Package Combiner
Class MaxDepthCombinerOptimizedCalls
- java.lang.Object
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- Combiner.MaxDepthCombinerOptimizedCalls
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- All Implemented Interfaces:
OptimizeCombiner<MaxDepthCombiner>
public class MaxDepthCombinerOptimizedCalls extends java.lang.Object implements OptimizeCombiner<MaxDepthCombiner>
Gets an optimized MaxDepthCombiner. That is it is used to get a MaxDepthCombiner with optimized w.
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Constructor Summary
Constructors Constructor Description MaxDepthCombinerOptimizedCalls(int maxDepth, AccuracyCalculator.AccuracyMethod method)
ConstructorMaxDepthCombinerOptimizedCalls(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
Creates the optimizer from the given configuration
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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 the optimizable combinerMaxDepthCombiner
getOptimized(java.util.List<SingleGenotypeProbability> called, java.util.List<SingleGenotypeProbability> imputed, java.util.List<SingleGenotypeReads> reads, java.util.List<SingleGenotypeCall> correct, java.util.List<SingleGenotypeMasked> masked)
Returns an optimized combiner for the given inputs
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Constructor Detail
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MaxDepthCombinerOptimizedCalls
public MaxDepthCombinerOptimizedCalls(int maxDepth, AccuracyCalculator.AccuracyMethod method)
Constructor- Parameters:
maxDepth
- The depth above which only called genotype probabilities are usedmethod
- The accuracy method to be used
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MaxDepthCombinerOptimizedCalls
public MaxDepthCombinerOptimizedCalls(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
Creates the optimizer from the given configuration- Parameters:
params
- The configuration
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Method Detail
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getOptimized
public MaxDepthCombiner getOptimized(java.util.List<SingleGenotypeProbability> called, java.util.List<SingleGenotypeProbability> imputed, java.util.List<SingleGenotypeReads> reads, java.util.List<SingleGenotypeCall> correct, java.util.List<SingleGenotypeMasked> masked)
Description copied from interface:OptimizeCombiner
Returns an optimized combiner for the given inputs- Specified by:
getOptimized
in interfaceOptimizeCombiner<MaxDepthCombiner>
- Parameters:
called
- The called genotype probabilitiesimputed
- The imputed genotype probabilitiesreads
- The read depthscorrect
- The correct genotypesmasked
- A list of masked genotypes- Returns:
- The optimized combiner
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getConfig
public org.apache.commons.configuration2.tree.ImmutableNode getConfig()
Description copied from interface:OptimizeCombiner
Get the config for the optimizable combiner- Specified by:
getConfig
in interfaceOptimizeCombiner<MaxDepthCombiner>
- Returns:
- The config
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