Package Imputers
Class KnniLDProbOptimizedCalls
- java.lang.Object
-
- Imputers.KnniLDProbOptimizedCalls
-
- All Implemented Interfaces:
OptimizeImputer<KnniLDProb>
public class KnniLDProbOptimizedCalls extends java.lang.Object implements OptimizeImputer<KnniLDProb>
Represents a KnniLDProb imputer that can be optimized to maximise the number of correctly called genotyped
-
-
Constructor Summary
Constructors Constructor Description KnniLDProbOptimizedCalls(int knownDepth, AccuracyCalculator.AccuracyMethod method)
ConstructorKnniLDProbOptimizedCalls(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
Constructor from a config (read in from a XML file)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description org.apache.commons.configuration2.tree.ImmutableNode
getConfig()
Get the config for this caseKnniLDProb
getOptimized(double[][][] callprobs, int[][][] readCounts, java.util.List<SingleGenotypeProbability> maskedprobs, java.util.List<SingleGenotypeMasked> list)
Get an optimized version of the imputer
-
-
-
Constructor Detail
-
KnniLDProbOptimizedCalls
public KnniLDProbOptimizedCalls(int knownDepth, AccuracyCalculator.AccuracyMethod method)
Constructor- Parameters:
knownDepth
- The read depth above which imputation is not performed and the called probabilities are used insteadmethod
- The accuracy method to be used
-
KnniLDProbOptimizedCalls
public KnniLDProbOptimizedCalls(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
Constructor from a config (read in from a XML file)- Parameters:
params
- The config
-
-
Method Detail
-
getOptimized
public KnniLDProb getOptimized(double[][][] callprobs, int[][][] readCounts, java.util.List<SingleGenotypeProbability> maskedprobs, java.util.List<SingleGenotypeMasked> list)
Description copied from interface:OptimizeImputer
Get an optimized version of the imputer- Specified by:
getOptimized
in interfaceOptimizeImputer<KnniLDProb>
- Parameters:
callprobs
- Original called genotype probabilitiesreadCounts
- Read countsmaskedprobs
- Masked genotype probabilitieslist
- List of masked sites and their genotype- Returns:
- An optimized imputer
-
getConfig
public org.apache.commons.configuration2.tree.ImmutableNode getConfig()
Description copied from interface:OptimizeImputer
Get the config for this case- Specified by:
getConfig
in interfaceOptimizeImputer<KnniLDProb>
- Returns:
- The config
-
-