Package Accuracy
Class AccuracyStats
- java.lang.Object
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- Accuracy.AccuracyStats
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public class AccuracyStats extends java.lang.Object
Represents accuracy statistics
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double
accuracy()
Returns the overall accuracyint
correct()
Return the total number of genotypes that are correctdouble
correlation()
Returns the overall correlationdouble
depthAccuracy(int depth)
Returns the accuracy for a certain depth (number of reads)int
depthCorrect(int depth)
Return the number of genotypes that are correct that have the given depth (read count)double
depthCorrelation(int depth)
Returns the correlation for a certain depth (number of reads)double
depthGenoAccuracy(int depth, byte geno)
Return the accuracy for a given depth (read count) and true genotypeint
depthGenoCorrect(int depth, byte geno)
Return the number of genotypes that are correct that have the given depth (read count) and true genotypeint
depthGenoTotal(int depth, byte geno)
Return the number of genotypes used in the accuracy calculation that have the give depth (read count) and true genotypeint
depthTotal(int depth)
Return the number of genotypes used in the accuracy calculation that have the given depth (read count)double
genoAccuracy(byte geno)
Return the accuracy for a given genotypeint
genoCorrect(byte geno)
Return the number of genotypes that are correct that have the give true genotypeint
genoTotal(byte geno)
Return the number of genotypes used in the accuracy calculation that have the give true genotypeint
getMaxDepth()
Gte the maximum depth (read count) of any genotype used in the accuracy calculationint
total()
Return the total number of genotypes used in the accuracy calculation
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Method Detail
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accuracy
public double accuracy()
Returns the overall accuracy- Returns:
- The overall accuracy
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correlation
public double correlation()
Returns the overall correlation- Returns:
- The overall correlation
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depthAccuracy
public double depthAccuracy(int depth)
Returns the accuracy for a certain depth (number of reads)- Parameters:
depth
- The depth to return the accuracy for- Returns:
- The accuracy
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depthCorrelation
public double depthCorrelation(int depth)
Returns the correlation for a certain depth (number of reads)- Parameters:
depth
- The depth to return the accuracy for- Returns:
- The correlation
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genoAccuracy
public double genoAccuracy(byte geno)
Return the accuracy for a given genotype- Parameters:
geno
- The true genotype to return the accuracy for- Returns:
- The accuracy
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depthGenoAccuracy
public double depthGenoAccuracy(int depth, byte geno)
Return the accuracy for a given depth (read count) and true genotype- Parameters:
depth
- The depth to return the accuracy forgeno
- The true genotype to return the accuracy for- Returns:
- The accuracy
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total
public int total()
Return the total number of genotypes used in the accuracy calculation- Returns:
- The number of genotypes
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depthTotal
public int depthTotal(int depth)
Return the number of genotypes used in the accuracy calculation that have the given depth (read count)- Parameters:
depth
- Depth- Returns:
- The number of genotypes
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genoTotal
public int genoTotal(byte geno)
Return the number of genotypes used in the accuracy calculation that have the give true genotype- Parameters:
geno
- The true genotype- Returns:
- The number of genotypes
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depthGenoTotal
public int depthGenoTotal(int depth, byte geno)
Return the number of genotypes used in the accuracy calculation that have the give depth (read count) and true genotype- Parameters:
depth
- Depthgeno
- The true genotype- Returns:
- The number of genotypes
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correct
public int correct()
Return the total number of genotypes that are correct- Returns:
- The number of genotypes
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depthCorrect
public int depthCorrect(int depth)
Return the number of genotypes that are correct that have the given depth (read count)- Parameters:
depth
- Depth- Returns:
- The number of genotypes
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genoCorrect
public int genoCorrect(byte geno)
Return the number of genotypes that are correct that have the give true genotype- Parameters:
geno
- The true genotype- Returns:
- The number of genotypes
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depthGenoCorrect
public int depthGenoCorrect(int depth, byte geno)
Return the number of genotypes that are correct that have the given depth (read count) and true genotype- Parameters:
depth
- Depthgeno
- The true genotype- Returns:
- The number of genotypes
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getMaxDepth
public int getMaxDepth()
Gte the maximum depth (read count) of any genotype used in the accuracy calculation- Returns:
- The maximum depth
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