OptimizeCombiner<MaxDepthCombiner>
public class MaxDepthCombinerOptimizedCalls extends java.lang.Object implements OptimizeCombiner<MaxDepthCombiner>
Constructor | Description |
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MaxDepthCombinerOptimizedCalls(int maxDepth,
AccuracyCalculator.AccuracyMethod method) |
Constructor
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MaxDepthCombinerOptimizedCalls(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params) |
Creates the optimizer from the given configuration
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Modifier and Type | Method | Description |
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org.apache.commons.configuration2.tree.ImmutableNode |
getConfig() |
Get the config for the optimizable combiner
|
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) |
Returns an optimized combiner for the given inputs
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public MaxDepthCombinerOptimizedCalls(int maxDepth, AccuracyCalculator.AccuracyMethod method)
maxDepth
- The depth above which only called genotype probabilities are usedmethod
- The accuracy method to be usedpublic MaxDepthCombinerOptimizedCalls(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
params
- The configurationpublic 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)
OptimizeCombiner
getOptimized
in interface OptimizeCombiner<MaxDepthCombiner>
called
- The called genotype probabilitiesimputed
- The imputed genotype probabilitiesreads
- The read depthscorrect
- The correct genotypesmasked
- A list of masked genotypespublic org.apache.commons.configuration2.tree.ImmutableNode getConfig()
OptimizeCombiner
getConfig
in interface OptimizeCombiner<MaxDepthCombiner>