BiasedBinomialCaller
public abstract class Caller
extends java.lang.Object
Constructor | Description |
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Caller() |
Modifier and Type | Method | Description |
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double[][][] |
call(int[][][] reads) |
Calls genotypes for every genotype
|
java.util.List<SingleGenotypeProbability> |
call(java.util.List<SingleGenotypeReads> list) |
Call the selected genotypes
|
abstract double[] |
callSingle(int[] reads,
int sample,
int snp) |
Call a single genotype
|
abstract org.apache.commons.configuration2.tree.ImmutableNode |
getConfig() |
Get the config for the caller
|
public abstract double[] callSingle(int[] reads, int sample, int snp)
reads
- Array of size two with the reads for the two allelessample
- The index of the sample of the genotype in the genotype tablesnp
- The index of tht snp of the genotypes in the genotype tablepublic double[][][] call(int[][][] reads)
reads
- Array of reads, dimensions are number of positions, number
of snps, 2 (i.e. counts for each allele)public java.util.List<SingleGenotypeProbability> call(java.util.List<SingleGenotypeReads> list)
list
- The genotypes to callpublic abstract org.apache.commons.configuration2.tree.ImmutableNode getConfig()