BinomialCaller
public class BiasedBinomialCaller extends Caller
Constructor | Description |
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BiasedBinomialCaller(double error,
double bias) |
Creates a biased caller with the given error and bias
|
BiasedBinomialCaller(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params) |
Creates the caller from the given configuration
|
Modifier and Type | Method | Description |
---|---|---|
double[] |
callSingle(int[] d) |
Calls a genotype based on reads
|
double[] |
callSingle(int[] depths,
int i,
int j) |
Call a single genotype
|
org.apache.commons.configuration2.tree.ImmutableNode |
getConfig() |
Get the config for the caller
|
public BiasedBinomialCaller(double error, double bias)
error
- The error ratebias
- The bias - given as the probability of the allele coded 0public BiasedBinomialCaller(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
params
- The configurationpublic double[] callSingle(int[] depths, int i, int j)
Caller
callSingle
in class Caller
depths
- Array of size two with the reads for the two allelesi
- The index of the sample of the genotype in the genotype tablej
- The index of tht snp of the genotypes in the genotype tablepublic double[] callSingle(int[] d)
d
- The reads