Package Utils
Class ProbToCallMinDepth
- java.lang.Object
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- Utils.ProbToCallMinDepth
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public class ProbToCallMinDepth extends java.lang.Object
Converts genotype probabilities to a called genotype
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Constructor Summary
Constructors Constructor Description ProbToCallMinDepth()
Default constructor - always calls a genotype, no matter the number of readsProbToCallMinDepth(int minDepth)
Creates an instance that will only call a genotype if there are more than the given number of reads for that genotype
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description byte[][]
call(double[][][] probs, int[][][] readCounts)
Call a table of genotypesbyte
callSingle(double[] prob, int[] readCounts)
Call a single genotype
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Constructor Detail
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ProbToCallMinDepth
public ProbToCallMinDepth()
Default constructor - always calls a genotype, no matter the number of reads
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ProbToCallMinDepth
public ProbToCallMinDepth(int minDepth)
Creates an instance that will only call a genotype if there are more than the given number of reads for that genotype- Parameters:
minDepth
- Minimum number of reads at which to call a genotype
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Method Detail
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callSingle
public byte callSingle(double[] prob, int[] readCounts)
Call a single genotype- Parameters:
prob
- Genotype probabilitiesreadCounts
- The read counts for that genotype- Returns:
- The called genotype
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call
public byte[][] call(double[][][] probs, int[][][] readCounts)
Call a table of genotypes- Parameters:
probs
- Table of genotype probabilitiesreadCounts
- Table of read counts- Returns:
- Table of called genotypes
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