OptimizeImputer<KnniLDProb>
public class KnniLDProbOptimizedCalls extends java.lang.Object implements OptimizeImputer<KnniLDProb>
Constructor | Description |
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KnniLDProbOptimizedCalls(int knownDepth,
AccuracyCalculator.AccuracyMethod method) |
Constructor
|
KnniLDProbOptimizedCalls(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params) |
Constructor from a config (read in from a XML file)
|
Modifier and Type | Method | Description |
---|---|---|
org.apache.commons.configuration2.tree.ImmutableNode |
getConfig() |
Get the config for this case
|
KnniLDProb |
getOptimized(double[][][] callprobs,
int[][][] readCounts,
java.util.List<SingleGenotypeProbability> maskedprobs,
java.util.List<SingleGenotypeMasked> list) |
Get an optimized version of the imputer
|
public KnniLDProbOptimizedCalls(int knownDepth, AccuracyCalculator.AccuracyMethod method)
knownDepth
- The read depth above which imputation is not performed
and the called probabilities are used insteadmethod
- The accuracy method to be usedpublic KnniLDProbOptimizedCalls(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
params
- The configpublic KnniLDProb getOptimized(double[][][] callprobs, int[][][] readCounts, java.util.List<SingleGenotypeProbability> maskedprobs, java.util.List<SingleGenotypeMasked> list)
OptimizeImputer
getOptimized
in interface OptimizeImputer<KnniLDProb>
callprobs
- Original called genotype probabilitiesreadCounts
- Read countsmaskedprobs
- Masked genotype probabilitieslist
- List of masked sites and their genotypepublic org.apache.commons.configuration2.tree.ImmutableNode getConfig()
OptimizeImputer
getConfig
in interface OptimizeImputer<KnniLDProb>