Package Imputers
Interface Imputer
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- All Known Implementing Classes:
KnniLDProb
public interface Imputer
Represents an imputer
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description org.apache.commons.configuration2.tree.ImmutableNode
getConfig()
Get the config for the imputerdouble[][][]
impute(double[][][] probs, int[][][] readCounts)
Imputes a genotype tablejava.util.List<SingleGenotypeProbability>
impute(double[][][] probs, int[][][] readCounts, java.util.List<SingleGenotypeProbability> maskedprobs, java.util.List<SingleGenotypeMasked> list)
Imputes a list of genotypes.
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Method Detail
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impute
double[][][] impute(double[][][] probs, int[][][] readCounts)
Imputes a genotype table- Parameters:
probs
- Genotype probabilities (from a caller)readCounts
- Read counts for each genotype- Returns:
- Table of imputed genotype probabilities
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impute
java.util.List<SingleGenotypeProbability> impute(double[][][] probs, int[][][] readCounts, java.util.List<SingleGenotypeProbability> maskedprobs, java.util.List<SingleGenotypeMasked> list)
Imputes a list of genotypes. Used to calculate accuracy. Need both unmasked probs (probs) and masked probs (maskedprobs) so that the calculation for each genotype is independent (i.e. using the full reads for the other masked genotypes if they're used in the imputation calculation).- Parameters:
probs
- Genotype probabilities (from a caller)readCounts
- Read counts for each genotypemaskedprobs
- Genotype probabilities (from a caller) using masked readslist
- List of genotypes to impute- Returns:
- List of imputed genotype probabilities
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getConfig
org.apache.commons.configuration2.tree.ImmutableNode getConfig()
Get the config for the imputer- Returns:
- The config
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