Package Combiner
Class MaxDepthCombiner
- java.lang.Object
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- Combiner.MaxDepthCombiner
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Constructor Summary
Constructors Constructor Description MaxDepthCombiner(double w, int maxDepth)
ConstructorMaxDepthCombiner(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
Creates the combiner from the given configuration
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double[][][]
combine(double[][][] called, double[][][] imputed, int[][][] reads)
Combines imputed and inferred genotypes for all genotypes in a tablejava.util.List<SingleGenotypeProbability>
combine(java.util.List<SingleGenotypeProbability> called, java.util.List<SingleGenotypeProbability> imputed, java.util.List<SingleGenotypeReads> reads)
Combines imputed and inferred genotypes for a list of genotypesorg.apache.commons.configuration2.tree.ImmutableNode
getConfig()
Get the config for the caller
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Constructor Detail
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MaxDepthCombiner
public MaxDepthCombiner(double w, int maxDepth)
Constructor- Parameters:
w
- The weight to give to the imputed probabilitiesmaxDepth
- The depth above which only called genotypes are used
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MaxDepthCombiner
public MaxDepthCombiner(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
Creates the combiner from the given configuration- Parameters:
params
- The configuration
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Method Detail
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combine
public double[][][] combine(double[][][] called, double[][][] imputed, int[][][] reads)
Description copied from interface:Combiner
Combines imputed and inferred genotypes for all genotypes in a table
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combine
public java.util.List<SingleGenotypeProbability> combine(java.util.List<SingleGenotypeProbability> called, java.util.List<SingleGenotypeProbability> imputed, java.util.List<SingleGenotypeReads> reads)
Description copied from interface:Combiner
Combines imputed and inferred genotypes for a list of genotypes
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