotypeProbability> call(java.util.List<SingleGenotypeReads> list)
Call the selected genotypes- Parameters:
list
- The genotypes to call- Returns:
- The probabilities of each genotype
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getConfig
public abstract org.apache.commons.configuration2.tree.ImmutableNode getConfig()
Get the config for the caller- Returns:
- The config
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