Package Utils.SingleGenotype
Class SingleGenotypeMasked
- java.lang.Object
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- Utils.SingleGenotype.SingleGenotypePosition
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- Utils.SingleGenotype.SingleGenotypeMasked
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public class SingleGenotypeMasked extends SingleGenotypePosition
Represents a single masked genotype
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Constructor Summary
Constructors Constructor Description SingleGenotypeMasked(int sample, int snp, int[] original, int[] maskedTo, double maf)
Constructor
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double
getMaf()
Get the minor allele frequency for the position of this genotypesint[]
getMasked()
Get the masked read countsint
getMaskedDepth()
Get the masked depthint[]
getOriginal()
Get the original read counts-
Methods inherited from class Utils.SingleGenotype.SingleGenotypePosition
getSample, getSNP, samePosition, samePositions
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Constructor Detail
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SingleGenotypeMasked
public SingleGenotypeMasked(int sample, int snp, int[] original, int[] maskedTo, double maf)
Constructor- Parameters:
sample
- The sample positionsnp
- The snp positionoriginal
- The original read countsmaskedTo
- The masked read countsmaf
- The minor allele frequency for the position of this genotype
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Method Detail
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getMasked
public int[] getMasked()
Get the masked read counts- Returns:
- The masked read counts
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getMaskedDepth
public int getMaskedDepth()
Get the masked depth- Returns:
- The masked depth
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getOriginal
public int[] getOriginal()
Get the original read counts- Returns:
- The original read counts
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getMaf
public double getMaf()
Get the minor allele frequency for the position of this genotypes- Returns:
- The minor allele frequency
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